Citrus Sinensis ID: 048593

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150
Protein Sequence
SSAIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIAVCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWAGTDDINLKMLVHIMQV
Secondary Structure (PSIPRED)
ccEEEEHHHHHHHHHccccccccEEEEEEEEEEEcccccEEcccccEEEEEEEEEEEEEEEcccEEEEEEEEEcccccccccccccccccccEEEEEEEEEEEEEccccccEEEEEEEEccccccccccccccccccccccEEEEEEEcc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHccEEEEEEEHHHHccccEEEEcccEEEEEEEEEEEEEccccccEEEEEEEEEccccccHcccHHHHHHcccEEEEEEEEEEEcHHHHHHHHHHHHHHEHcccccccEEEccccccHHHcHHHHHHHHcc
Coil and Loop (DISEMBL)
SSAIFVTRLLKGLinekackdqcyfLSVTNLKsigrergtvnesgvvfFPVTFLCRTFLPVKGEILHGVIHIAvceqpffsneQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRvegeslgpvslsgwagtddiNLKMLVHIMQV
Flexible Loop (DISEMBL)
SSAIFVTRLLKglinekackdqcYFLSVTNLKsigrergtvnesGVVFFPVTFLCRTFLPVKGEILHGVIHIAVCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVegeslgpvslsgwagtddiNLKMLVHIMQV
Low Complexity Region (SEG)
SSAIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIAVCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWAGTDDINLKMLVHIMQV
Disordered region (IsUnstruct)
***IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIAVCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWAGTDDINLKMLVHI***
Disordered Region (DISOPRED)
**AIFVTRLLKGLINEKACKDQCYFLSVTNLKSI*********SGVVFFPVTFLCRTFLPVKGEILHGVIHIAVCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWAGTDDINLKMLVHIMQV
Disordered Region (DISEMBL)
SSAIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIAVCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWAGTDDINLKMLVHIMQV
Disordered Region (DISPRO)
SSAIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIAVCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWAGTDDINLKMLVHIMQV
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
SSAIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIAVCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWAGTDDINLKMLVHIMQV
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	150
224107919	189	predicted protein [Populus trichocarpa]	0.88	0.698	0.402	5e-24
449432628	190	PREDICTED: DNA-directed RNA polymerase I	0.873	0.689	0.421	1e-21
297804848	194	hypothetical protein ARALYDRAFT_493454 [	0.833	0.644	0.321	4e-15
30682881	200	DNA-directed RNA polymerase II-like prot	0.833	0.625	0.315	5e-15
2244808	194	hypothetical protein [Arabidopsis thalia	0.833	0.644	0.315	5e-15
297737162	242	unnamed protein product [Vitis vinifera]	0.793	0.491	0.348	1e-12
225432916	177	PREDICTED: DNA-directed RNA polymerase I	0.793	0.672	0.348	2e-12
449465372	175	PREDICTED: DNA-directed RNA polymerase I	0.786	0.674	0.342	3e-12
255563208	176	DNA-directed RNA polymerase II 19 kD pol	0.786	0.670	0.346	8e-12
388498028	180	unknown [Medicago truncatula]	0.78	0.65	0.313	4e-10

>gi|224107919|ref|XP_002314653.1| predicted protein [Populus trichocarpa] gi|222863693|gb|EEF00824.1| predicted protein [Populus trichocarpa]

 Score =  115 bits (289), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 66/164 (40%), Positives = 98/164 (59%), Gaps = 32/164 (19%)

Query: 6   VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEI 65
           VT LLK L++ KA KD  YFL+VTNLKSIG+    VN+SG V F V F CRTF+P+KGEI
Sbjct: 30  VTHLLKDLLSMKASKDHGYFLAVTNLKSIGKGE-VVNKSGDVLFHVEFKCRTFMPMKGEI 88

Query: 66  LHGVIH-------IAVC---------------------EQPFFSNEQQAKIRNGLVVQFL 97
           L GV+H       +  C                     E P F N++ A+I N ++V+F 
Sbjct: 89  LQGVVHRTFRHGVLLRCGPVKYIFLSARKMPNYQYTSEENPVFLNDELARIENNVLVRFS 148

Query: 98  VTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWAGTDDINL 141
           V  V+WI++  ++++ +++   + G+SLGP+SL    G+D+++L
Sbjct: 149 VLDVRWIEKMWDMRRDFMMLASLVGDSLGPISL---CGSDELDL 189

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449432628|ref|XP_004134101.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Cucumis sativus] gi|449432630|ref|XP_004134102.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Cucumis sativus] gi|449504102|ref|XP_004162253.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Cucumis sativus] gi|449504105|ref|XP_004162254.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Cucumis sativus]

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 70/166 (42%), Positives = 99/166 (59%), Gaps = 35/166 (21%)

Query: 6   VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTV-NESGVVFFPVTFLCRTFLPVKGE 64
           +T LL+ L+ EKA KD  YFLSVT+L+SIG+  G V NES  V FP+TF+CRTFLP +GE
Sbjct: 30  ITCLLENLLKEKANKDHGYFLSVTSLRSIGK--GIVKNESQCVSFPITFICRTFLPFEGE 87

Query: 65  ILHGVIH-------IAVC---------------------EQPFFSNEQQAKIRNGLVVQF 96
           ILHGV+        +  C                     E P FS+++ A I N +VV+F
Sbjct: 88  ILHGVVRHIFQRGLLLKCGPIKYVFLSARKMPTYQYVGGENPVFSSKEFATIGNDVVVRF 147

Query: 97  LVTAVQWIDEGRNLKKKYLVFGRVEG-ESLGPVSLSGWAGTDDINL 141
            V  V+WI++   +KK++++   +EG  SLGP+SLS    +D+ +L
Sbjct: 148 SVLGVRWIEKRGCIKKEFVMLASLEGNNSLGPISLS---DSDEFDL 190

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297804848|ref|XP_002870308.1| hypothetical protein ARALYDRAFT_493454 [Arabidopsis lyrata subsp. lyrata] gi|297316144|gb|EFH46567.1| hypothetical protein ARALYDRAFT_493454 [Arabidopsis lyrata subsp. lyrata]

 Score = 86.3 bits (212), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 53/165 (32%), Positives = 85/165 (51%), Gaps = 40/165 (24%)

Query: 8   RLLKGLINEKACKDQCYFLSVTNLKSIGRERGTV------NESGVVFFPVTFLCRTFLPV 61
           RLLK LI+EKAC++  ++L +T LKSIG  +         +++ ++ FPV+F CRTFLP 
Sbjct: 24  RLLKDLIHEKACREHGFYLGITALKSIGNNKNNNDENKDNHQAHLLTFPVSFTCRTFLPA 83

Query: 62  KGEILHGV-------------------------------IHIAVC--EQPFFSNEQQAKI 88
           +G+IL G                                +H  +   E+P+F  +  +KI
Sbjct: 84  RGDILQGTVKKVLWNGAFIRSGPLRYAYLSFLKMPDYHYVHSPLLEDEKPYFQKDDLSKI 143

Query: 89  RNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVE-GESLGPVSLSG 132
             G+VV+F V AV++ ++    +  Y V   +E  +S GP+SL+G
Sbjct: 144 AVGVVVRFGVLAVRFKEKPHKRRNDYYVLATLERNDSFGPISLTG 188

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30682881|ref|NP_193188.2| DNA-directed RNA polymerase II-like protein [Arabidopsis thaliana] gi|30682886|ref|NP_849385.1| DNA-directed RNA polymerase II-like protein [Arabidopsis thaliana] gi|334186527|ref|NP_001190729.1| DNA-directed RNA polymerase II-like protein [Arabidopsis thaliana] gi|38603938|gb|AAR24714.1| At4g14520 [Arabidopsis thaliana] gi|44681416|gb|AAS47648.1| At4g14520 [Arabidopsis thaliana] gi|110741153|dbj|BAE98669.1| hypothetical protein [Arabidopsis thaliana] gi|332658054|gb|AEE83454.1| DNA-directed RNA polymerase II-like protein [Arabidopsis thaliana] gi|332658055|gb|AEE83455.1| DNA-directed RNA polymerase II-like protein [Arabidopsis thaliana] gi|332658056|gb|AEE83456.1| DNA-directed RNA polymerase II-like protein [Arabidopsis thaliana]

 Score = 85.9 bits (211), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 52/165 (31%), Positives = 83/165 (50%), Gaps = 40/165 (24%)

Query: 8   RLLKGLINEKACKDQCYFLSVTNLKSIGRERGTV------NESGVVFFPVTFLCRTFLPV 61
           RLL+ LI+EKAC++  ++L +T LKSIG  +         +++ ++ FPV+F CRTFLP 
Sbjct: 30  RLLQDLIHEKACREHGFYLGITALKSIGNNKNNNIDNENNHQAKILTFPVSFTCRTFLPA 89

Query: 62  KGEILHGVIH---------------------------------IAVCEQPFFSNEQQAKI 88
           +G+IL G +                                  ++  E+P F  +  +KI
Sbjct: 90  RGDILQGTVKKVLWNGAFIRSGPLRYAYLSLLKMPHYHYVHSPLSEDEKPHFQKDDLSKI 149

Query: 89  RNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGE-SLGPVSLSG 132
             G+VV+F V AV++ +     +  Y V   +EG  S GP+SL+G
Sbjct: 150 AVGVVVRFQVLAVRFKERPHKRRNDYYVLATLEGNGSFGPISLTG 194

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2244808|emb|CAB10231.1| hypothetical protein [Arabidopsis thaliana] gi|7268158|emb|CAB78494.1| hypothetical protein [Arabidopsis thaliana]

 Score = 85.9 bits (211), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 52/165 (31%), Positives = 83/165 (50%), Gaps = 40/165 (24%)

Query: 8   RLLKGLINEKACKDQCYFLSVTNLKSIGRERGTV------NESGVVFFPVTFLCRTFLPV 61
           RLL+ LI+EKAC++  ++L +T LKSIG  +         +++ ++ FPV+F CRTFLP 
Sbjct: 24  RLLQDLIHEKACREHGFYLGITALKSIGNNKNNNIDNENNHQAKILTFPVSFTCRTFLPA 83

Query: 62  KGEILHGVIH---------------------------------IAVCEQPFFSNEQQAKI 88
           +G+IL G +                                  ++  E+P F  +  +KI
Sbjct: 84  RGDILQGTVKKVLWNGAFIRSGPLRYAYLSLLKMPHYHYVHSPLSEDEKPHFQKDDLSKI 143

Query: 89  RNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGE-SLGPVSLSG 132
             G+VV+F V AV++ +     +  Y V   +EG  S GP+SL+G
Sbjct: 144 AVGVVVRFQVLAVRFKERPHKRRNDYYVLATLEGNGSFGPISLTG 188

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737162|emb|CBI26363.3| unnamed protein product [Vitis vinifera]

 Score = 77.8 bits (190), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 53/152 (34%), Positives = 75/152 (49%), Gaps = 33/152 (21%)

Query: 6   VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEI 65
           + RLL    N+KA ++  YFL+VT L++IG E      SG V FPV F C TF   +GEI
Sbjct: 95  IIRLLDAFSNKKATQELGYFLAVTTLENIG-EGKVRQHSGDVLFPVVFSCVTFKLFRGEI 153

Query: 66  LHGVIH-------IAVC---------------------EQPFFSNEQQAKIRNGLVVQFL 97
           L GV+H       I  C                     E P F NE+ +KI   +VV+F+
Sbjct: 154 LDGVVHKVLKHGVILRCGPVENIYLSCQKMPDYRYVPGENPVFLNEKLSKIEKDVVVRFI 213

Query: 98  VTAVQWIDEGRNLKKKYLVFGRVEGESLGPVS 129
           V   +W++  R    ++     +EG+ LGP+S
Sbjct: 214 VMGTKWLEAER----EFQALVSLEGDYLGPLS 241

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225432916|ref|XP_002284221.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7 [Vitis vinifera] gi|147822056|emb|CAN61549.1| hypothetical protein VITISV_043525 [Vitis vinifera]

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 53/152 (34%), Positives = 74/152 (48%), Gaps = 33/152 (21%)

Query: 6   VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEI 65
           + RLL    N+KA ++  YFL+VT L++IG E      SG V FPV F C TF   +GEI
Sbjct: 30  IIRLLDAFSNKKATQELGYFLAVTTLENIG-EGKVRQHSGDVLFPVVFSCVTFKLFRGEI 88

Query: 66  LHGVIH-------IAVC---------------------EQPFFSNEQQAKIRNGLVVQFL 97
           L GV+H       I  C                     E P F NE+ +KI   +VV+F+
Sbjct: 89  LDGVVHKVLKHGVILRCGPVENIYLSCQKMPDYRYVPGENPVFLNEKLSKIEKDVVVRFI 148

Query: 98  VTAVQWIDEGRNLKKKYLVFGRVEGESLGPVS 129
           V   +W++  R  +        +EG+ LGP+S
Sbjct: 149 VMGTKWLEAEREFQ----ALVSLEGDYLGPLS 176

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449465372|ref|XP_004150402.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Cucumis sativus] gi|449522228|ref|XP_004168129.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Cucumis sativus]

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 52/152 (34%), Positives = 74/152 (48%), Gaps = 34/152 (22%)

Query: 6   VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEI 65
           + RLL     +KA KD  YFL+VT L++IG   G V ++G V FPV F   TF   +GEI
Sbjct: 30  IIRLLDEFATKKATKDLGYFLAVTTLENIGE--GKVRQTGDVLFPVIFSGITFKLYRGEI 87

Query: 66  LHGVIHIAV-------C---------------------EQPFFSNEQQAKIRNGLVVQFL 97
           L GV+H  +       C                     E P F N++ +KI   +VV+F+
Sbjct: 88  LEGVVHKVLKHGVFLRCGPVENIYLSYLKMPDYRYVPGENPVFLNDKLSKIEKDVVVRFI 147

Query: 98  VTAVQWIDEGRNLKKKYLVFGRVEGESLGPVS 129
           V   +W++  R  +        +EG+ LGPVS
Sbjct: 148 VIGTKWLEAEREFQ----ALVSLEGDYLGPVS 175

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563208|ref|XP_002522607.1| DNA-directed RNA polymerase II 19 kD polypeptide rpb7, putative [Ricinus communis] gi|223538083|gb|EEF39694.1| DNA-directed RNA polymerase II 19 kD polypeptide rpb7, putative [Ricinus communis]

 Score = 75.5 bits (184), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 53/153 (34%), Positives = 76/153 (49%), Gaps = 35/153 (22%)

Query: 6   VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNE-SGVVFFPVTFLCRTFLPVKGE 64
           + RLL+   ++KA KD  Y+L+VT L+SIG   G V E +G V FPV F   TF   +GE
Sbjct: 30  IIRLLEDFASKKATKDLGYYLAVTTLESIGE--GKVREHTGDVLFPVVFNGITFKIFRGE 87

Query: 65  ILHGVIHIAV-----------------C-----------EQPFFSNEQQAKIRNGLVVQF 96
           IL GV+H  +                 C           E P F N++ +KI   +VV+F
Sbjct: 88  ILEGVVHKVLKHGVFIRCGPIENIYLSCMKMPDYHYVPGENPVFLNDKTSKIEKDVVVRF 147

Query: 97  LVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVS 129
           +V   +W++  R  +        +EG+ LGPVS
Sbjct: 148 IVIGTKWLEAEREFQ----ALVSLEGDYLGPVS 176

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388498028|gb|AFK37080.1| unknown [Medicago truncatula]

 Score = 69.7 bits (169), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 47/150 (31%), Positives = 66/150 (44%), Gaps = 33/150 (22%)

Query: 8   RLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILH 67
           RLL     +KA KD  YFL+VT L  IG E      +G V FPV F   TF   KGE+L 
Sbjct: 32  RLLSDFAAKKATKDMGYFLAVTTLDKIG-EGKVRQHTGDVLFPVVFNAVTFKIFKGEVLE 90

Query: 68  GVIH----------------------------IAVCEQPFFSNEQQAKIRNGLVVQFLVT 99
           GV+H                              + E P+F N++  KI   + V+ +V 
Sbjct: 91  GVVHKVLKHGVFMRIGPIENAYLSSSKMPGYVYVLGENPYFMNQKMPKIAKDVKVRVVVI 150

Query: 100 AVQWIDEGRNLKKKYLVFGRVEGESLGPVS 129
             +W++  R  +        +EG+ LGP+S
Sbjct: 151 GTKWMEAEREFQ----ALVGLEGDYLGPIS 176

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	150
TAIR|locus:2084573	174	NRPD7 [Arabidopsis thaliana (t	0.426	0.367	0.447	4.1e-16
TAIR|locus:2130060	178	NRPE7 [Arabidopsis thaliana (t	0.44	0.370	0.457	8.4e-16
TAIR|locus:2168514	176	NRPB7 [Arabidopsis thaliana (t	0.52	0.443	0.329	0.00022

TAIR|locus:2084573 NRPD7 [Arabidopsis thaliana (taxid:3702)]

 Score = 122 (48.0 bits), Expect = 4.1e-16, Sum P(2) = 4.1e-16
 Identities = 30/67 (44%), Positives = 40/67 (59%)

Query:     6 VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNE-SGVVFFPVTFLCRTFLPVKGE 64
             V RLL+    EKA KD  Y ++ T L++IG   G + E +G + FPV F    F   KGE
Sbjct:    29 VIRLLEAFSKEKATKDLGYLITPTILENIGE--GKIKEQTGEIQFPVVFNGICFKMFKGE 86

Query:    65 ILHGVIH 71
             I+HGV+H
Sbjct:    87 IVHGVVH 93

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS

GO:0000418 "DNA-directed RNA polymerase IV complex" evidence=IPI

TAIR|locus:2130060 NRPE7 [Arabidopsis thaliana (taxid:3702)]

 Score = 131 (51.2 bits), Expect = 8.4e-16, Sum P(2) = 8.4e-16
 Identities = 32/70 (45%), Positives = 43/70 (61%)

Query:     3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNE-SGVVFFPVTFLCRTFLPV 61
             AI V  LL+   ++KA K+  Y+++VT L  IG   G + E +G V FPV F   TF   
Sbjct:    28 AILV-ELLEAFASKKATKELGYYVAVTTLDKIGE--GKIREHTGEVLFPVMFSGMTFKIF 84

Query:    62 KGEILHGVIH 71
             KGEI+HGV+H
Sbjct:    85 KGEIIHGVVH 94

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS

GO:0000419 "DNA-directed RNA polymerase V complex" evidence=IPI

TAIR|locus:2168514 NRPB7 [Arabidopsis thaliana (taxid:3702)]

 Score = 101 (40.6 bits), Expect = 0.00022, P = 0.00022
 Identities = 28/85 (32%), Positives = 48/85 (56%)

Query:     6 VTRLLKGLINEKACKDQCYFL-SVTNLKSIGRERGTVNE-SGVVFFPVTFLCRTFLPVKG 63
             V++L+K +  E  C  +  F+ ++T + +IG+  G + + +G V FPV + C  F P KG
Sbjct:    27 VSKLMKDV--EGTCSGRHGFVVAITGIDTIGK--GLIRDGTGFVTFPVKYQCVVFRPFKG 82

Query:    64 EILHGVIHIAVCEQPFFSNEQQAKI 88
             EIL  V+ + V +  FF+     +I
Sbjct:    83 EILEAVVTL-VNKMGFFAEAGPVQI 106


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   0.141   0.422    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      150       150   0.00087  104 3  11 22  0.42    31
                                                     30  0.39    34


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:  3
  No. of states in DFA:  589 (63 KB)
  Total size of DFA:  140 KB (2086 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:  12.65u 0.11s 12.76t   Elapsed:  00:00:00
  Total cpu time:  12.65u 0.11s 12.76t   Elapsed:  00:00:00
  Start:  Sat May 11 08:47:46 2013   End:  Sat May 11 08:47:46 2013

GO:0003723 "RNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IPI

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

---

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

Your Input: grail3.0144004501 hypothetical protein (189 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	150
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	100.0
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	100.0
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	100.0
KOG3297	202	consensus DNA-directed RNA polymerase subunit E' [	100.0
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	100.0
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	100.0
cd04329	80	RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ri	99.85
cd04330	80	RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-termin	99.85
cd00655	80	RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved	99.84
cd04331	80	RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprot	99.82
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	99.75
PF03876	70	SHS2_Rpb7-N: SHS2 domain found in N terminus of Rp	99.53
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	99.45
cd04328	89	RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal r	99.18
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	97.55
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	96.21
KOG4134	253	consensus DNA-dependent RNA polymerase I [Transcri	96.2
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	95.91
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	95.76
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	95.67
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	95.34
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	94.98
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	94.14
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	91.86
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	91.66
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	90.79
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	90.41
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	89.83
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	89.78
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	89.39
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	89.08
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	89.08
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	88.62
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	88.43
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	87.9
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	87.79
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	87.22
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	86.14
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	86.12
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	85.95
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	84.84
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	84.2
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	84.11
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	83.98
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	83.78
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	83.72
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	83.39
PRK08582	139	hypothetical protein; Provisional	82.3
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	81.54
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	80.64
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	80.06
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	80.03

>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional

Probab=100.00  E-value=1.7e-36  Score=239.57  Aligned_cols=120  Identities=15%  Similarity=0.296  Sum_probs=108.3

Q ss_pred             HHHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe---------
Q 048593            3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA---------   73 (150)
Q Consensus         3 ~~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v---------   73 (150)
                      ..+++++|+++|+|||.+++||||||+|++++++|+|.| |||++||+|+|||+|||||+|||++|+|++|         
T Consensus        23 ~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~-gdG~~~~~V~FraivFrPf~gEVv~g~V~~v~~~G~~v~~  101 (176)
T PTZ00162         23 QQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQD-GTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFFAQA  101 (176)
T ss_pred             HHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEc-CCCCEEEEEEEEEEEEecCCCCEEEEEEEEEecceEEEEe
Confidence            357899999999999999999999999999999999999 9999999999999999999999999999999         


Q ss_pred             -------------------cCCCceee--ccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCcccccc
Q 048593           74 -------------------VCEQPFFS--NEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVS  129 (150)
Q Consensus        74 -------------------~~~~~~~~--~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i~  129 (150)
                                         +++++|.|  ++++.+|++|+.|||||++++|+..      .++++|||++||||++.
T Consensus       102 Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~------~~~~i~T~~~~~LG~~~  172 (176)
T PTZ00162        102 GPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDAS------NLFAIATINSDYLGPIE  172 (176)
T ss_pred             eCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCC------CcEEEEEecCCCcCccc
Confidence                               33455655  3445789999999999999999543      58999999999999983

>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]

Probab=100.00  E-value=5.2e-36  Score=233.80  Aligned_cols=118  Identities=31%  Similarity=0.566  Sum_probs=108.8

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe----------
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA----------   73 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v----------   73 (150)
                      .++.++|.+..+|||++++||+|||+++++||+|+|+| ++|.+.|+|+|+|++||||||||++|+|++|          
T Consensus        24 ~~l~~~L~~~veg~ctg~~Gyvi~vt~ld~Ig~g~I~~-~~G~v~FpVky~av~FkpfKGEVvdgvV~~Vnk~G~F~~~G  102 (170)
T KOG3298|consen   24 AILKRKLLAEVEGKCTGKYGYVIAVTTLDNIGEGRIRP-GTGFVTFPVKYKAVTFKPFKGEVVDGVVTKVNKMGVFARSG  102 (170)
T ss_pred             HHHHHHHHHHhhccccccccEEEEEEEhhhccCCcccc-CCceEEEEEEEEEEEEeecCCcEEEEEEEEEeeeeEEEecc
Confidence            46788888888899999999999999999999999999 9999999999999999999999999999999          


Q ss_pred             ------------------cCCC-ceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccc
Q 048593           74 ------------------VCEQ-PFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPV  128 (150)
Q Consensus        74 ------------------~~~~-~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i  128 (150)
                                        +++| |.|..++...|++|+.||++|+|++| +.     ++|+|+|||++|||||+
T Consensus       103 Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~-~~-----~~i~algtl~~D~LG~i  170 (170)
T KOG3298|consen  103 PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRV-DE-----TEIFALGTLKGDYLGPI  170 (170)
T ss_pred             ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEE-ee-----eeEEEEEEecCcccccC
Confidence                              5556 77887776799999999999999999 44     37999999999999986

>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]

Probab=100.00  E-value=7.6e-35  Score=231.35  Aligned_cols=126  Identities=19%  Similarity=0.208  Sum_probs=111.8

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe----------
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA----------   73 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v----------   73 (150)
                      -++++.|++.|+|||++++|+||+|+|+++|++|+|.| |||++||+|+||||+|+||+|||++|+|++|          
T Consensus        24 ~~v~~~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~-GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~~~G~fV~ig  102 (183)
T COG1095          24 EAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVP-GDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVEFGAFVRIG  102 (183)
T ss_pred             HHHHHHHHHHhcceEccccCEEEEEEEeeEeeccEEec-CCCcEEEEEEEEEEEEEeccccEEEEEEEEEeecceEEEec
Confidence            46889999999999999999999999999999999999 9999999999999999999999999999999          


Q ss_pred             -----------------cCCCc--eeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccccCCCCC
Q 048593           74 -----------------VCEQP--FFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWA  134 (150)
Q Consensus        74 -----------------~~~~~--~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i~w~~w~  134 (150)
                                       .++++  |..++++++|++||.|||||+++++.+..   .....|.+||+++|||...|  |.
T Consensus       103 p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~---~~~~~I~lTmrq~~LGklew--~~  177 (183)
T COG1095         103 PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR---PRESKIGLTMRQPGLGKLEW--IE  177 (183)
T ss_pred             cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCc---cccceEEEEeccccCCcchh--hh
Confidence                             22233  33466777999999999999999996542   24689999999999999999  85


Q ss_pred             C
Q 048593          135 G  135 (150)
Q Consensus       135 ~  135 (150)
                      +
T Consensus       178 ~  178 (183)
T COG1095         178 E  178 (183)
T ss_pred             h
Confidence            3

>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]

Probab=100.00  E-value=1.9e-34  Score=229.02  Aligned_cols=129  Identities=19%  Similarity=0.307  Sum_probs=116.3

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe----------
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA----------   73 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v----------   73 (150)
                      .+|++.|+.++.+|+..|+|||||||||.++++|.|.| |||+.|++|.||++|||||.|||+.|+|+++          
T Consensus        24 ~ai~~eL~~k~anKvl~nvGLCI~vyDi~~v~e~~v~p-GDGas~~~V~FR~vVFrPF~gEVi~gki~~cs~eG~rvtl~  102 (202)
T KOG3297|consen   24 DAIKEELNRKLANKVLPNVGLCICVYDILEVEEGIVLP-GDGASYARVWFRVVVFRPFVGEVITGKIKECSEEGLRVTLG  102 (202)
T ss_pred             HHHHHHHHHHHHhhhcccccEEEEEeEeeeecceEEec-CCCceEEEEEEEEEEEecccceEEEEEeecCCccceEEEEE
Confidence            57899999999999999999999999999999999999 9999999999999999999999999999999          


Q ss_pred             -------------------cCCCceeeccc-------cceecCCCEEEEEEEEEEeeecCcC-------------ccCcE
Q 048593           74 -------------------VCEQPFFSNEQ-------QAKIRNGLVVQFLVTAVQWIDEGRN-------------LKKKY  114 (150)
Q Consensus        74 -------------------~~~~~~~~~~~-------~~~i~~gd~VR~RI~~v~~~d~~~~-------------~~~~~  114 (150)
                                         +++..|+|...       +.+++.|+.|||||...+|.|.++.             ..+||
T Consensus       103 FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e~f~d~~p~~~~~~~t~~e~~e~~~py  182 (202)
T KOG3297|consen  103 FFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDESFVDVSPEGNSTAITGAEDPEKESPY  182 (202)
T ss_pred             eeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeeecccccCccccccccccccccccCCCe
Confidence                               45567887433       3479999999999999999876532             45899


Q ss_pred             EEEEEccCCccccccCCCCCC
Q 048593          115 LVFGRVEGESLGPVSLSGWAG  135 (150)
Q Consensus       115 ~~igsi~~d~LG~i~w~~w~~  135 (150)
                      .++|+|++|||||++|  |..
T Consensus       183 ~l~gs~~~~GLG~lsW--W~~  201 (202)
T KOG3297|consen  183 TLLGSMNEDGLGPLSW--WDS  201 (202)
T ss_pred             EEEEEecCCCCccchh--hhc
Confidence            9999999999999999  964

>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form

Probab=100.00  E-value=1.1e-33  Score=222.63  Aligned_cols=125  Identities=18%  Similarity=0.231  Sum_probs=110.2

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe----------
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA----------   73 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v----------   73 (150)
                      -++++.|.++|+|||.+++||||||+|++++++|+|.| |||++||+|+|||++||||+|||++|+|+++          
T Consensus        24 ~~i~~~l~~~~~gk~~~~~G~~i~v~di~~i~~g~i~~-gdG~~~~~V~f~~i~f~p~~gEvv~G~V~~v~~~GifV~lg  102 (179)
T TIGR00448        24 EVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVIP-GDGSAYHNVTFRALVFKPELGEIVEGEVIEIVEFGAFVSLG  102 (179)
T ss_pred             HHHHHHHHHHhcCcCcCCcCEEEEEEEeEEecCCEEEC-CCCCEEEEEEEEEEEEeccCCCEEEEEEEEEEeeEEEEEeC
Confidence            47889999999999999999999999999999999999 9999999999999999999999999999999          


Q ss_pred             -------------------cCCCceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccccCCCCC
Q 048593           74 -------------------VCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWA  134 (150)
Q Consensus        74 -------------------~~~~~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i~w~~w~  134 (150)
                                         ..++.|++++.+.++++||.|||||.++++.+..+   ..-.+.+||+++|||++.|  ++
T Consensus       103 ~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~---~~~~I~lt~k~~~LG~~~w--~~  177 (179)
T TIGR00448       103 PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP---EGSKIGLTMRQPLLGKLEW--IE  177 (179)
T ss_pred             CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC---CcceEEEEeccCcCCcccc--cc
Confidence                               22234556666678999999999999999865421   2455799999999999999  74

This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.

>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional

Probab=100.00  E-value=1.2e-33  Score=222.80  Aligned_cols=127  Identities=17%  Similarity=0.189  Sum_probs=109.2

Q ss_pred             HHHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe---------
Q 048593            3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA---------   73 (150)
Q Consensus         3 ~~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v---------   73 (150)
                      .-++.++|+++|+|||.+++||||||+|++++++|+|.| |||+++|+|+|||++|+||+|||++|+|+++         
T Consensus        23 ~~~i~~~l~~~~~~k~~~~~G~~v~v~di~~i~~g~i~~-gdg~~~~~v~f~~lvf~P~~GEVv~g~V~~v~~~Gi~V~l  101 (187)
T PRK08563         23 EEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVP-GDGATYHEVEFDALVFKPELQEVVEGEVVEVVEFGAFVRI  101 (187)
T ss_pred             HHHHHHHHHHHhhCcCcCCcCEEEEEEEeEEecccEEec-CCCCcEEEEEEEEEEEeccCCCEEEEEEEEEEccEEEEEE
Confidence            346899999999999999999999999999999999999 9999999999999999999999999999999         


Q ss_pred             --------------------cCCCceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccccCCCC
Q 048593           74 --------------------VCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGW  133 (150)
Q Consensus        74 --------------------~~~~~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i~w~~w  133 (150)
                                          +.++.|.+++....+++|+.||+||.++++.+..  + ....+.+||+++|||+++|  |
T Consensus       102 g~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~--~-~~~~I~ls~~~~~LG~~~w--~  176 (187)
T PRK08563        102 GPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERR--P-RGSKIGLTMRQPGLGKLEW--I  176 (187)
T ss_pred             eCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCC--C-CCCEEEEEecCCCCCcHHH--H
Confidence                                1112234455556899999999999999985432  0 1147888999999999999  9


Q ss_pred             CC
Q 048593          134 AG  135 (150)
Q Consensus       134 ~~  135 (150)
                      ++
T Consensus       177 ~~  178 (187)
T PRK08563        177 EE  178 (187)
T ss_pred             HH
Confidence            64

>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain

Probab=99.85  E-value=3.3e-21  Score=135.06  Aligned_cols=59  Identities=25%  Similarity=0.426  Sum_probs=56.4

Q ss_pred             HHHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeec
Q 048593            3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVK   62 (150)
Q Consensus         3 ~~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~   62 (150)
                      .-++.+.|+++++||+.+++||||||+|++++++|+|.| |||++||+|+|||++||||+
T Consensus        22 ~~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~~G~I~~-gdG~~~~~V~F~aivfrPf~   80 (80)
T cd04329          22 KEYLEQKLLEEVEGTCTGDYGYIIAVTDIDDIGEGKILP-GTGSVEFPVKYKAIVFKPFK   80 (80)
T ss_pred             HHHHHHHHHHHhCCcCcCceeEEEEEEEeeEecCcEEEc-CCCCEEEEEEEEEEEEEccC
Confidence            347889999999999999999999999999999999999 99999999999999999996

Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter.

>cd04330 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain

Probab=99.85  E-value=3.5e-21  Score=134.91  Aligned_cols=59  Identities=14%  Similarity=0.130  Sum_probs=56.9

Q ss_pred             HHHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeec
Q 048593            3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVK   62 (150)
Q Consensus         3 ~~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~   62 (150)
                      .-++++.|+++|+||+++++||||||+|+.++++|+|.| |||++||+|+|||++||||+
T Consensus        22 ~~~i~~~L~~ky~gkv~~~~Gl~v~v~di~~i~eG~I~~-gdG~~~~~V~Fr~lvFrPf~   80 (80)
T cd04330          22 NDAIEDELNKKYANKVIQNVGLCICLYDILEVEDGYILP-GDGASHYKVTFRMVVFRPFV   80 (80)
T ss_pred             HHHHHHHHHHHhCCcEeCCccEEEEEEEeEEEcCCEEEC-CCCCEEEEEEEEEEEEECCC
Confidence            457899999999999999999999999999999999999 99999999999999999996

Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis.

>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP

Probab=99.84  E-value=4.6e-21  Score=134.25  Aligned_cols=59  Identities=17%  Similarity=0.142  Sum_probs=56.6

Q ss_pred             HHHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeec
Q 048593            3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVK   62 (150)
Q Consensus         3 ~~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~   62 (150)
                      .-++.++|+++|+||+.+++||||||+|++++++|+|.| |||++||+|+|||++||||+
T Consensus        22 ~~~i~~~L~~k~~gkv~~~~G~~v~v~di~~i~~G~I~~-gdG~~~~~V~F~~ivFrPf~   80 (80)
T cd00655          22 KGVKKCLLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRP-GDGSAYVNVSFRAVVFKPFS   80 (80)
T ss_pred             HHHHHHHHHHHhCCeEeCCccEEEEEEEeEEEcCCEEEC-CCCCEEEEEEEEEEEEEcCC
Confidence            357899999999999999999999999999999999999 99999999999999999996

These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.

>cd04331 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain

Probab=99.82  E-value=4.5e-20  Score=129.44  Aligned_cols=58  Identities=26%  Similarity=0.301  Sum_probs=55.3

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeec
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVK   62 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~   62 (150)
                      -++.+.|+++++|||.+++||||||+|++++|+|+|.| |||++||+|+|||++|||..
T Consensus        23 ~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~eG~I~~-gdG~~~~~V~F~~ivFrP~~   80 (80)
T cd04331          23 EAVLEILKEKYEGRLDKDLGKIVSVLDVKDVGEGKIVH-GDGAVYHEVRFDALVFKPEL   80 (80)
T ss_pred             HHHHHHHHHHhcCcCcCCCCEEEEEEEEEEecCCEEEc-CCCCEEEEEEEEEEEEecCC
Confidence            46889999999999999999999999999999999999 99999999999999999963

RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA.

>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit

Probab=99.75  E-value=4.5e-18  Score=127.96  Aligned_cols=72  Identities=29%  Similarity=0.439  Sum_probs=49.8

Q ss_pred             eecCcEEEEEEEEe-----------------------------cCCCceeecc---ccceecCCCEEEEEEEEEEeeecC
Q 048593           60 PVKGEILHGVIHIA-----------------------------VCEQPFFSNE---QQAKIRNGLVVQFLVTAVQWIDEG  107 (150)
Q Consensus        60 Pf~gEVv~G~V~~v-----------------------------~~~~~~~~~~---~~~~i~~gd~VR~RI~~v~~~d~~  107 (150)
                      ||+||||.|+|+++                             .+++.|+|..   +..+++.|+.|||||.++.|.|.+
T Consensus         1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f~d~~   80 (122)
T PF08292_consen    1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIFPDVP   80 (122)
T ss_dssp             --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE----
T ss_pred             CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEEecCC
Confidence            99999999999999                             4556687754   334799999999999999997533


Q ss_pred             ------------------cCccCcEEEEEEccCCccccccCCCC
Q 048593          108 ------------------RNLKKKYLVFGRVEGESLGPVSLSGW  133 (150)
Q Consensus       108 ------------------~~~~~~~~~igsi~~d~LG~i~w~~w  133 (150)
                                        .++++||.++|||+++|||+++|  |
T Consensus        81 p~~~~~~~~~~~~~~~~~~~~~~Py~I~gs~~~~GLG~~sW--W  122 (122)
T PF08292_consen   81 PTPPPSAEASGEEEEEEEDEPKPPYQIIGSINEDGLGLVSW--W  122 (122)
T ss_dssp             -----------------------SEEEEEEB-STT-EEGGG--C
T ss_pred             CCCcccccccccccccccccCCCCeEEEEEecCCCCccccc--C
Confidence                              23679999999999999999999  9

Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.

>PF03876 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; InterPro: IPR005576 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core

Probab=99.53  E-value=4.5e-14  Score=95.16  Aligned_cols=53  Identities=25%  Similarity=0.308  Sum_probs=49.2

Q ss_pred             HHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEe
Q 048593            5 FVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTF   58 (150)
Q Consensus         5 ~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivF   58 (150)
                      .+.+.|.+.++||+.+++|+|||++|+..+++|+|.+ +||.++|+|+|+|++|
T Consensus        18 ~i~~~L~~~~~~k~~~~~G~~i~v~~i~~~~~g~I~~-~~g~~~~~V~f~~lvF   70 (70)
T PF03876_consen   18 GIKEQLLDKYEGKYIPELGVVIAVTDIKEISEGKIIP-GDGFVYFKVTFRALVF   70 (70)
T ss_dssp             HHHHHHHHHHTTEEETTTEEEEEEEEEEEESCEEE-T-TTSSEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHhCcCcCCceEEEEEeeeeEecCcEEEC-CCCCEEEEEEEEEEEC
Confidence            5677888888899999999999999999999999999 9999999999999998

Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable []. This entry represents the N-terminal, heterodimerisation domain of RPB7.; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2C35_F 3HKZ_E 2PMZ_T 2CKZ_D 2Y0S_E 2RF4_A 2JA7_G 1Y1V_G 2JA5_G 4A3D_G ....

>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain

Probab=99.45  E-value=4.4e-13  Score=95.24  Aligned_cols=59  Identities=17%  Similarity=0.356  Sum_probs=49.6

Q ss_pred             cCcEEEEEEEEe----------------------------cCCCceeec-cccceecCCCEEEEEEEEEEeeecCcCccC
Q 048593           62 KGEILHGVIHIA----------------------------VCEQPFFSN-EQQAKIRNGLVVQFLVTAVQWIDEGRNLKK  112 (150)
Q Consensus        62 ~gEVv~G~V~~v----------------------------~~~~~~~~~-~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~  112 (150)
                      +|||++|+|++|                            +++++|.|. +++.+|++|+.|||||++++| ++     .
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~-~~-----~   74 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRV-DA-----T   74 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEE-cc-----C
Confidence            699999999999                            224556553 456789999999999999999 55     3


Q ss_pred             cEEEEEEccCCccc
Q 048593          113 KYLVFGRVEGESLG  126 (150)
Q Consensus       113 ~~~~igsi~~d~LG  126 (150)
                      .++++|||++||||
T Consensus        75 ~~~~igt~~~~~LG   88 (88)
T cd04462          75 DIFAIGTIKDDYLG   88 (88)
T ss_pred             ceEEEEEccCCCCC
Confidence            79999999999998

RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.

>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain

Probab=99.18  E-value=6.3e-11  Score=83.86  Aligned_cols=56  Identities=16%  Similarity=0.085  Sum_probs=52.7

Q ss_pred             HHHHHHHhHHhceecCCc-eEEEEEeeeceeCC--eeeeeCCCcceEEEEEEEEEEeeeec
Q 048593            5 FVTRLLKGLINEKACKDQ-CYFLSVTNLKSIGR--ERGTVNESGVVFFPVTFLCRTFLPVK   62 (150)
Q Consensus         5 ~i~~ll~~~~~gk~~~~~-GliV~V~di~~i~~--G~I~~~gdG~v~~~V~FraivFrPf~   62 (150)
                      +|++.|...+- |+.+++ |+|+|.+|+..+++  |+|.+ ++|..+++|+||++|||||.
T Consensus        31 ~i~~~l~~~l~-ky~~~l~Gv~l~~~di~~~~~~~~~i~~-~~~~~~~~V~~~~lVFrP~~   89 (89)
T cd04328          31 GIKAQLLNPLL-KYSPKLKGVVLAYSNIKLLEGELAKIVD-DSPFIFVWISADFLVFRPKI   89 (89)
T ss_pred             HHHHHHhhhHh-hhcccCCeEEEEecceEeccccceeeeC-CCcEEEEEEEEEEEEEecCC
Confidence            68888899988 999999 99999999999977  99999 99999999999999999985

Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, invo

>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain

Probab=97.55  E-value=0.00025  Score=50.39  Aligned_cols=42  Identities=19%  Similarity=0.207  Sum_probs=31.9

Q ss_pred             cceecCCCEEEEEEEEEEeeecCcCccCcEE-EEEEccCCccccccC
Q 048593           85 QAKIRNGLVVQFLVTAVQWIDEGRNLKKKYL-VFGRVEGESLGPVSL  130 (150)
Q Consensus        85 ~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~-~igsi~~d~LG~i~w  130 (150)
                      ...++.||.|+++|.++.. +..   .|... +.-|+++++|||+.|
T Consensus        51 ~~~~~~Gd~v~vkI~~vd~-~~~---~~~~~~i~ls~k~~~~g~~~~   93 (99)
T cd04460          51 KRVLKVGDVVRARIVAVSL-KER---RPRESKIGLTMRQPGLGKLEW   93 (99)
T ss_pred             CCEECCCCEEEEEEEEEeH-HHC---cCCCceEEEEEecCCCCcHHH
Confidence            4679999999999999885 321   01234 444999999999999

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.

>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain

Probab=96.21  E-value=0.014  Score=39.79  Aligned_cols=62  Identities=19%  Similarity=0.244  Sum_probs=42.8

Q ss_pred             eeeecCcEEEEEEEEecCCCce---------------eec----cccceecCCCEEEEEEEEEEeeecCcCccCcEEEEE
Q 048593           58 FLPVKGEILHGVIHIAVCEQPF---------------FSN----EQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFG  118 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~~~~---------------~~~----~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~ig  118 (150)
                      |.|.+|.++.|+|+++.++...               +..    +-...+++||.|++||..+.- +        ..+.=
T Consensus         2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~-~--------~~i~L   72 (82)
T cd04454           2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGD-D--------MNVLL   72 (82)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCC-C--------CCEEE
Confidence            6799999999999999333211               111    112358999999999998652 1        23666


Q ss_pred             EccCCccccc
Q 048593          119 RVEGESLGPV  128 (150)
Q Consensus       119 si~~d~LG~i  128 (150)
                      |++++.||.+
T Consensus        73 S~~~~~~Gvi   82 (82)
T cd04454          73 TTADNELGVI   82 (82)
T ss_pred             EECCCCCccC
Confidence            7788888864

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]

Probab=96.20  E-value=0.037  Score=46.17  Aligned_cols=97  Identities=13%  Similarity=0.096  Sum_probs=70.5

Q ss_pred             HHHHHHHHhHHhceecCCc-eEEEEEeeecee-CCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEecCC-----
Q 048593            4 IFVTRLLKGLINEKACKDQ-CYFLSVTNLKSI-GRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIAVCE-----   76 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~-GliV~V~di~~i-~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v~~~-----   76 (150)
                      +++++.|..+.. ++...+ |++++.-+|+-. ..++|.+ .||..+-.+.=..+||+|-.|.+|+|.|-.+...     
T Consensus        49 ~~i~ehld~~vl-~y~~~l~GivLgydnIKvLg~~aki~~-D~pf~hlwi~adfyVf~Pk~Gd~LeG~Vn~vS~sHIglL  126 (253)
T KOG4134|consen   49 ALIEEHLDTKVL-FYDSGLDGIVLGYDNIKVLGQTAKIRA-DDPFMHLWINADFYVFRPKAGDILEGVVNHVSRSHIGLL  126 (253)
T ss_pred             HHHHHHhhHHHh-hhccCCCceEEeecceEeeccccceec-CCCceEEEEeeeEEEECCCCCCeeeeeeeecchhhhcee
Confidence            356677777764 666554 788888778765 4589999 9999999999999999999999999999887111     


Q ss_pred             -----Ccee----eccccceecCCCEEEEEEEEEE
Q 048593           77 -----QPFF----SNEQQAKIRNGLVVQFLVTAVQ  102 (150)
Q Consensus        77 -----~~~~----~~~~~~~i~~gd~VR~RI~~v~  102 (150)
                           |+..    ...+-..|..++..-+||....
T Consensus       127 Ihg~FNASIpk~nip~dw~fI~md~eee~~v~ntD  161 (253)
T KOG4134|consen  127 IHGVFNASIPKTNIPADWEFIAMDQEEEIRVKNTD  161 (253)
T ss_pred             ehhhhhccCCCCCCccceeeecCCchhhhceeecc
Confidence                 1111    1222336788888888887654

>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain

Probab=95.91  E-value=0.026  Score=40.17  Aligned_cols=66  Identities=18%  Similarity=0.409  Sum_probs=46.5

Q ss_pred             eeeecCcEEEEEEEEecC---------CCc-e-----e---eccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEE
Q 048593           58 FLPVKGEILHGVIHIAVC---------EQP-F-----F---SNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGR  119 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~---------~~~-~-----~---~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igs  119 (150)
                      |.|-.|.+|-|+|+++..         ..+ .     |   .+..+..+++||.|-+||..+.- +.    .+...++.+
T Consensus         2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~~~~~-~~----~~eLtc~~~   76 (86)
T cd05790           2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANR-DM----EPELSCVDS   76 (86)
T ss_pred             CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccccccccccCCCCCEEEEEEEecCC-CC----CeEEEEeCC
Confidence            789999999999999911         111 1     1   12334579999999999988764 32    257778764


Q ss_pred             c-cCCccccc
Q 048593          120 V-EGESLGPV  128 (150)
Q Consensus       120 i-~~d~LG~i  128 (150)
                      - +.++||+.
T Consensus        77 ~~k~~g~G~L   86 (86)
T cd05790          77 SGKADGFGPL   86 (86)
T ss_pred             CCcccccccC
Confidence            3 67889874

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain

Probab=95.76  E-value=0.037  Score=37.81  Aligned_cols=61  Identities=15%  Similarity=0.146  Sum_probs=40.1

Q ss_pred             eeeecCcEEEEEEEEecCCCce---------ee-----c---------cccceecCCCEEEEEEEEEEeeecCcCccCcE
Q 048593           58 FLPVKGEILHGVIHIAVCEQPF---------FS-----N---------EQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKY  114 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~~~~---------~~-----~---------~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~  114 (150)
                      |.|-+|+++.|+|+++.+....         +.     .         +-...+.+||.|++||..+.-         .-
T Consensus         2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~---------~~   72 (86)
T cd05789           2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDS---------DG   72 (86)
T ss_pred             CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECC---------CC
Confidence            6799999999999999222110         10     0         011258999999999988641         13


Q ss_pred             EEEEEccCCcccc
Q 048593          115 LVFGRVEGESLGP  127 (150)
Q Consensus       115 ~~igsi~~d~LG~  127 (150)
                      .+.=|++..+||.
T Consensus        73 ~i~LS~~~~~~g~   85 (86)
T cd05789          73 SVSLHTRSLKYGK   85 (86)
T ss_pred             CEEEEeCcccccC
Confidence            4455667777775

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=95.67  E-value=0.041  Score=36.25  Aligned_cols=45  Identities=20%  Similarity=0.228  Sum_probs=32.1

Q ss_pred             eeecCcEEEEEEEEecCCCce---------ee----------ccccceecCCCEEEEEEEEEEe
Q 048593           59 LPVKGEILHGVIHIAVCEQPF---------FS----------NEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        59 rPf~gEVv~G~V~~v~~~~~~---------~~----------~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      +|..|++++|+|+++...+.+         |.          .+....+.+|+.|+++|.++..
T Consensus         1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~   64 (74)
T PF00575_consen    1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDK   64 (74)
T ss_dssp             -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEET
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEEC
Confidence            578999999999999322111         11          1123479999999999999875

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....

>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain

Probab=95.34  E-value=0.032  Score=39.65  Aligned_cols=62  Identities=23%  Similarity=0.274  Sum_probs=41.1

Q ss_pred             eeeecCcEEEEEEEEecCCC---------------ce---ee-c---c---c----cceecCCCEEEEEEEEEEeeecCc
Q 048593           58 FLPVKGEILHGVIHIAVCEQ---------------PF---FS-N---E---Q----QAKIRNGLVVQFLVTAVQWIDEGR  108 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~~---------------~~---~~-~---~---~----~~~i~~gd~VR~RI~~v~~~d~~~  108 (150)
                      +.|..|.++-|+|+++....               ++   +- +   +   +    ...+++||.||+||.+..  +.  
T Consensus         2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~--~~--   77 (92)
T cd05791           2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLG--DA--   77 (92)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcC--CC--
Confidence            67999999999999991110               10   00 0   0   0    135899999999999865  32  


Q ss_pred             CccCcEEEEEEccCCccccc
Q 048593          109 NLKKKYLVFGRVEGESLGPV  128 (150)
Q Consensus       109 ~~~~~~~~igsi~~d~LG~i  128 (150)
                         ++|.  =|++++.||.+
T Consensus        78 ---~~~~--Lst~~~~lGVv   92 (92)
T cd05791          78 ---SSYY--LSTAENELGVV   92 (92)
T ss_pred             ---CCcE--EEecCCCCccC
Confidence               2333  46688888864

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=94.98  E-value=0.065  Score=44.09  Aligned_cols=63  Identities=16%  Similarity=0.333  Sum_probs=42.7

Q ss_pred             eeeecCcEEEEEEEEecCCC----------cee------ec-------cccceecCCCEEEEEEEEEEeeecCcCccCcE
Q 048593           58 FLPVKGEILHGVIHIAVCEQ----------PFF------SN-------EQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKY  114 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~~----------~~~------~~-------~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~  114 (150)
                      |.|..|.+|.|+|+++....          ..+      +.       +-...+++||.|++||..+.- +.      + 
T Consensus        59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~-~~------~-  130 (235)
T PRK04163         59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR-TR------D-  130 (235)
T ss_pred             ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC-CC------c-
Confidence            89999999999999992111          111      11       111258999999999998762 21      2 


Q ss_pred             EEEEEccCCcccccc
Q 048593          115 LVFGRVEGESLGPVS  129 (150)
Q Consensus       115 ~~igsi~~d~LG~i~  129 (150)
                       +.=|+++++||.+.
T Consensus       131 -~~LS~k~~~lG~L~  144 (235)
T PRK04163        131 -VVLTLKGKGLGKIE  144 (235)
T ss_pred             -EEEEEcCCCCCccC
Confidence             34456888899876

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

Probab=94.14  E-value=0.33  Score=39.37  Aligned_cols=82  Identities=21%  Similarity=0.178  Sum_probs=50.6

Q ss_pred             CeeeeeCCCcceEEEEEEEEEEeeeecC--------cEEEEEEEEe------------cC-C------Cce-e--e----
Q 048593           36 RERGTVNESGVVFFPVTFLCRTFLPVKG--------EILHGVIHIA------------VC-E------QPF-F--S----   81 (150)
Q Consensus        36 ~G~I~~~gdG~v~~~V~FraivFrPf~g--------EVv~G~V~~v------------~~-~------~~~-~--~----   81 (150)
                      +|.|...-.|-+.++..=+.+.-+|++.        -++-|.|+++            .+ +      +.- +  +    
T Consensus        30 ~g~i~Aa~~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~  109 (188)
T COG1096          30 GGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRD  109 (188)
T ss_pred             CCEEEEeecccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEeccc
Confidence            4555532357777766656665555554        8999999999            11 1      110 1  1    


Q ss_pred             ---ccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccc
Q 048593           82 ---NEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPV  128 (150)
Q Consensus        82 ---~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i  128 (150)
                         +.....|+.||.||+||++.-  +       ||++  |+++..||.+
T Consensus       110 ~~~~~~~d~f~~GDivrA~Vis~~--~-------~~~L--st~~~dlGVI  148 (188)
T COG1096         110 GYVEKLSDAFRIGDIVRARVISTG--D-------PIQL--STKGNDLGVI  148 (188)
T ss_pred             ccccccccccccccEEEEEEEecC--C-------CeEE--EecCCcceEE
Confidence               122236999999999999976  2       3433  4566677766

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=91.86  E-value=0.075  Score=50.09  Aligned_cols=73  Identities=15%  Similarity=0.145  Sum_probs=51.7

Q ss_pred             eeeceeCCeeeeeCCCcceEEEE--EEEEEEeeeecCcEEEEEEEEecCCCcee-------------------eccccce
Q 048593           29 TNLKSIGRERGTVNESGVVFFPV--TFLCRTFLPVKGEILHGVIHIAVCEQPFF-------------------SNEQQAK   87 (150)
Q Consensus        29 ~di~~i~~G~I~~~gdG~v~~~V--~FraivFrPf~gEVv~G~V~~v~~~~~~~-------------------~~~~~~~   87 (150)
                      +||.+-|..+|.. .++..+..+  .++.+++.|.+|+++.|+|+++.+...++                   .+.-...
T Consensus       584 I~i~ddG~V~i~~-~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~  662 (684)
T TIGR03591       584 IDIEDDGTVKIAA-SDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDV  662 (684)
T ss_pred             EEEecCeEEEEEE-CcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhc
Confidence            3455556666667 788777777  67777889999999999999992221111                   1111235


Q ss_pred             ecCCCEEEEEEEEEE
Q 048593           88 IRNGLVVQFLVTAVQ  102 (150)
Q Consensus        88 i~~gd~VR~RI~~v~  102 (150)
                      ++.||.|++||.++.
T Consensus       663 ~kvGD~V~VkVi~id  677 (684)
T TIGR03591       663 LKEGDEVKVKVLEID  677 (684)
T ss_pred             cCCCCEEEEEEEEEC
Confidence            899999999999876

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>smart00316 S1 Ribosomal protein S1-like RNA-binding domain

Probab=91.66  E-value=0.52  Score=29.47  Aligned_cols=42  Identities=14%  Similarity=0.158  Sum_probs=28.2

Q ss_pred             cCcEEEEEEEEecCCCc---------eee-----cc-----ccceecCCCEEEEEEEEEEe
Q 048593           62 KGEILHGVIHIAVCEQP---------FFS-----NE-----QQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        62 ~gEVv~G~V~~v~~~~~---------~~~-----~~-----~~~~i~~gd~VR~RI~~v~~  103 (150)
                      .|+++.|+|+++.+...         .+.     .+     ....++.|+.|+++|..+..
T Consensus         2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~   62 (72)
T smart00316        2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE   62 (72)
T ss_pred             CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeC
Confidence            58899999999822211         111     00     11358999999999999874

>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=90.79  E-value=0.89  Score=29.75  Aligned_cols=18  Identities=22%  Similarity=0.206  Sum_probs=15.5

Q ss_pred             ceecCCCEEEEEEEEEEe
Q 048593           86 AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        86 ~~i~~gd~VR~RI~~v~~  103 (150)
                      ..+.+||.|+++|..+..
T Consensus        46 ~~~~~Gd~v~~~V~~~d~   63 (73)
T cd05706          46 YKFKKNDIVRACVLSVDV   63 (73)
T ss_pred             cccCCCCEEEEEEEEEeC
Confidence            358999999999998774

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain

Probab=90.41  E-value=0.87  Score=30.25  Aligned_cols=17  Identities=18%  Similarity=0.036  Sum_probs=14.7

Q ss_pred             eecCCCEEEEEEEEEEe
Q 048593           87 KIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        87 ~i~~gd~VR~RI~~v~~  103 (150)
                      .++.||.|++||..+..
T Consensus        48 ~~~~Gd~v~vkv~~vd~   64 (73)
T cd05686          48 VVDVGEKVWVKVIGREM   64 (73)
T ss_pred             EECCCCEEEEEEEEECC
Confidence            58999999999988764

pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.

>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

Probab=89.83  E-value=0.98  Score=29.59  Aligned_cols=44  Identities=14%  Similarity=0.062  Sum_probs=28.6

Q ss_pred             eecCcEEEEEEEEecCCCc-----------eee----------ccccceecCCCEEEEEEEEEEe
Q 048593           60 PVKGEILHGVIHIAVCEQP-----------FFS----------NEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        60 Pf~gEVv~G~V~~v~~~~~-----------~~~----------~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      |-+|+++.|+|+++.+...           -+.          .+....+..||.|++||..+..
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~   65 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDK   65 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEEC
Confidence            5578899999998821111           111          0111358999999999998764

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c

>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain

Probab=89.78  E-value=0.89  Score=29.40  Aligned_cols=18  Identities=22%  Similarity=0.254  Sum_probs=15.6

Q ss_pred             ceecCCCEEEEEEEEEEe
Q 048593           86 AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        86 ~~i~~gd~VR~RI~~v~~  103 (150)
                      ..+++||.|++||..+..
T Consensus        43 ~~~~~Gd~v~~~v~~~d~   60 (73)
T cd05691          43 ERFKVGDEVEAKITNVDR   60 (73)
T ss_pred             HccCCCCEEEEEEEEEeC
Confidence            358999999999999875

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=89.39  E-value=0.96  Score=29.39  Aligned_cols=18  Identities=33%  Similarity=0.366  Sum_probs=15.7

Q ss_pred             ceecCCCEEEEEEEEEEe
Q 048593           86 AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        86 ~~i~~gd~VR~RI~~v~~  103 (150)
                      ..+..|+.+.+||.++..
T Consensus        43 ~~~~~Gd~i~~~V~~id~   60 (69)
T cd05697          43 KKFKPGLKVKCRVLSVEP   60 (69)
T ss_pred             HcCCCCCEEEEEEEEEEC
Confidence            469999999999999874

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=89.08  E-value=1.2  Score=28.99  Aligned_cols=18  Identities=22%  Similarity=0.086  Sum_probs=15.6

Q ss_pred             ceecCCCEEEEEEEEEEe
Q 048593           86 AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        86 ~~i~~gd~VR~RI~~v~~  103 (150)
                      ..+.+||.|++||..+..
T Consensus        46 ~~~~~Gd~v~v~i~~vd~   63 (77)
T cd05708          46 KLFRVGDKVRAKVLKIDA   63 (77)
T ss_pred             HeecCCCEEEEEEEEEeC
Confidence            368999999999999874

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain

Probab=89.08  E-value=1.7  Score=28.70  Aligned_cols=18  Identities=28%  Similarity=0.200  Sum_probs=16.1

Q ss_pred             ceecCCCEEEEEEEEEEe
Q 048593           86 AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        86 ~~i~~gd~VR~RI~~v~~  103 (150)
                      ..++.||.||+||.++..
T Consensus        56 ~~~~~gd~v~v~v~~vd~   73 (83)
T cd04471          56 KVFRLGDKVKVRVVRVDL   73 (83)
T ss_pred             CEEcCCCEEEEEEEEecc
Confidence            578999999999999875

RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.

>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=88.62  E-value=0.96  Score=29.33  Aligned_cols=18  Identities=11%  Similarity=0.213  Sum_probs=15.0

Q ss_pred             ceecCCCEEEEEEEEEEe
Q 048593           86 AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        86 ~~i~~gd~VR~RI~~v~~  103 (150)
                      ..+.+||.|++||..+..
T Consensus        43 ~~~~~Gd~v~~~v~~~d~   60 (68)
T cd05707          43 KRFKVGQLVKGKIVSIDP   60 (68)
T ss_pred             hccCCCCEEEEEEEEEeC
Confidence            358999999999988763

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain

Probab=88.43  E-value=1.2  Score=28.94  Aligned_cols=16  Identities=25%  Similarity=0.362  Sum_probs=14.5

Q ss_pred             eecCCCEEEEEEEEEE
Q 048593           87 KIRNGLVVQFLVTAVQ  102 (150)
Q Consensus        87 ~i~~gd~VR~RI~~v~  102 (150)
                      .+++||.++++|..+.
T Consensus        44 ~~~~Gd~i~~~i~~~~   59 (70)
T cd05687          44 EVKVGDEVEVYVLRVE   59 (70)
T ss_pred             cCCCCCEEEEEEEEEE
Confidence            5899999999999876

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=87.90  E-value=6.1  Score=33.19  Aligned_cols=47  Identities=19%  Similarity=0.276  Sum_probs=33.7

Q ss_pred             EeeeecCcEEEEEEEEec---------CCCcee-----------e---ccccceecCCCEEEEEEEEEEe
Q 048593           57 TFLPVKGEILHGVIHIAV---------CEQPFF-----------S---NEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        57 vFrPf~gEVv~G~V~~v~---------~~~~~~-----------~---~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      -|.|-.|.+|-|.|.++.         ...+.+           .   .+-+.++++||.|-+||..+--
T Consensus        59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~  128 (239)
T COG1097          59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR  128 (239)
T ss_pred             cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC
Confidence            588999999999999991         100101           1   1223479999999999998763

>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

Probab=87.79  E-value=1.9  Score=27.19  Aligned_cols=18  Identities=17%  Similarity=0.104  Sum_probs=15.5

Q ss_pred             ceecCCCEEEEEEEEEEe
Q 048593           86 AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        86 ~~i~~gd~VR~RI~~v~~  103 (150)
                      ..++.||.|+++|..+..
T Consensus        43 ~~~~~Gd~v~v~i~~vd~   60 (68)
T cd05688          43 EVVNVGDEVEVKVLKIDK   60 (68)
T ss_pred             HEECCCCEEEEEEEEEEC
Confidence            368999999999999864

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=87.22  E-value=1.2  Score=29.70  Aligned_cols=16  Identities=13%  Similarity=0.306  Sum_probs=13.9

Q ss_pred             eecCCCEEEEEEEEEE
Q 048593           87 KIRNGLVVQFLVTAVQ  102 (150)
Q Consensus        87 ~i~~gd~VR~RI~~v~  102 (150)
                      .+++||.||++|.++.
T Consensus        48 ~~~~Gd~v~~kV~~~~   63 (72)
T cd05704          48 GFKPGKIVRCCILSKK   63 (72)
T ss_pred             hCCCCCEEEEEEEEec
Confidence            5889999999998864

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

Probab=86.14  E-value=1.8  Score=27.12  Aligned_cols=17  Identities=18%  Similarity=0.239  Sum_probs=14.6

Q ss_pred             eecCCCEEEEEEEEEEe
Q 048593           87 KIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        87 ~i~~gd~VR~RI~~v~~  103 (150)
                      .++.||.|++||..+..
T Consensus        44 ~~~~Gd~v~v~v~~~~~   60 (69)
T cd05692          44 VLKEGDKVKVKVLSIDA   60 (69)
T ss_pred             ccCCCCEEEEEEEEECC
Confidence            58999999999988763

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []

Probab=86.12  E-value=2.3  Score=29.90  Aligned_cols=14  Identities=21%  Similarity=0.385  Sum_probs=10.5

Q ss_pred             eecCcEEEEEEEEe
Q 048593           60 PVKGEILHGVIHIA   73 (150)
Q Consensus        60 Pf~gEVv~G~V~~v   73 (150)
                      |-.|-++.|+|+++
T Consensus         2 P~vGdiV~~rVtrv   15 (82)
T PF10447_consen    2 PKVGDIVIARVTRV   15 (82)
T ss_dssp             --TT-EEEEEEEEE
T ss_pred             CCCCCEEEEEEEEE
Confidence            88899999999999

The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.

>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=85.95  E-value=2.3  Score=27.83  Aligned_cols=16  Identities=19%  Similarity=0.183  Sum_probs=14.3

Q ss_pred             eecCCCEEEEEEEEEE
Q 048593           87 KIRNGLVVQFLVTAVQ  102 (150)
Q Consensus        87 ~i~~gd~VR~RI~~v~  102 (150)
                      .+..||.|++||.++.
T Consensus        46 ~~~~Gd~i~~kVl~~d   61 (70)
T cd05702          46 KFKIGQKIKARVIGGH   61 (70)
T ss_pred             hCCCCCEEEEEEEEEe
Confidence            5899999999998875

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain

Probab=84.84  E-value=3.9  Score=26.14  Aligned_cols=18  Identities=17%  Similarity=0.217  Sum_probs=15.6

Q ss_pred             ceecCCCEEEEEEEEEEe
Q 048593           86 AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        86 ~~i~~gd~VR~RI~~v~~  103 (150)
                      ..+++|+.|+++|..+..
T Consensus        44 ~~~~~G~~v~v~v~~id~   61 (69)
T cd05690          44 EIYKKGQEVEAVVLNIDV   61 (69)
T ss_pred             hEECCCCEEEEEEEEEEC
Confidence            468999999999998874

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]

Probab=84.20  E-value=2.9  Score=33.85  Aligned_cols=52  Identities=21%  Similarity=0.235  Sum_probs=33.5

Q ss_pred             EEEEEEEEEeeeecCcEEEEEEEEe-----------cCCC---cee---e-cc-------cc----ceecCCCEEEEEEE
Q 048593           49 FPVTFLCRTFLPVKGEILHGVIHIA-----------VCEQ---PFF---S-NE-------QQ----AKIRNGLVVQFLVT   99 (150)
Q Consensus        49 ~~V~FraivFrPf~gEVv~G~V~~v-----------~~~~---~~~---~-~~-------~~----~~i~~gd~VR~RI~   99 (150)
                      .+..|..+  -||.|-|+.++|+.+           -++.   ..|   . ++       ++    ..+++||.||+||+
T Consensus        57 ~~~~~~~~--LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVi  134 (193)
T KOG3409|consen   57 EKQLFNEL--LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVI  134 (193)
T ss_pred             cccchhhc--CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEe
Confidence            44455554  599999999999998           1110   011   1 11       11    14889999999999


Q ss_pred             EEE
Q 048593          100 AVQ  102 (150)
Q Consensus       100 ~v~  102 (150)
                      +..
T Consensus       135 s~~  137 (193)
T KOG3409|consen  135 SLG  137 (193)
T ss_pred             ecC
Confidence            943

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=84.11  E-value=3.3  Score=32.68  Aligned_cols=46  Identities=17%  Similarity=0.221  Sum_probs=31.9

Q ss_pred             EeeeecCcEEEEEEEEecCCCce-------------------ee--c---cc-----cceecCCCEEEEEEEEEE
Q 048593           57 TFLPVKGEILHGVIHIAVCEQPF-------------------FS--N---EQ-----QAKIRNGLVVQFLVTAVQ  102 (150)
Q Consensus        57 vFrPf~gEVv~G~V~~v~~~~~~-------------------~~--~---~~-----~~~i~~gd~VR~RI~~v~  102 (150)
                      .+.|-.|+++.|+|+++.+....                   +.  +   +.     ...+.+||.|++||..+.
T Consensus        59 ~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~  133 (189)
T PRK09521         59 PPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT  133 (189)
T ss_pred             CCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence            47788999999999999222111                   10  0   00     235899999999999875

>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa

Probab=83.98  E-value=2.8  Score=26.23  Aligned_cols=17  Identities=18%  Similarity=0.225  Sum_probs=15.0

Q ss_pred             eecCCCEEEEEEEEEEe
Q 048593           87 KIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        87 ~i~~gd~VR~RI~~v~~  103 (150)
                      .+++||.|++||..+..
T Consensus        44 ~~~~Gd~v~v~i~~vd~   60 (68)
T cd05685          44 VVSVGDIVEVKVISIDE   60 (68)
T ss_pred             hcCCCCEEEEEEEEEEC
Confidence            58999999999998874

The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.

>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=83.78  E-value=2.3  Score=27.44  Aligned_cols=18  Identities=28%  Similarity=0.270  Sum_probs=15.3

Q ss_pred             ceecCCCEEEEEEEEEEe
Q 048593           86 AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        86 ~~i~~gd~VR~RI~~v~~  103 (150)
                      ..+.+|+.+++||.++..
T Consensus        43 ~~~~~G~~i~v~v~~~d~   60 (70)
T cd05698          43 EHFRVGQVVKVKVLSCDP   60 (70)
T ss_pred             HcccCCCEEEEEEEEEcC
Confidence            358999999999998763

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=83.72  E-value=3.9  Score=27.52  Aligned_cols=18  Identities=17%  Similarity=0.150  Sum_probs=15.8

Q ss_pred             ceecCCCEEEEEEEEEEe
Q 048593           86 AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        86 ~~i~~gd~VR~RI~~v~~  103 (150)
                      ..+.+|+.|+++|.++.-
T Consensus        49 ~~~~~G~~v~~kVl~id~   66 (74)
T cd05705          49 KYLPEGKLLTAKVLSVNS   66 (74)
T ss_pred             cccCCCCEEEEEEEEEEC
Confidence            468999999999999874

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains

Probab=83.39  E-value=2.7  Score=28.35  Aligned_cols=44  Identities=18%  Similarity=0.154  Sum_probs=28.7

Q ss_pred             eecCcEEEEEEEEecCCCc---------eee----------ccccceecCCCEEEEEEEEEEe
Q 048593           60 PVKGEILHGVIHIAVCEQP---------FFS----------NEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        60 Pf~gEVv~G~V~~v~~~~~---------~~~----------~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      +-.|+++.|+|+++.+...         -|.          .+-...+.+|+.|++||..+..
T Consensus        12 ~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~   74 (83)
T cd04461          12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE   74 (83)
T ss_pred             CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcC
Confidence            4578888888888822111         111          1112368999999999999774

Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK08582 hypothetical protein; Provisional

Probab=82.30  E-value=4  Score=31.07  Aligned_cols=41  Identities=20%  Similarity=0.261  Sum_probs=27.1

Q ss_pred             cCcEEEEEEEEecCCCce-------------------eeccccceecCCCEEEEEEEEEE
Q 048593           62 KGEILHGVIHIAVCEQPF-------------------FSNEQQAKIRNGLVVQFLVTAVQ  102 (150)
Q Consensus        62 ~gEVv~G~V~~v~~~~~~-------------------~~~~~~~~i~~gd~VR~RI~~v~  102 (150)
                      .|++++|+|+++.....+                   +..+....+.+||.|+++|..+.
T Consensus         5 vG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id   64 (139)
T PRK08582          5 VGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE   64 (139)
T ss_pred             CCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEEC
Confidence            588888888888111111                   01111246899999999999976

>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

Probab=81.54  E-value=4.1  Score=25.65  Aligned_cols=16  Identities=25%  Similarity=0.258  Sum_probs=14.2

Q ss_pred             eecCCCEEEEEEEEEE
Q 048593           87 KIRNGLVVQFLVTAVQ  102 (150)
Q Consensus        87 ~i~~gd~VR~RI~~v~  102 (150)
                      .++.||.|+++|..+.
T Consensus        44 ~~~~Gd~v~v~v~~~d   59 (68)
T cd04472          44 VLKVGDEVKVKVIEVD   59 (68)
T ss_pred             ccCCCCEEEEEEEEEC
Confidence            5799999999998875

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.

>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain

Probab=80.64  E-value=7.8  Score=25.09  Aligned_cols=18  Identities=17%  Similarity=0.150  Sum_probs=15.5

Q ss_pred             ceecCCCEEEEEEEEEEe
Q 048593           86 AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        86 ~~i~~gd~VR~RI~~v~~  103 (150)
                      ..+++|+.|+++|..+..
T Consensus        47 ~~~~~Gd~v~v~v~~id~   64 (72)
T cd05689          47 KVVSLGDEVEVMVLDIDE   64 (72)
T ss_pred             cEeCCCCEEEEEEEEeeC
Confidence            468999999999988774

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=80.06  E-value=6.6  Score=25.62  Aligned_cols=18  Identities=17%  Similarity=0.126  Sum_probs=15.3

Q ss_pred             ceecCCCEEEEEEEEEEe
Q 048593           86 AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        86 ~~i~~gd~VR~RI~~v~~  103 (150)
                      ..++.|+.|.+||..+..
T Consensus        41 ~~~~~G~~i~~kVi~id~   58 (66)
T cd05695          41 STYKEGQKVRARILYVDP   58 (66)
T ss_pred             cCcCCCCEEEEEEEEEeC
Confidence            469999999999998763

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain

Probab=80.03  E-value=9.6  Score=24.80  Aligned_cols=42  Identities=21%  Similarity=0.274  Sum_probs=29.4

Q ss_pred             ecCcEEEEEEEEecCCCcee--------e--cc--ccceecCCCEEEEEEEEEE
Q 048593           61 VKGEILHGVIHIAVCEQPFF--------S--NE--QQAKIRNGLVVQFLVTAVQ  102 (150)
Q Consensus        61 f~gEVv~G~V~~v~~~~~~~--------~--~~--~~~~i~~gd~VR~RI~~v~  102 (150)
                      ..|+++.|+|.++.+...++        .  ++  ....+++|+.|++-|..+.
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~~~~~~~Gd~v~v~v~~v~   55 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPGESYRPGDRIKAYVLEVR   55 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCCCCcCCCCCEEEEEEEEEe
Confidence            57999999999994433222        1  00  0125799999999999987

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.

---

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

ID	Length	Definition	E-value
Query	150
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	3e-05
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	1e-04
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	2e-04
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	3e-04
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	3e-04
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	5e-04
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	9e-04

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} Length = 218

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 22/133 (16%), Positives = 39/133 (29%), Gaps = 34/133 (25%)

Query: 6   VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEI 65
           +T  L      K   +    +++ +L ++  E       G  +  VTF    F P  GEI
Sbjct: 26  ITHQLNNKFANKIIPNVGLCITIYDLLTVE-EGQLKPGDGSSYINVTFRAVVFKPFLGEI 84

Query: 66  LHGVIH------IAVCEQPFFSN---------------------------EQQAKIRNGL 92
           + G I       I V     F +                           E +       
Sbjct: 85  VTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNE 144

Query: 93  VVQFLVTAVQWID 105
            ++F +    ++D
Sbjct: 145 KIRFRIEREVFVD 157

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} Length = 203

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 14/66 (21%), Positives = 24/66 (36%), Gaps = 1/66 (1%)

Query: 6  VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEI 65
          +   +      K  ++    + V +   IG E       G  +  V F    F P +GE+
Sbjct: 26 LAEEIHKKYANKVIQNIGLAICVYDFLKIG-EGIIKYGDGSSYMNVVFRLIIFRPFRGEV 84

Query: 66 LHGVIH 71
          + G I 
Sbjct: 85 MLGKIK 90

>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 Length = 215

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 6  VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTV-NESGVVFFPVTFLCRTFLPVKGE 64
          +   L   +         Y L V +  +I  +RG +    G   F V +    F P KGE
Sbjct: 26 LKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGE 85

Query: 65 ILHGVIH 71
          ++ G + 
Sbjct: 86 VVDGTVV 92

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ... Length = 171

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 22/152 (14%), Positives = 41/152 (26%), Gaps = 35/152 (23%)

Query: 6   VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTV-NESGVVFFPVTFLCRTFLPVKGE 64
           +   L   +         Y L V +  +I  +RG +    G   F V +    F P KGE
Sbjct: 26  LKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGE 85

Query: 65  ILHGVI------HIAVC----------------------EQPFFSNEQQAKIRNGLVVQF 96
           ++ G +         V                         P      +  I     ++ 
Sbjct: 86  VVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRV 145

Query: 97  LVTAVQWIDEGRNLKKKYLVFGRVEGESLGPV 128
            +          +        G ++ + LG +
Sbjct: 146 KIEGC------ISQVSSIHAIGSIKEDYLGAI 171

>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1 Length = 172

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 23/154 (14%), Positives = 48/154 (31%), Gaps = 37/154 (24%)

Query: 6   VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEI 65
           V + L   +         + ++VT + +IG         G V +PV +    F P KGE+
Sbjct: 26  VKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGV-IQPGRGFVLYPVKYKAIVFRPFKGEV 84

Query: 66  LHGV-------------------IHIAVCEQP-----------FFSNEQQAKIRNGLVVQ 95
           +  V                   I                   + + ++   I+    ++
Sbjct: 85  VDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIR 144

Query: 96  FLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVS 129
             +   +      +    + + G +  + LG VS
Sbjct: 145 LKIVGTRV-----DKNDIFAI-GSLMDDYLGLVS 172

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1 Length = 187

 Score = 37.6 bits (87), Expect = 5e-04
 Identities = 27/153 (17%), Positives = 50/153 (32%), Gaps = 33/153 (21%)

Query: 6   VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEI 65
           V ++L      +  KD  + LS+ ++K IG E   V+  G  + PV F    ++P   E+
Sbjct: 26  VKKILMEKYEGRLDKDVGFVLSIVDVKDIG-EGKVVHGDGSAYHPVVFETLVYIPEMYEL 84

Query: 66  LHGVIHIAVC-----------------------------EQPFFSNEQQAKIRNGLVVQF 96
           + G +   V                               +     E    +  G  V+ 
Sbjct: 85  IEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRA 144

Query: 97  LVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVS 129
            + A+    E    K+   +   +    LG + 
Sbjct: 145 RIVAISLKAER---KRGSKIALTMRQPYLGKLE 174

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 172

 Score = 36.9 bits (85), Expect = 9e-04
 Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 6  VTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTV-NESGVVFFPVTFLCRTFLPVKGE 64
          +   L   +         Y + V +  +I  ++G V    G   F V +    + P +GE
Sbjct: 27 LKAKLLADVEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLWRPFRGE 86

Query: 65 ILHGVIH 71
          ++  ++ 
Sbjct: 87 VVDAIVT 93

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	150
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	100.0
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	100.0
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	99.98
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	99.96
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.94
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	99.92
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	99.91
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	99.9
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	99.81
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	96.88
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	96.16
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	95.77
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	95.4
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	94.82
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	94.78
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	94.45
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	93.83
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	93.36
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	92.39
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	91.46
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	90.63
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	90.39
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	89.4
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	87.29
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	87.07
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	87.05
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	86.56
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	83.59
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	81.94
2bh8_A	101	1B11; transcription, molecular evolution, unique a	81.62

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.3e-35  Score=239.98  Aligned_cols=130  Identities=19%  Similarity=0.306  Sum_probs=113.0

Q ss_pred             HHHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe---------
Q 048593            3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA---------   73 (150)
Q Consensus         3 ~~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v---------   73 (150)
                      .-+|++.|.++|+|||.+++||||||+||.++++|+|.| |||++||+|+|+|++||||+||+++|+|++|         
T Consensus        23 ~~~i~~~L~~kyegkv~~~~Gl~I~v~di~~i~eG~I~~-GdG~~~~~V~fk~~~f~p~vGEv~~G~Is~Vt~fGifVeL  101 (218)
T 2ckz_B           23 ISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLKP-GDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEGIKVSL  101 (218)
T ss_dssp             HHHHHHHHHHHHTTEEETTTEEEEEEEEEEEECCCEECS-SSSCEEEEEEEEEEEECCCTTCEEEEEEEEEETTEEEEEC
T ss_pred             HHHHHHHHHHHhcCcCcCCccEEEEEEEeeeccCcEEeC-CCCCEEEEEEEEEEEecCCCCCEEEEEEEEEccCcEEEEc
Confidence            357889999999999999999999999999999999999 9999999999999999999999999999999         


Q ss_pred             ---------------------cCCCceee---ccccceecCCCEEEEEEEEEEeeecCc---------------------
Q 048593           74 ---------------------VCEQPFFS---NEQQAKIRNGLVVQFLVTAVQWIDEGR---------------------  108 (150)
Q Consensus        74 ---------------------~~~~~~~~---~~~~~~i~~gd~VR~RI~~v~~~d~~~---------------------  108 (150)
                                           ..+++|++   ++++..++.||.|||||.++++.+..+                     
T Consensus       102 ~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~~~~~p~~~~~~~~~~~~~~~~~~~~~  181 (218)
T 2ckz_B          102 LGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVDVKPKSPKERELEERAQLENEIEGK  181 (218)
T ss_dssp             TTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEECCCCC---------------------
T ss_pred             cCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEcccCCCCCccccccccccccccccccc
Confidence                                 23345666   555678999999999999999976421                     


Q ss_pred             -------CccCcEEEEEEccCCccccccCCCCCC
Q 048593          109 -------NLKKKYLVFGRVEGESLGPVSLSGWAG  135 (150)
Q Consensus       109 -------~~~~~~~~igsi~~d~LG~i~w~~w~~  135 (150)
                             ++++||.++|||++||||+++|  |+-
T Consensus       182 ~~~~~~~~~~~p~~i~gs~~~~GLG~~~w--w~~  213 (218)
T 2ckz_B          182 NEETPQNEKPPAYALLGSCQTDGMGLVSW--WEH  213 (218)
T ss_dssp             ----------CSEEEEEECCSTTCEEGGG--CC-
T ss_pred             cccccccCCCCCeEEEEEecCCCCchhhh--hhc
Confidence                   2468999999999999999999  964

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=100.00  E-value=2.6e-35  Score=235.08  Aligned_cols=129  Identities=16%  Similarity=0.254  Sum_probs=113.0

Q ss_pred             HHHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe---------
Q 048593            3 AIFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA---------   73 (150)
Q Consensus         3 ~~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v---------   73 (150)
                      .-+|++.|.+.|+|||.+++||||||+|+.++++|+|.| |||++||+|+|||++||||+||+++|+|++|         
T Consensus        23 ~~~i~~~L~~~~egkv~~~~Gl~I~v~di~~i~~g~I~~-GdG~~~~~V~fk~~~f~p~~GEv~~G~Vs~vt~~GifV~l  101 (203)
T 3ayh_B           23 KEALAEEIHKKYANKVIQNIGLAICVYDFLKIGEGIIKY-GDGSSYMNVVFRLIIFRPFRGEVMLGKIKSCSEEGIRVTI  101 (203)
T ss_dssp             HHHHHHHHHHHHTTEEETTTEEEEEEEEEEEECCCEECT-TTCCEEEEEEEEEEEECCCTTCEEEEEEEEEETTEEEEEC
T ss_pred             HHHHHHHhhhhhCCEEeCCccEEEEEEEeeEecccEEeC-CCCCEEEEEEEEEEEEccCCCCEEEEEEEEEeccEEEEEE
Confidence            457889999999999999999999999999999999999 9999999999999999999999999999999         


Q ss_pred             --------------------cCCCceee--------ccccceecCCCEEEEEEEEEEeeecCc---------------Cc
Q 048593           74 --------------------VCEQPFFS--------NEQQAKIRNGLVVQFLVTAVQWIDEGR---------------NL  110 (150)
Q Consensus        74 --------------------~~~~~~~~--------~~~~~~i~~gd~VR~RI~~v~~~d~~~---------------~~  110 (150)
                                          ..+++|++        ++++..++.||.||+||.++++.+..+               +.
T Consensus       102 g~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~p~~~~~~~~~~~~~~~~~  181 (203)
T 3ayh_B          102 SFFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQIESEDFVDISPKRNKNATAITGTEALES  181 (203)
T ss_dssp             SSCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEEEEEEECC--------------------
T ss_pred             eCceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEEEEEEccccCCCCccccccccccccccC
Confidence                                23345666        455668999999999999999965322               14


Q ss_pred             cCcEEEEEEccCCccccccCCCCC
Q 048593          111 KKKYLVFGRVEGESLGPVSLSGWA  134 (150)
Q Consensus       111 ~~~~~~igsi~~d~LG~i~w~~w~  134 (150)
                      .+||+++|||++||||+++|  |+
T Consensus       182 ~~~~~i~gs~~~~gLG~~~W--w~  203 (203)
T 3ayh_B          182 VSPYTLIASCSRDGLGIPAW--WK  203 (203)
T ss_dssp             CCSEEEEEEBCSTTCBCGGG--GC
T ss_pred             CCCeEEEEEecCCCCceeee--cC
Confidence            57999999999999999999  94

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E

Probab=99.98  E-value=2.8e-32  Score=212.34  Aligned_cols=127  Identities=20%  Similarity=0.211  Sum_probs=108.3

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe----------
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA----------   73 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v----------   73 (150)
                      -++++.|.++++|||.+++|||||++|+.++++|+|.| |||+++|+|+|+|++||||+|||++|+|+++          
T Consensus        24 ~~i~~~L~~k~~~kv~~~~G~~I~v~di~~~~~g~I~~-gdg~~~~~v~~~~iv~~p~~Gev~~G~V~~v~~~G~fv~l~  102 (180)
T 4ayb_E           24 EIALNELRQQYQEKILKDLGLVLAILNVKTSEEGMLVF-GDGATYHEVEFDMITYVPVVQEVVEGEVLQVDNYGVFVNLG  102 (180)
T ss_dssp             HHHHHHHHHHTTTCBCSSSCEEEEEEEEEEEEEEEECS-SCSSEEEEEEEEEEEECCCTTCEEEEEEEEEETTEEEEECS
T ss_pred             HHHHHHHHHHhcCeEcCCCcEEEEeeeEeecCceeEcc-CchHHHHHHhhheeeeeccCCCEEEEEEeeeccceEEEEEC
Confidence            46889999999999999999999999999999999999 9999999999999999999999999999999          


Q ss_pred             -------------------cCCCceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccccCCCCC
Q 048593           74 -------------------VCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWA  134 (150)
Q Consensus        74 -------------------~~~~~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i~w~~w~  134 (150)
                                         ...+.|++++.+..++.||.||+||.+++....+    ....+.+||++||||+++|  |+
T Consensus       103 ~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~~~----~~~rI~ls~k~~gLG~~~W--~~  176 (180)
T 4ayb_E          103 PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTG----RLPRIALTMRQPYLGKLEW--IT  176 (180)
T ss_dssp             SSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC-----------CEEEECCSTTCEEHHH--HT
T ss_pred             CccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCCCCc----ccCcEEEEcCCCCCCCChh--Hh
Confidence                               2223455666667899999999999999863322    2456888999999999999  98


Q ss_pred             CCc
Q 048593          135 GTD  137 (150)
Q Consensus       135 ~~~  137 (150)
                      +++
T Consensus       177 ~~~  179 (180)
T 4ayb_E          177 QAK  179 (180)
T ss_dssp             TC-
T ss_pred             hhh
Confidence            654

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=99.96  E-value=4.7e-29  Score=194.09  Aligned_cols=118  Identities=16%  Similarity=0.273  Sum_probs=103.3

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEe--eeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe--------
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVT--NLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA--------   73 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~--di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v--------   73 (150)
                      -++++.|.+.++|+|.+++|+||||+  |+.++++|+|.| |||+++|+|+|+|++||||+||+++|+|+++        
T Consensus        25 ~~i~~~l~~~~~g~vi~~~G~~I~i~~idi~~i~~G~I~~-gdg~~~~~v~f~~ivf~p~~Gev~~G~V~~v~~fG~FV~  103 (172)
T 3h0g_G           25 DYLKAKLLADVEGTCSGQYGYIICVLDSNTIDIDKGRVVP-GQGFAEFEVKYRAVLWRPFRGEVVDAIVTTVNKMGFFAN  103 (172)
T ss_dssp             HHHHHHHHHHHTTCEETTTEEEEEECTTTSEEECCCEECT-TTCCEEEEEEEEEEEECCCTTCEEECCCCEEETTEEECC
T ss_pred             HHHHHHHHHHhCCcCcCCccEEEEEEeeeeeEeeCCEEEC-CCCcEEEEEEEEEeeeccCCCCEEEEEEEEEEcceEEEE
Confidence            46888899999999999999999999  999999999999 9999999999999999999999999999999        


Q ss_pred             -------------cC-------CCceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccc
Q 048593           74 -------------VC-------EQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPV  128 (150)
Q Consensus        74 -------------~~-------~~~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i  128 (150)
                                   ++       ++.|.++..+..++.||.||+||.++++ +.     ++++++|||++||||++
T Consensus       104 l~~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~-~~-----~~~~~Igtm~~~~LG~~  172 (172)
T 3h0g_G          104 IGPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRT-DA-----TEIFAIATMKEDYLGVL  172 (172)
T ss_dssp             BTTBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEE-SS-----SCEEEEEECCSTTCEEC
T ss_pred             eCCeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEEC-CC-----CCceEEEEcCCCCCCCC
Confidence                         10       0122224445689999999999999998 43     37899999999999985

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=99.94  E-value=4.8e-27  Score=183.49  Aligned_cols=126  Identities=20%  Similarity=0.266  Sum_probs=105.9

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEec---------
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIAV---------   74 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v~---------   74 (150)
                      -+|+++|.+.++|||.+++|+|||++|+.++++|+|.+ +||+++|++.|++++|+|++||+++|+|+++.         
T Consensus        24 ~~I~~~L~~~~~gk~~~~~G~~i~~idi~~~g~~~I~~-~d~~~~~~~~~~~i~~~~~~Gev~~G~V~~v~~~G~fV~l~  102 (187)
T 1go3_E           24 ETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVH-GDGSAYHPVVFETLVYIPEMYELIEGEVVDVVEFGSFVRLG  102 (187)
T ss_dssp             HHHHHHHHHHHTTCEETTTEEEEEEEEEEEECCCBCCT-TCCSEEEEEEEEEEEECCCTTCEEEEEEEEEETTEEEEECS
T ss_pred             HHHHHHHHHHhCCeEcCCccEEEEEEEEeeccCCEEeC-CCccEEEEEEEEEEEEccCCCCEEEEEEEEEeCcEEEEEEc
Confidence            36888899999999999999999999999999999999 99999999999999999999999999999991         


Q ss_pred             --------------------CCCceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccccCCCCC
Q 048593           75 --------------------CEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVSLSGWA  134 (150)
Q Consensus        75 --------------------~~~~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i~w~~w~  134 (150)
                                          .++.|++++....+++||.||+||.++...+..   ..++.+..|+++++||+++|  |.
T Consensus       103 ~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~---p~~~~I~lS~k~~~LG~~~w--~~  177 (187)
T 1go3_E          103 PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAER---KRGSKIALTMRQPYLGKLEW--IE  177 (187)
T ss_dssp             SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC--------CEEEEECCSTTCEEHHH--HH
T ss_pred             CccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccCC---CCccEEEEEEcCCCCCcHHH--Hh
Confidence                                111222334446899999999999999974432   01578999999999999999  95


Q ss_pred             C
Q 048593          135 G  135 (150)
Q Consensus       135 ~  135 (150)
                      +
T Consensus       178 ~  178 (187)
T 1go3_E          178 E  178 (187)
T ss_dssp             H
T ss_pred             h
Confidence            3

>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1

Probab=99.92  E-value=1.7e-24  Score=167.40  Aligned_cols=119  Identities=20%  Similarity=0.326  Sum_probs=102.3

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe----------
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA----------   73 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v----------   73 (150)
                      -+++..|...+.+++.++.|+||+++|+.++++|+|.| +||.++++++|++++|+|++||+++|+|+++          
T Consensus        24 ~~i~~~l~~~~~~~vi~~~G~~I~~~di~~i~~g~i~~-~d~~~~~~~~~~~~~~~~~~Gev~~G~V~~v~~fG~fV~l~  102 (172)
T 2c35_B           24 NTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQP-GRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIG  102 (172)
T ss_dssp             HHHHHHHHHHHTTCEETTTEEEEEEEEEEEECCCBCCT-TCSSEEEEEEEEEEEECCCTTCEEEEEEEEEETTEEEEEET
T ss_pred             HHHHHHHHHHHcCcCcCCceEEEEEEEeeecCCeEEeC-CCCCEEEEEEEEEEEeeCCCCCEEEEEEEEEeCCEEEEEEC
Confidence            46777888888899999999999999999999999999 9999999999999999999999999999999          


Q ss_pred             ------------------cCCCceee--ccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCcccccc
Q 048593           74 ------------------VCEQPFFS--NEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVS  129 (150)
Q Consensus        74 ------------------~~~~~~~~--~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i~  129 (150)
                                        +.+++|.|  +.++..++.||.||+||.++.+ +.     +++.++|||++||||+++
T Consensus       103 ~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~-~~-----~~~~~igsm~~~~LG~~~  172 (172)
T 2c35_B          103 PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV-DK-----NDIFAIGSLMDDYLGLVS  172 (172)
T ss_dssp             TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEE-ET-----TEEEEEEECCSTTCEEC-
T ss_pred             CEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEc-CC-----CCcEEEEEecCCCCCCCC
Confidence                              11222222  2335589999999999999998 43     479999999999999985

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...

Probab=99.91  E-value=4.9e-24  Score=165.12  Aligned_cols=118  Identities=18%  Similarity=0.251  Sum_probs=87.5

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeeec--eeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe--------
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNLK--SIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA--------   73 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~--~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v--------   73 (150)
                      -+++..|...+.+++.++.|+||+++||.  ++++|+|.| |||+++|++.|++++|+|+.||+++|+|+++        
T Consensus        24 ~~i~~~i~~~~i~~vig~~G~~I~~~di~~~di~~g~i~~-~d~~~~~~~~~~~~~~~~~~Gev~~G~V~~v~~fG~FV~  102 (171)
T 1y14_B           24 QYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILP-TDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQ  102 (171)
T ss_dssp             HHHHHHHHHHHTTEEETTTEEEEEECCGGGCBCC-------------CEEEEEEEEECCCTTCEEEEEEEEEETTEEEEE
T ss_pred             HHHHHHHHHHHcCcCcCCceEEEEEEEecccccCccEEeC-CCCCEEEEEEEEEEEccCCCCCEEEEEEEEEecCEEEEE
Confidence            35677777788899999999999999999  999999999 9999999999999999999999999999999        


Q ss_pred             -------------c-------CCCceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCccccc
Q 048593           74 -------------V-------CEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPV  128 (150)
Q Consensus        74 -------------~-------~~~~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i  128 (150)
                                   +       .+++|.+..+...++.||.||+||.++.+ +.     +++.++|||++||||++
T Consensus       103 l~~~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~-~~-----~~~~~igsm~~~~LG~~  171 (171)
T 1y14_B          103 VGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCIS-QV-----SSIHAIGSIKEDYLGAI  171 (171)
T ss_dssp             ETTEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEE-ET-----TEEEEEEECCSTTCEEC
T ss_pred             ecCeEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEEc-CC-----CCcEEEEEcCCCCCCCC
Confidence                         1       11222221111569999999999999998 43     47999999999999985

>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1

Probab=99.90  E-value=2.3e-23  Score=168.02  Aligned_cols=119  Identities=18%  Similarity=0.255  Sum_probs=101.3

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeeec--eeCCeeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEEEEe--------
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNLK--SIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVIHIA--------   73 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~--~i~~G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V~~v--------   73 (150)
                      -+++..|...+.|+|.++.|+||+++||.  ++++|+|.| |||+++|++.|++++|+|++||+++|+|+++        
T Consensus        24 ~~i~~~I~~~~ig~vIg~~G~vI~~~dI~~~di~dG~I~~-gdg~~~~~v~~~~i~~~p~vGev~~G~V~~vt~fG~FVe  102 (215)
T 2b8k_G           24 QYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILP-TDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQ  102 (215)
T ss_dssp             HHHHHHHHHSSTTCEETTTEEEEEECCSTTCBCCCEEECS-SSCCEEEEEECCEEEECCCTTEEEEEEEEEEETTEEEEE
T ss_pred             HHHHhcCCHHHCCeEcCCCCEEEEEEEeeecccccceEeC-CCHHHHHHHHhhhheeccCCCCEEEEEEEEEecceEEEE
Confidence            35677777777789999999999999999  999999999 9999999999999999999999999999999        


Q ss_pred             -------------c-------CCCceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEEEccCCcccccc
Q 048593           74 -------------V-------CEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFGRVEGESLGPVS  129 (150)
Q Consensus        74 -------------~-------~~~~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~igsi~~d~LG~i~  129 (150)
                                   +       .+++|.+......++.||.||+||.++.+ +.     .++..+|||++||||+++
T Consensus       103 lg~~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~-~~-----~~i~~IgSmk~~~LG~~~  172 (215)
T 2b8k_G          103 VGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCIS-QV-----SSIHAIGSIKEDYLGAIS  172 (215)
T ss_dssp             CTTSEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEE-ET-----TEEEEEEECCSTTCEEC-
T ss_pred             ecCcEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEc-CC-----CccEEEEEcCCCCCCCcc
Confidence                         1       12233222112579999999999999998 43     479999999999999996

>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae}

Probab=99.81  E-value=1.9e-19  Score=144.73  Aligned_cols=107  Identities=18%  Similarity=0.134  Sum_probs=77.0

Q ss_pred             HHHHHHHHhHHhceecCCc-eEEEEEeeeceeCC------------eeeeeCCCcceEEEEEEEEEEeeeecCcEEEEEE
Q 048593            4 IFVTRLLKGLINEKACKDQ-CYFLSVTNLKSIGR------------ERGTVNESGVVFFPVTFLCRTFLPVKGEILHGVI   70 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~-GliV~V~di~~i~~------------G~I~~~gdG~v~~~V~FraivFrPf~gEVv~G~V   70 (150)
                      .++.+.|..+.+ |++.++ |+|+|++|+..+++            |+|.| ++|.++|+|+||++|||||+||||+|+|
T Consensus        60 ~i~~~~L~~ll~-ky~~~~~Gv~la~~di~~~~~~~~~~d~~~~~~g~I~~-~~g~~~~~V~~~~iVFrPf~GevL~G~V  137 (214)
T 2rf4_A           60 GVMKQHLNPLVM-KYNNKVGGVVLGYEGLKILDADPLSKEDTSEKLIKITP-DTPFGFTWCHVNLYVWQPQVGDVLEGYI  137 (214)
T ss_dssp             HHHHHHHHHHBT-SEETTTTEEEEEEEEEETTSCCC------------------CCCEEEEEEEEEEECCCTTCEEEEEE
T ss_pred             HHHHHHHHHHHh-cccCCCCEEEEEEECeEeccCCCcCccccccceeEEeC-CCceEEEEEEEEEEEEecCCCCEEEEEE
Confidence            355667877765 777776 89999999976665            79999 9999999999999999999999999999


Q ss_pred             EEe-----------------------------cCC-----CceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEE
Q 048593           71 HIA-----------------------------VCE-----QPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLV  116 (150)
Q Consensus        71 ~~v-----------------------------~~~-----~~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~  116 (150)
                      +.+                             +.+     +.|.+.++ ..  .|+.|||||.+++....      -..+
T Consensus       138 ~~~s~~~Ig~~~~G~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~-~~--ig~~IRFrV~~~~~~~~------~lsI  208 (214)
T 2rf4_A          138 FIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNG-EP--IDGKLRFTVRNVHTTGR------VVSV  208 (214)
T ss_dssp             CCCCSSCEEEEETTTEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSC-CB--CCSEEEEEEEEEECCSS------SCEE
T ss_pred             EEECCCcEEEEEeCCEEEEEcHHHCCCcccccccccccCCCceEcCCC-CC--CCCEEEEEEEEEEecCC------EEEE
Confidence            998                             111     22333322 22  59999999999997432      4778


Q ss_pred             EEEcc
Q 048593          117 FGRVE  121 (150)
Q Consensus       117 igsi~  121 (150)
                      .|||-
T Consensus       209 ~Gsll  213 (214)
T 2rf4_A          209 DGTLI  213 (214)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            88874

>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1

Probab=96.88  E-value=0.00074  Score=52.45  Aligned_cols=67  Identities=15%  Similarity=0.231  Sum_probs=45.2

Q ss_pred             eeeecCcEEEEEEEEecCC----------C-cee--------eccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEE
Q 048593           58 FLPVKGEILHGVIHIAVCE----------Q-PFF--------SNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFG  118 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~----------~-~~~--------~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~ig  118 (150)
                      |.|..|++|.|+|+++..+          . ..+        .+..+..++.||.||+||.++.- +..    +...++.
T Consensus         3 Y~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~g~~k~~r~~l~~GDlV~ArV~~~~~-~~~----~~Ltc~~   77 (175)
T 2ja9_A            3 YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEK-ELE----AEIECFD   77 (175)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCT-TSC----CEEESSC
T ss_pred             ccCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCCchhhhhhccCCCCCEEEEEEEEecC-CCc----eEEEecc
Confidence            7899999999999999111          1 111        12233469999999999998874 321    2332222


Q ss_pred             --EccCCcccccc
Q 048593          119 --RVEGESLGPVS  129 (150)
Q Consensus       119 --si~~d~LG~i~  129 (150)
                        ++++++||.+.
T Consensus        78 ~~~~r~~~lG~L~   90 (175)
T 2ja9_A           78 STTGRDAGFGILE   90 (175)
T ss_dssp             TTTCSCTTCEEEC
T ss_pred             cccccccCCcCcC
Confidence              37888999875

>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=96.16  E-value=0.01  Score=47.49  Aligned_cols=63  Identities=14%  Similarity=0.261  Sum_probs=43.5

Q ss_pred             eeeecCcEEEEEEEEecCCCc----------ee-----e-----ccccceecCCCEEEEEEEEEEeeecCcCccCcEEEE
Q 048593           58 FLPVKGEILHGVIHIAVCEQP----------FF-----S-----NEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVF  117 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~~~----------~~-----~-----~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~i  117 (150)
                      |.|-.|++|.|+|+++.+...          .+     .     .+-...+++||.|++||..+.- +      .++.+ 
T Consensus        53 y~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~-~------~~i~L-  124 (229)
T 2ba0_A           53 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-K------MKVTL-  124 (229)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-T------CCEEE-
T ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECC-C------CcEEE-
Confidence            889999999999999922211          11     0     0112369999999999999862 2      23444 


Q ss_pred             EEccCCcccccc
Q 048593          118 GRVEGESLGPVS  129 (150)
Q Consensus       118 gsi~~d~LG~i~  129 (150)
                       |+++.+||.+.
T Consensus       125 -S~r~~~lG~L~  135 (229)
T 2ba0_A          125 -TMKDRICRPIR  135 (229)
T ss_dssp             -ECCSSSCEEES
T ss_pred             -EEccccCCccc
Confidence             67888999763

>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1

Probab=95.77  E-value=0.016  Score=46.35  Aligned_cols=62  Identities=24%  Similarity=0.397  Sum_probs=42.5

Q ss_pred             eeeecCcEEEEEEEEecCCCce---------ee-----cc---------ccceecCCCEEEEEEEEEEeeecCcCccCcE
Q 048593           58 FLPVKGEILHGVIHIAVCEQPF---------FS-----NE---------QQAKIRNGLVVQFLVTAVQWIDEGRNLKKKY  114 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~~~~---------~~-----~~---------~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~  114 (150)
                      |.|-.|+++.|+|+++.+...+         +.     .+         -...+++||.|++||.++.  +.     .++
T Consensus        62 y~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~--~~-----~~i  134 (235)
T 2z0s_A           62 YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFD--KT-----RSP  134 (235)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEEC--TT-----SCE
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEEC--CC-----CcE
Confidence            7999999999999999222111         10     11         0126999999999999986  22     134


Q ss_pred             EEEEEccCCccccc
Q 048593          115 LVFGRVEGESLGPV  128 (150)
Q Consensus       115 ~~igsi~~d~LG~i  128 (150)
                      .+  |+++..||.+
T Consensus       135 ~L--S~k~~~lG~l  146 (235)
T 2z0s_A          135 LL--TVQGEGLGRI  146 (235)
T ss_dssp             EE--ECCSSSCEEC
T ss_pred             EE--EEecccCccc
Confidence            43  6788888865

>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C

Probab=95.40  E-value=0.049  Score=44.14  Aligned_cols=63  Identities=16%  Similarity=0.190  Sum_probs=42.8

Q ss_pred             EeeeecCcEEEEEEEEecCCCce---------ee-----ccc--------cceecCCCEEEEEEEEEEeeecCcCccCcE
Q 048593           57 TFLPVKGEILHGVIHIAVCEQPF---------FS-----NEQ--------QAKIRNGLVVQFLVTAVQWIDEGRNLKKKY  114 (150)
Q Consensus        57 vFrPf~gEVv~G~V~~v~~~~~~---------~~-----~~~--------~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~  114 (150)
                      .|.|-.|++|.|+|+++.+...+         +.     .+.        ...+++||.|++||.++.- +      .++
T Consensus        69 ~y~p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~-~------~~i  141 (251)
T 2je6_I           69 FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-S------IDP  141 (251)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-T------EEE
T ss_pred             ccCCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECC-C------CcE
Confidence            47899999999999999222111         10     101        1268999999999999872 2      123


Q ss_pred             EEEEEccCCccccc
Q 048593          115 LVFGRVEGESLGPV  128 (150)
Q Consensus       115 ~~igsi~~d~LG~i  128 (150)
                      ..  |+++..||.+
T Consensus       142 ~L--S~r~~~lG~L  153 (251)
T 2je6_I          142 VL--SVKGKDLGRV  153 (251)
T ss_dssp             EE--ECCSTTCEEC
T ss_pred             EE--EEccccCCcc
Confidence            33  6788899965

>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=94.82  E-value=0.02  Score=48.04  Aligned_cols=62  Identities=15%  Similarity=0.227  Sum_probs=41.2

Q ss_pred             eeeecCcEEEEEEEEecCC----------Cce-------ee-----c-------cccceecCCCEEEEEEEEEEeeecCc
Q 048593           58 FLPVKGEILHGVIHIAVCE----------QPF-------FS-----N-------EQQAKIRNGLVVQFLVTAVQWIDEGR  108 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~----------~~~-------~~-----~-------~~~~~i~~gd~VR~RI~~v~~~d~~~  108 (150)
                      |.|..|++|.|+|+++...          ...       |.     .       +-...+++||.||+||.++.  +.  
T Consensus        91 Y~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~--~~--  166 (308)
T 2nn6_H           91 YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVF--SD--  166 (308)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEE--TT--
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcC--CC--
Confidence            7899999999999999111          100       10     0       00135899999999999988  22  


Q ss_pred             CccCcEEEEEEccCCccccc
Q 048593          109 NLKKKYLVFGRVEGESLGPV  128 (150)
Q Consensus       109 ~~~~~~~~igsi~~d~LG~i  128 (150)
                         .++..  |+++++||.+
T Consensus       167 ---~~i~L--Str~~~LGkL  181 (308)
T 2nn6_H          167 ---GAVSL--HTRSLKYGKL  181 (308)
T ss_dssp             ---TEEEE--ECCSSTTCEE
T ss_pred             ---CCEEE--EecCcCCccc
Confidence               23443  6677888843

>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2

Probab=94.78  E-value=0.061  Score=42.43  Aligned_cols=63  Identities=21%  Similarity=0.187  Sum_probs=41.5

Q ss_pred             eeeecCcEEEEEEEEecCCCceee---------------------------c--cccceecCCCEEEEEEEEEEeeecCc
Q 048593           58 FLPVKGEILHGVIHIAVCEQPFFS---------------------------N--EQQAKIRNGLVVQFLVTAVQWIDEGR  108 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~~~~~~---------------------------~--~~~~~i~~gd~VR~RI~~v~~~d~~~  108 (150)
                      |.|-.|++|.|+|+++.+...+..                           +  +-...+++||.|++||+++.  +.  
T Consensus        77 y~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~--~~--  152 (209)
T 2nn6_I           77 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLG--DA--  152 (209)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEE--TT--
T ss_pred             CCCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEe--CC--
Confidence            789999999999999922211100                           0  01124899999999999985  32  


Q ss_pred             CccCcEEEEEEccCCccccc
Q 048593          109 NLKKKYLVFGRVEGESLGPV  128 (150)
Q Consensus       109 ~~~~~~~~igsi~~d~LG~i  128 (150)
                          .-.+.=|+++..||.+
T Consensus       153 ----~~~i~LS~k~~~lGVv  168 (209)
T 2nn6_I          153 ----QSNYLLTTAENELGVV  168 (209)
T ss_dssp             ----TTEEEEECCSSSCEEC
T ss_pred             ----CCeEEEEEecCCCcEE
Confidence                1134446777777776

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=94.45  E-value=0.027  Score=40.08  Aligned_cols=53  Identities=15%  Similarity=0.098  Sum_probs=36.1

Q ss_pred             EEEEEEEeeeecCcEEEEEEEEecCCCce---------ee-----------ccccceecCCCEEEEEEEEEEe
Q 048593           51 VTFLCRTFLPVKGEILHGVIHIAVCEQPF---------FS-----------NEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        51 V~FraivFrPf~gEVv~G~V~~v~~~~~~---------~~-----------~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      ..|..+.++|..|++++|+|+++.+-..+         +.           .+....+++||.|++||..+..
T Consensus        19 ~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~   91 (115)
T 2khi_A           19 SHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDE   91 (115)
T ss_dssp             --CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEET
T ss_pred             CCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEEC
Confidence            44566667889999999999999221111         10           1112369999999999999874

>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=93.83  E-value=0.048  Score=39.26  Aligned_cols=52  Identities=13%  Similarity=0.088  Sum_probs=37.5

Q ss_pred             EEEEEEeeeecCcEEEEEEEEecCCCce----------ee----------ccccceecCCCEEEEEEEEEEe
Q 048593           52 TFLCRTFLPVKGEILHGVIHIAVCEQPF----------FS----------NEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        52 ~FraivFrPf~gEVv~G~V~~v~~~~~~----------~~----------~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      .|+.+.+.|..|+++.|+|+++.+...+          |.          .+....++.||.|++||..+..
T Consensus        12 ~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~   83 (119)
T 2cqo_A           12 RPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREM   83 (119)
T ss_dssp             CCCCSCCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEE
T ss_pred             chhhhhcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEec
Confidence            4667789999999999999999222211          11          0111258999999999999875

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}

Probab=93.36  E-value=0.22  Score=32.88  Aligned_cols=45  Identities=13%  Similarity=0.090  Sum_probs=31.7

Q ss_pred             eeecCcEEEEEEEEecCCCcee---------e--ccc-c---ceecCCCEEEEEEEEEEe
Q 048593           59 LPVKGEILHGVIHIAVCEQPFF---------S--NEQ-Q---AKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        59 rPf~gEVv~G~V~~v~~~~~~~---------~--~~~-~---~~i~~gd~VR~RI~~v~~  103 (150)
                      .|..|+++.|+|+++.+...++         .  ++- .   ..++.||.|++||..+..
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel~~~~~~~~~~Gd~V~v~V~~vd~   61 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRLENLNVGDEIIVQAIDVRP   61 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSCCGGGCCTTCEEEEEEEEEET
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCcccceeeCCCCEEEEEEEEEEC
Confidence            5778999999999993332221         1  110 0   258999999999999874

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=92.39  E-value=0.27  Score=34.30  Aligned_cols=46  Identities=20%  Similarity=0.188  Sum_probs=31.7

Q ss_pred             eeeecCcEEEEEEEEecCCCceee-------------------ccccceecCCCEEEEEEEEEEe
Q 048593           58 FLPVKGEILHGVIHIAVCEQPFFS-------------------NEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~~~~~~-------------------~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      ..|..|+++.|+|+++.+...++.                   ......+++||.|++||..+..
T Consensus        27 ~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~   91 (109)
T 2khj_A           27 ALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDR   91 (109)
T ss_dssp             TTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEET
T ss_pred             hcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEEC
Confidence            356689999999999932222110                   1112358999999999999874

>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=91.46  E-value=0.3  Score=40.52  Aligned_cols=64  Identities=14%  Similarity=0.274  Sum_probs=41.7

Q ss_pred             eeeecCcEEEEEEEEecCCC----------ce-----ee---ccccceecCCCEEEEEEEEEEeeecCcCccCcEEEE--
Q 048593           58 FLPVKGEILHGVIHIAVCEQ----------PF-----FS---NEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVF--  117 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~~----------~~-----~~---~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~i--  117 (150)
                      |.|-+|.+|-|+|+++..+.          ..     |.   +.....++.||.|++||..+.- +.      ++.+.  
T Consensus       123 YiP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~Gatk~~r~~f~~GDlV~ArV~s~~~-~~------~~eLsc~  195 (289)
T 2nn6_G          123 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANK-DM------EPEMVCI  195 (289)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCSSCSSSSSCTTCEEEEEEEECCT-TS------CCEEECS
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcCcchhhhhhhcCCCCEEEEEEEEcCC-CC------ceEEEec
Confidence            78999999999999992211          11     11   1223369999999999997642 21      23331  


Q ss_pred             E-EccCCccccc
Q 048593          118 G-RVEGESLGPV  128 (150)
Q Consensus       118 g-si~~d~LG~i  128 (150)
                      . +.++.+||++
T Consensus       196 ~~~~k~~~lG~L  207 (289)
T 2nn6_G          196 DSCGRANGMGVI  207 (289)
T ss_dssp             BTTTTBCCCCSC
T ss_pred             ccccccccCCEe
Confidence            1 2367889987

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=90.63  E-value=0.71  Score=32.57  Aligned_cols=62  Identities=18%  Similarity=0.154  Sum_probs=41.2

Q ss_pred             eeecCcEEEEEEEEecCCCce----------ee--c---------cccceecCCCEEEEEEEEEEeeecCcCccCcEEEE
Q 048593           59 LPVKGEILHGVIHIAVCEQPF----------FS--N---------EQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVF  117 (150)
Q Consensus        59 rPf~gEVv~G~V~~v~~~~~~----------~~--~---------~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~i  117 (150)
                      .+..|++++|+|+++.+-..+          +.  +         +....++.||.|++||..+.. +       .-.+.
T Consensus        18 ~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~-~-------~~~i~   89 (119)
T 1wi5_A           18 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKG-N-------GGVVS   89 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCT-T-------SCEEE
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeC-C-------CCEEE
Confidence            357899999999999222211          11  1         112469999999999998753 1       22455


Q ss_pred             EEccCCccccc
Q 048593          118 GRVEGESLGPV  128 (150)
Q Consensus       118 gsi~~d~LG~i  128 (150)
                      =|++...||..
T Consensus        90 Lslk~~~l~~~  100 (119)
T 1wi5_A           90 LSVGHSEVSTA  100 (119)
T ss_dssp             EECCCCCSCCC
T ss_pred             EEEchhhcccc
Confidence            67777777754

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}

Probab=90.39  E-value=0.57  Score=33.86  Aligned_cols=45  Identities=20%  Similarity=0.124  Sum_probs=31.2

Q ss_pred             eeecCcEEEEEEEEecCCCcee---------e----------ccccceecCCCEEEEEEEEEEe
Q 048593           59 LPVKGEILHGVIHIAVCEQPFF---------S----------NEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        59 rPf~gEVv~G~V~~v~~~~~~~---------~----------~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      .+..|+++.|+|+++.+-..++         .          .+-...+.+||.|++||..+..
T Consensus         4 ~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~   67 (130)
T 2k4k_A            4 KFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDE   67 (130)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEET
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeC
Confidence            4678999999999992222111         0          1112469999999999999874

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.40  E-value=0.71  Score=31.94  Aligned_cols=46  Identities=17%  Similarity=0.201  Sum_probs=32.1

Q ss_pred             EeeeecCcEEEEEEEEecCCCce------------ee--c---------cccceecCCCEEEEEEEEEE
Q 048593           57 TFLPVKGEILHGVIHIAVCEQPF------------FS--N---------EQQAKIRNGLVVQFLVTAVQ  102 (150)
Q Consensus        57 vFrPf~gEVv~G~V~~v~~~~~~------------~~--~---------~~~~~i~~gd~VR~RI~~v~  102 (150)
                      .+.|..|+++.|+|+++.+-..+            +.  +         +....++.||.|++||..+.
T Consensus         7 ~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd   75 (103)
T 2eqs_A            7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFT   75 (103)
T ss_dssp             CSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEE
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEE
Confidence            45788999999999999222111            11  0         01135899999999999986

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=87.29  E-value=0.029  Score=51.98  Aligned_cols=73  Identities=14%  Similarity=0.100  Sum_probs=7.3

Q ss_pred             eeceeCCeeeeeCCCcceEEE--EEEEEEEeeeecCcEEEEEEEEecCCCcee-------------------ecccccee
Q 048593           30 NLKSIGRERGTVNESGVVFFP--VTFLCRTFLPVKGEILHGVIHIAVCEQPFF-------------------SNEQQAKI   88 (150)
Q Consensus        30 di~~i~~G~I~~~gdG~v~~~--V~FraivFrPf~gEVv~G~V~~v~~~~~~~-------------------~~~~~~~i   88 (150)
                      ||.+-|..+|.. .|+.+...  -.++.++..|..|++++|+|+++.+-..++                   .++-...+
T Consensus       604 di~ddG~v~I~~-~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~~rv~~~~d~~  682 (726)
T 4aid_A          604 DINDDGVVKVSA-SDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVL  682 (726)
T ss_dssp             ----------CC-SCHHHHHHHHHC-------------------------------------------------------
T ss_pred             eEECCceEEEEe-CCHHHHHHHHHHHHHHhhhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCcccccCccccC
Confidence            455555556656 66666554  568889999999999999999992111111                   11122369


Q ss_pred             cCCCEEEEEEEEEEe
Q 048593           89 RNGLVVQFLVTAVQW  103 (150)
Q Consensus        89 ~~gd~VR~RI~~v~~  103 (150)
                      +.||.|++||..+.-
T Consensus       683 kvGD~V~VkVi~iD~  697 (726)
T 4aid_A          683 KEGQMVKVKLLGFDD  697 (726)
T ss_dssp             ---------------
T ss_pred             CCCCEEEEEEEEECC
Confidence            999999999999863

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=87.07  E-value=0.85  Score=34.73  Aligned_cols=43  Identities=9%  Similarity=0.033  Sum_probs=29.7

Q ss_pred             EeeeecCcEEEEEEEEecCCCce-------------------ee----------ccccceecCCCEEEEEEEE
Q 048593           57 TFLPVKGEILHGVIHIAVCEQPF-------------------FS----------NEQQAKIRNGLVVQFLVTA  100 (150)
Q Consensus        57 vFrPf~gEVv~G~V~~v~~~~~~-------------------~~----------~~~~~~i~~gd~VR~RI~~  100 (150)
                      -|.|- |+++.|+|+++.+...+                   +.          ++-...++.||.|++||++
T Consensus        53 ~y~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~  124 (179)
T 3m7n_A           53 PEIVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG  124 (179)
T ss_dssp             CCCCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE
T ss_pred             cccCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC
Confidence            46788 99999999999222111                   10          0112368999999999997

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=87.05  E-value=0.12  Score=47.84  Aligned_cols=81  Identities=14%  Similarity=0.034  Sum_probs=0.0

Q ss_pred             cCCceEEEEEeeeceeCCeeeeeCCCcceEEEE--EEEEEEeeeecCcEEEEEEEEecCCCcee----------------
Q 048593           19 CKDQCYFLSVTNLKSIGRERGTVNESGVVFFPV--TFLCRTFLPVKGEILHGVIHIAVCEQPFF----------------   80 (150)
Q Consensus        19 ~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V--~FraivFrPf~gEVv~G~V~~v~~~~~~~----------------   80 (150)
                      ..+.|..   +||.+-+.-.|.. .|.......  .++.++..|..|++++|+|+++.+-..++                
T Consensus       586 ~~~~G~~---IdI~~dg~v~I~~-~~~~~~~~a~~~i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~  661 (723)
T 3cdi_A          586 TEETGTT---IEIEDDGTVKIAA-TDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIA  661 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ehhhCce---EEecCCccEEEec-CCHHHHHHHHHHHHHHhhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcC
Confidence            3456644   3565544444444 555555433  57788999999999999999992221111                


Q ss_pred             ---eccccceecCCCEEEEEEEEEEe
Q 048593           81 ---SNEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        81 ---~~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                         .++-...++.||.|++||.++.-
T Consensus       662 ~~~v~~~~~~~~vGd~V~VkVi~vd~  687 (723)
T 3cdi_A          662 DKRVEKVTDYLQMGQEVPVKVLEVDR  687 (723)
T ss_dssp             --------------------------
T ss_pred             CccccCcccccCCCCEEEEEEEEECC
Confidence               11112368999999999999873

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5

Probab=86.56  E-value=1.2  Score=34.36  Aligned_cols=44  Identities=16%  Similarity=0.096  Sum_probs=28.6

Q ss_pred             eecCcEEEEEEEEecCCCceee---------------------ccccceecCCCEEEEEEEEEEe
Q 048593           60 PVKGEILHGVIHIAVCEQPFFS---------------------NEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        60 Pf~gEVv~G~V~~v~~~~~~~~---------------------~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      |..|+++.|+|+++.+-..++.                     .+-...+++||.|++||..+..
T Consensus        13 p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~   77 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDK   77 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEET
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEEC
Confidence            7899999999999922222211                     1112368999999999999863

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A

Probab=83.59  E-value=2.1  Score=32.64  Aligned_cols=44  Identities=18%  Similarity=0.088  Sum_probs=30.3

Q ss_pred             eecCcEEEEEEEEecCCCce-----------ee----------ccccceecCCCEEEEEEEEEEe
Q 048593           60 PVKGEILHGVIHIAVCEQPF-----------FS----------NEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        60 Pf~gEVv~G~V~~v~~~~~~-----------~~----------~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      |-.|+++.|+|+++.+-..+           +.          .+-...+++||.|++||..+..
T Consensus        13 p~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~   77 (175)
T 2a19_A           13 PEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDK   77 (175)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEEET
T ss_pred             CCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEEC
Confidence            55899999999999221111           10          1112468999999999999863

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=81.94  E-value=1  Score=30.53  Aligned_cols=43  Identities=21%  Similarity=0.370  Sum_probs=28.8

Q ss_pred             eeecCcEEEEEEEEecCCCce-----------ee--c-c--------ccceecCCCEEEEEEEEEEe
Q 048593           59 LPVKGEILHGVIHIAVCEQPF-----------FS--N-E--------QQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        59 rPf~gEVv~G~V~~v~~~~~~-----------~~--~-~--------~~~~i~~gd~VR~RI~~v~~  103 (150)
                      .|..|++++|+|+ +.+-..+           +.  + +        ....+ .|+.|++||..+..
T Consensus         8 ~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~   72 (88)
T 1luz_A            8 LPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDY   72 (88)
T ss_dssp             CCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEET
T ss_pred             CCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEEC
Confidence            3899999999999 9222111           11  1 0        01246 99999999999874

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}

Probab=81.62  E-value=0.93  Score=31.47  Aligned_cols=45  Identities=22%  Similarity=0.121  Sum_probs=37.0

Q ss_pred             eCCeeeeeCCCcceEEEEEEEEEE---e---eeecCcEEEEEEEEecCCCce
Q 048593           34 IGRERGTVNESGVVFFPVTFLCRT---F---LPVKGEILHGVIHIAVCEQPF   79 (150)
Q Consensus        34 i~~G~I~~~gdG~v~~~V~Fraiv---F---rPf~gEVv~G~V~~v~~~~~~   79 (150)
                      -+-|.|.| .+|...+-|.+++|.   |   +|..|++++++|+++.+-..+
T Consensus        28 kGfGFI~~-~~gg~dvfvH~s~l~~~~~~~~~l~~Ge~V~g~V~~i~~fG~f   78 (101)
T 2bh8_A           28 KGFGFITP-DDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITDFGIF   78 (101)
T ss_dssp             GTEEEEEE-SSSSCEEEEECCCSCSSSCCCCCCCTTCEEEEEEEECCSEEEE
T ss_pred             CCCEEEEe-CCCCcEEEEEEEEEecCCccccCCCCCCEEEEEEEEeCCcEEE
Confidence            46789999 899899999999998   4   788999999999988544433

---

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	150
d1go3e2	78	N-terminal, heterodimerisation domain of RBP7 (Rpo	99.73
d1y14b2	80	N-terminal, heterodimerisation domain of RBP7 (Rpo	99.68
d2c35b2	77	N-terminal, heterodimerisation domain of RBP7 (Rpo	99.68
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	99.64
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	99.58
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	98.13
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	97.39
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	97.29
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	97.1
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	95.72
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	95.43
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	95.39
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	93.41
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	92.91
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	92.32
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	92.23
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	89.79
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	86.87

>d1go3e2 d.230.1.1 (E:1-78) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a+b)
fold: Dodecin subunit-like
superfamily: N-terminal, heterodimerisation domain of RBP7 (RpoE)
family: N-terminal, heterodimerisation domain of RBP7 (RpoE)
domain: N-terminal, heterodimerisation domain of RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.73  E-value=3e-18  Score=116.70  Aligned_cols=54  Identities=24%  Similarity=0.394  Sum_probs=52.5

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEe
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTF   58 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivF   58 (150)
                      -++++.|+++|+|||.+++||||||+|+.++++|+|.| |||++||+|+|||+||
T Consensus        24 ~~i~~~L~~~~egkv~~~~G~ii~v~di~~i~eG~I~~-gdG~~~~~V~F~~lvF   77 (78)
T d1go3e2          24 ETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVH-GDGSAYHPVVFETLVY   77 (78)
T ss_dssp             HHHHHHHHHHHTTCEETTTEEEEEEEEEEEECCCBCCT-TCCSEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHhCCcCcCCcCEEEEEEEeeEecCCEEEc-CCCCEEEEEEEEEEEE
Confidence            47899999999999999999999999999999999999 9999999999999999

>d1y14b2 d.230.1.1 (B:1-80) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Dodecin subunit-like
superfamily: N-terminal, heterodimerisation domain of RBP7 (RpoE)
family: N-terminal, heterodimerisation domain of RBP7 (RpoE)
domain: N-terminal, heterodimerisation domain of RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.68  E-value=1.4e-17  Score=113.80  Aligned_cols=55  Identities=20%  Similarity=0.225  Sum_probs=39.8

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeee--ceeCCeeeeeCCCcceEEEEEEEEEEee
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNL--KSIGRERGTVNESGVVFFPVTFLCRTFL   59 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di--~~i~~G~I~~~gdG~v~~~V~FraivFr   59 (150)
                      -++.++|+++++|||.+++||||||+++  .++|+|+|.| |||++||+|+|||++||
T Consensus        24 ~~i~~~L~~~~egkv~~~~G~vi~V~~~~~~~i~~G~I~~-gdG~~~~~V~F~alvFr   80 (80)
T d1y14b2          24 QYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILP-TDGSAEFNVKYRAVVFK   80 (80)
T ss_dssp             HHHHHHHHHHHTTEEETTTEEEEEECCGGGCBCC-------------CEEEEEEEEEC
T ss_pred             HHHHHHHHHHhCCcCcCCcCEEEEEEEEeeeeccCCEEEC-CCCCEEEEEEEEEEEEC
Confidence            5789999999999999999999999766  6899999999 99999999999999998

>d2c35b2 d.230.1.1 (B:1-77) N-terminal, heterodimerisation domain of RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Dodecin subunit-like
superfamily: N-terminal, heterodimerisation domain of RBP7 (RpoE)
family: N-terminal, heterodimerisation domain of RBP7 (RpoE)
domain: N-terminal, heterodimerisation domain of RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=3.5e-17  Score=110.61  Aligned_cols=54  Identities=20%  Similarity=0.308  Sum_probs=52.2

Q ss_pred             HHHHHHHHhHHhceecCCceEEEEEeeeceeCCeeeeeCCCcceEEEEEEEEEEe
Q 048593            4 IFVTRLLKGLINEKACKDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTF   58 (150)
Q Consensus         4 ~~i~~ll~~~~~gk~~~~~GliV~V~di~~i~~G~I~~~gdG~v~~~V~FraivF   58 (150)
                      -++.+.|++.++|||.+++|+|++++|+.++++|+|.| |||+++|+|+|||+||
T Consensus        24 ~~i~~~L~~~~egk~~~~~G~~i~v~~i~~i~~G~I~~-gdG~~~~~V~F~~lvF   77 (77)
T d2c35b2          24 NTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQP-GRGFVLYPVKYKAIVF   77 (77)
T ss_dssp             HHHHHHHHHHHTTCEETTTEEEEEEEEEEEECCCBCCT-TCSSEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHhCCEEeCCCCEEEEEEEEEEecCCEEEc-CCCCEEEEEEEEEEEC
Confidence            46889999999999999999999999999999999999 9999999999999998

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=3.1e-16  Score=109.01  Aligned_cols=64  Identities=19%  Similarity=0.334  Sum_probs=53.8

Q ss_pred             eeecCcEEEEEEEEe----------------------------cCCCceee--ccccceecCCCEEEEEEEEEEeeecCc
Q 048593           59 LPVKGEILHGVIHIA----------------------------VCEQPFFS--NEQQAKIRNGLVVQFLVTAVQWIDEGR  108 (150)
Q Consensus        59 rPf~gEVv~G~V~~v----------------------------~~~~~~~~--~~~~~~i~~gd~VR~RI~~v~~~d~~~  108 (150)
                      |||+|||++|+|++|                            .+++.|.|  ++++..+++||.||+||+++++ +.  
T Consensus         1 rPf~Gev~~g~V~~v~~~G~fv~lg~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~-~~--   77 (94)
T d2c35b1           1 RPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV-DK--   77 (94)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEE-ET--
T ss_pred             CCCCCCEEEEEEEEEEeeEEEEEecCceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEec-Cc--
Confidence            899999999999999                            23334333  5556689999999999999998 54  


Q ss_pred             CccCcEEEEEEccCCccccc
Q 048593          109 NLKKKYLVFGRVEGESLGPV  128 (150)
Q Consensus       109 ~~~~~~~~igsi~~d~LG~i  128 (150)
                         ..++++|||++||||++
T Consensus        78 ---~~I~~igt~~~d~LG~i   94 (94)
T d2c35b1          78 ---NDIFAIGSLMDDYLGLV   94 (94)
T ss_dssp             ---TEEEEEEECCSTTCEEC
T ss_pred             ---CcceEEEEccCCCcccC
Confidence               48999999999999986

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.58  E-value=2.3e-15  Score=103.74  Aligned_cols=63  Identities=16%  Similarity=0.270  Sum_probs=51.6

Q ss_pred             eecCcEEEEEEEEe----------------------------cCCCceeeccccceecCCCEEEEEEEEEEeeecCcCcc
Q 048593           60 PVKGEILHGVIHIA----------------------------VCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLK  111 (150)
Q Consensus        60 Pf~gEVv~G~V~~v----------------------------~~~~~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~  111 (150)
                      ||+|||++|+|+++                            ...+.+.+.+++..++.|+.||+||.++++ +.     
T Consensus         1 Pf~Gev~~g~I~~v~~~G~fv~lg~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~-~~-----   74 (91)
T d1y14b1           1 PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCIS-QV-----   74 (91)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEE-ET-----
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEEcCeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEec-cc-----
Confidence            99999999999999                            222344455666789999999999999998 54     


Q ss_pred             CcEEEEEEccCCccccc
Q 048593          112 KKYLVFGRVEGESLGPV  128 (150)
Q Consensus       112 ~~~~~igsi~~d~LG~i  128 (150)
                      ..++++|||++||||++
T Consensus        75 ~~i~~ig~~~~d~LG~i   91 (91)
T d1y14b1          75 SSIHAIGSIKEDYLGAI   91 (91)
T ss_dssp             TEEEEEEECCSTTCEEC
T ss_pred             CccEEEEEccCCCCCcC
Confidence            47999999999999986

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=98.13  E-value=3e-06  Score=58.97  Aligned_cols=67  Identities=15%  Similarity=0.188  Sum_probs=46.4

Q ss_pred             eecCcEEEEEEEEe---------------------cCCC--------ceeeccccceecCCCEEEEEEEEEEeeecCcCc
Q 048593           60 PVKGEILHGVIHIA---------------------VCEQ--------PFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNL  110 (150)
Q Consensus        60 Pf~gEVv~G~V~~v---------------------~~~~--------~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~  110 (150)
                      |-.|||++|+|+++                     .++.        .+.....+..+++|+.|++||.++.. +..   
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~-~~~---   76 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISL-KAE---   76 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEEC-CC----
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEeeCeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEch-hhc---
Confidence            78999999999999                     1110        01113334689999999999999986 331   


Q ss_pred             cCcEEEEE-EccCCccccccC
Q 048593          111 KKKYLVFG-RVEGESLGPVSL  130 (150)
Q Consensus       111 ~~~~~~ig-si~~d~LG~i~w  130 (150)
                      +.....++ |++.+++||..|
T Consensus        77 ~~~~~~i~ls~K~~~~~~~e~   97 (106)
T d1go3e1          77 RKRGSKIALTMRQPYLGKLEW   97 (106)
T ss_dssp             ----CEEEEECCSTTCEEHHH
T ss_pred             cccCceeecccccCCCCcchh
Confidence            12344555 999999999877

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=97.39  E-value=0.00032  Score=46.29  Aligned_cols=64  Identities=17%  Similarity=0.202  Sum_probs=45.3

Q ss_pred             EeeeecCcEEEEEEEEecCCCc----------ee------e------ccccceecCCCEEEEEEEEEEeeecCcCccCcE
Q 048593           57 TFLPVKGEILHGVIHIAVCEQP----------FF------S------NEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKY  114 (150)
Q Consensus        57 vFrPf~gEVv~G~V~~v~~~~~----------~~------~------~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~  114 (150)
                      .|.|-.|+++.|+|+++.+...          ..      +      .+-...++.||.|++||..+.   .      .-
T Consensus         2 ~Y~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd---~------~~   72 (87)
T d2je6i1           2 FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFD---R------SI   72 (87)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEE---T------TE
T ss_pred             cccCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEEC---C------CC
Confidence            3789999999999999922111          11      0      011236899999999999875   1      24


Q ss_pred             EEEEEccCCcccccc
Q 048593          115 LVFGRVEGESLGPVS  129 (150)
Q Consensus       115 ~~igsi~~d~LG~i~  129 (150)
                      .+.=|+++..||-++
T Consensus        73 ~i~LS~k~~~lgkl~   87 (87)
T d2je6i1          73 DPVLSVKGKDLGRVS   87 (87)
T ss_dssp             EEEEECCSTTCEECC
T ss_pred             CEEEEEecCCCccCC
Confidence            577799999999763

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.29  E-value=0.00026  Score=46.22  Aligned_cols=62  Identities=16%  Similarity=0.271  Sum_probs=43.9

Q ss_pred             eeeecCcEEEEEEEEecCCCc----------ee----------eccccceecCCCEEEEEEEEEEeeecCcCccCcEEEE
Q 048593           58 FLPVKGEILHGVIHIAVCEQP----------FF----------SNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVF  117 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~~~----------~~----------~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~i  117 (150)
                      |.|-.|+++.|+|+++.+.+.          .+          ..+....+.+||.|++||..+.  +       .-.+.
T Consensus         1 Y~Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd--~-------~~~i~   71 (83)
T d2ba0a1           1 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNID--P-------KMKVT   71 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEEC--T-------TCCEE
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEEEEEC--C-------CCCEE
Confidence            679999999999999922111          11          0111235999999999999975  2       13466


Q ss_pred             EEccCCccccc
Q 048593          118 GRVEGESLGPV  128 (150)
Q Consensus       118 gsi~~d~LG~i  128 (150)
                      =|+++.+||++
T Consensus        72 LS~k~~~~~k~   82 (83)
T d2ba0a1          72 LTMKDRICRPI   82 (83)
T ss_dssp             EECCSSSCEEE
T ss_pred             EEecCCCCCCC
Confidence            69999999875

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.10  E-value=0.00033  Score=46.24  Aligned_cols=63  Identities=21%  Similarity=0.300  Sum_probs=44.2

Q ss_pred             EeeeecCcEEEEEEEEecCCCc---------eee--------------ccccceecCCCEEEEEEEEEEeeecCcCccCc
Q 048593           57 TFLPVKGEILHGVIHIAVCEQP---------FFS--------------NEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKK  113 (150)
Q Consensus        57 vFrPf~gEVv~G~V~~v~~~~~---------~~~--------------~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~  113 (150)
                      +|.|-.|+++.|+|+++.+...         -+.              .+.+..++.||.|++||..+. .+        
T Consensus         2 ~Y~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd-~~--------   72 (88)
T d2z0sa1           2 IYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFD-KT--------   72 (88)
T ss_dssp             CCCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEEC-TT--------
T ss_pred             CcCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEEC-CC--------
Confidence            5899999999999999922111         110              011236899999999999986 22        


Q ss_pred             EEEEEEccCCccccc
Q 048593          114 YLVFGRVEGESLGPV  128 (150)
Q Consensus       114 ~~~igsi~~d~LG~i  128 (150)
                      -.+.=|++++.||-+
T Consensus        73 ~~i~Ls~k~~~~gkl   87 (88)
T d2z0sa1          73 RSPLLTVQGEGLGRI   87 (88)
T ss_dssp             SCEEEECCSSSCEEC
T ss_pred             CCEEEEEecCCCccc
Confidence            235558999999864

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.72  E-value=0.004  Score=41.51  Aligned_cols=66  Identities=12%  Similarity=0.255  Sum_probs=42.9

Q ss_pred             eeeecCcEEEEEEEEecCC----------C--------ceeeccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEE-
Q 048593           58 FLPVKGEILHGVIHIAVCE----------Q--------PFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFG-  118 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~----------~--------~~~~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~ig-  118 (150)
                      |.|-.|.++.|+|+++...          .        +...+..+..++.||.|.+||..+.- +.    .+...++= 
T Consensus         2 Y~P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~g~~k~~r~~l~~GD~V~arV~~v~~-~~----~~~Lscvd~   76 (88)
T d2nn6g1           2 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANK-DM----EPEMVCIDS   76 (88)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCSSCSSSSSCTTCEEEEEEEECCT-TS----CCEEECSBT
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcCccccccCcccCCCCEEEEEEEEeCC-CC----CEEEEEEcc
Confidence            6799999999999999111          1        11123344579999999999988762 32    13333222 


Q ss_pred             EccCCccccc
Q 048593          119 RVEGESLGPV  128 (150)
Q Consensus       119 si~~d~LG~i  128 (150)
                      +.+.++||.+
T Consensus        77 ~~k~~g~G~L   86 (88)
T d2nn6g1          77 CGRANGMGVI   86 (88)
T ss_dssp             TTTBCCCCSC
T ss_pred             cCcccCCccc
Confidence            2267888865

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=95.43  E-value=0.0053  Score=41.04  Aligned_cols=66  Identities=15%  Similarity=0.239  Sum_probs=43.2

Q ss_pred             eeeecCcEEEEEEEEecC----------CCcee---------eccccceecCCCEEEEEEEEEEeeecCcCccCcEEEEE
Q 048593           58 FLPVKGEILHGVIHIAVC----------EQPFF---------SNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLVFG  118 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~----------~~~~~---------~~~~~~~i~~gd~VR~RI~~v~~~d~~~~~~~~~~~ig  118 (150)
                      |.|-.|.++-|+|+++..          ....+         .+..+..++.||.|-+||..+.- +..    +..+++.
T Consensus         3 Y~P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~-~~~----~~Lsc~~   77 (90)
T d2ja9a1           3 YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEK-ELE----AEIECFD   77 (90)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCT-TSC----CEEESSC
T ss_pred             ccCCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCccccccCCccCCCCEEEEEEEEECC-CCC----EEEEEec
Confidence            679999999999999911          11111         12223479999999999998763 321    4454444


Q ss_pred             Ec--cCCccccc
Q 048593          119 RV--EGESLGPV  128 (150)
Q Consensus       119 si--~~d~LG~i  128 (150)
                      +.  ++.+||+.
T Consensus        78 ~~~gK~~g~G~L   89 (90)
T d2ja9a1          78 STTGRDAGFGIL   89 (90)
T ss_dssp             TTTCSCTTCEEE
T ss_pred             cccCcccccccc
Confidence            33  56777764

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.39  E-value=0.025  Score=39.70  Aligned_cols=63  Identities=22%  Similarity=0.285  Sum_probs=40.1

Q ss_pred             eeeecCcEEEEEEEEecCC---------------Cc---eee-------ccc----cceecCCCEEEEEEEEEEeeecCc
Q 048593           58 FLPVKGEILHGVIHIAVCE---------------QP---FFS-------NEQ----QAKIRNGLVVQFLVTAVQWIDEGR  108 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~---------------~~---~~~-------~~~----~~~i~~gd~VR~RI~~v~~~d~~~  108 (150)
                      +-|..|.++.|+|+++...               .+   ...       +.+    ...+++||.||+||+++.  +.. 
T Consensus         3 ~vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~--~~~-   79 (125)
T d2nn6i1           3 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLG--DAQ-   79 (125)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEE--TTT-
T ss_pred             cCCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEcc--CCC-
Confidence            3599999999999999111               01   010       001    125889999999999976  321 


Q ss_pred             CccCcEEEEEEccCCccccc
Q 048593          109 NLKKKYLVFGRVEGESLGPV  128 (150)
Q Consensus       109 ~~~~~~~~igsi~~d~LG~i  128 (150)
                         ++|+  -|.+++-||.+
T Consensus        80 ---~~~~--Lst~~~~LGVv   94 (125)
T d2nn6i1          80 ---SNYL--LTTAENELGVV   94 (125)
T ss_dssp             ---TEEE--EECCSSSCEEC
T ss_pred             ---ccEE--EEecCCCcEEE
Confidence               2333  35566778876

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.41  E-value=0.071  Score=35.18  Aligned_cols=62  Identities=16%  Similarity=0.207  Sum_probs=40.5

Q ss_pred             eeeecCcEEEEEEEEecCC----------Cceee-c-------------c-----ccceecCCCEEEEEEEEEEeeecCc
Q 048593           58 FLPVKGEILHGVIHIAVCE----------QPFFS-N-------------E-----QQAKIRNGLVVQFLVTAVQWIDEGR  108 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~----------~~~~~-~-------------~-----~~~~i~~gd~VR~RI~~v~~~d~~~  108 (150)
                      |.|..|.++.|+|+++.+.          +..+- +             +     -...++.||.|.+||.++.- +   
T Consensus         4 Y~P~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~-d---   79 (95)
T d2nn6h1           4 YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-D---   79 (95)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-T---
T ss_pred             ccCCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECC-C---
Confidence            6799999999999999111          11110 0             0     01249999999999999862 2   


Q ss_pred             CccCcEEEEEEccCCccccc
Q 048593          109 NLKKKYLVFGRVEGESLGPV  128 (150)
Q Consensus       109 ~~~~~~~~igsi~~d~LG~i  128 (150)
                         ..+..  |+....||-+
T Consensus        80 ---g~i~L--s~r~~~~gkl   94 (95)
T d2nn6h1          80 ---GAVSL--HTRSLKYGKL   94 (95)
T ss_dssp             ---TEEEE--ECCSSTTCEE
T ss_pred             ---CCEEE--EeccccCCcC
Confidence               13333  6777777753

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.91  E-value=0.1  Score=33.46  Aligned_cols=45  Identities=13%  Similarity=0.090  Sum_probs=28.2

Q ss_pred             eeecCcEEEEEEEEecCCCce-----------ee----------ccccceecCCCEEEEEEEEEEe
Q 048593           59 LPVKGEILHGVIHIAVCEQPF-----------FS----------NEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        59 rPf~gEVv~G~V~~v~~~~~~-----------~~----------~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      .|-.|+++.|+|+++.+...+           |.          ++-...+.+|+.|++||..+..
T Consensus        10 ~p~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd~   75 (86)
T d1kl9a2          10 FPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDK   75 (86)
T ss_dssp             SCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEET
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEEEC
Confidence            366799999999999222211           11          1112358999999999999763

>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Thermotoga maritima [TaxId: 2336]

Probab=92.32  E-value=0.16  Score=32.15  Aligned_cols=47  Identities=15%  Similarity=0.215  Sum_probs=34.9

Q ss_pred             eeeecCcEEEEEEEEecCCCcee---------eccc---cceecCCCEEEEEEEEEEee
Q 048593           58 FLPVKGEILHGVIHIAVCEQPFF---------SNEQ---QAKIRNGLVVQFLVTAVQWI  104 (150)
Q Consensus        58 FrPf~gEVv~G~V~~v~~~~~~~---------~~~~---~~~i~~gd~VR~RI~~v~~~  104 (150)
                      |+...||++.|+|..++..+...         ...+   +..+++||.||+=|..|+-.
T Consensus         4 f~~~~geiv~G~V~r~~~~~~~Vdlg~~eaiLp~~eqip~E~~~~Gdrik~~i~~V~~~   62 (72)
T d1hh2p1           4 YSELKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWIPGEEIKAGDLVKVYIIDVVKT   62 (72)
T ss_dssp             TTCCTTCEEEEEEEEECSSEEEEEETTEEEEEEGGGSCTTCCCCTTCEEEEEEEEEEEE
T ss_pred             HhhccCcEEEEEEEEEcCCCEEEEECCcEEECCHHHcCCCCCCCCCCEEEEEEEEEEEc
Confidence            67789999999999994443322         1111   23699999999999999853

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=92.23  E-value=0.054  Score=34.59  Aligned_cols=44  Identities=20%  Similarity=0.277  Sum_probs=30.6

Q ss_pred             eecCcEEEEEEEEecCCCce-----------ee----------ccccceecCCCEEEEEEEEEEe
Q 048593           60 PVKGEILHGVIHIAVCEQPF-----------FS----------NEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        60 Pf~gEVv~G~V~~v~~~~~~-----------~~----------~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      |-.|+++.|+|+++.+...+           +.          ++-...+.+|+.|++||..+..
T Consensus         9 p~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~   73 (84)
T d2ahob2           9 PSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDR   73 (84)
T ss_dssp             CCTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEET
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEEEC
Confidence            77899999999999222211           11          1112358999999999999863

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Escherichia coli [TaxId: 562]

Probab=89.79  E-value=0.19  Score=31.50  Aligned_cols=42  Identities=19%  Similarity=0.188  Sum_probs=28.6

Q ss_pred             ecCcEEEEEEEEecCCCcee-------------------eccccceecCCCEEEEEEEEEE
Q 048593           61 VKGEILHGVIHIAVCEQPFF-------------------SNEQQAKIRNGLVVQFLVTAVQ  102 (150)
Q Consensus        61 f~gEVv~G~V~~v~~~~~~~-------------------~~~~~~~i~~gd~VR~RI~~v~  102 (150)
                      -.|+++.|+|+++.+...++                   .++-...+.+|+.|++||+.+.
T Consensus         4 kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id   64 (76)
T d1sroa_           4 EVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVD   64 (76)
T ss_dssp             CTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECC
T ss_pred             CCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEEC
Confidence            46999999999992221111                   1111235899999999999863

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Tex S1-domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=86.87  E-value=0.43  Score=30.87  Aligned_cols=42  Identities=21%  Similarity=0.324  Sum_probs=28.5

Q ss_pred             cCcEEEEEEEEecCCCcee-------------------eccccceecCCCEEEEEEEEEEe
Q 048593           62 KGEILHGVIHIAVCEQPFF-------------------SNEQQAKIRNGLVVQFLVTAVQW  103 (150)
Q Consensus        62 ~gEVv~G~V~~v~~~~~~~-------------------~~~~~~~i~~gd~VR~RI~~v~~  103 (150)
                      .|+++.|+|+++.+.+.+.                   .++-...+.+|+.|++||..+.-
T Consensus        18 ~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~   78 (94)
T d3bzka4          18 PGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDI   78 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEET
T ss_pred             CCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEEC
Confidence            4889999999992222111                   11112368999999999999863