Citrus Sinensis ID: 042741

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160------
Protein Sequence
MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGVCGPMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAKGESI
Secondary Structure (PSIPRED)
cEEEEEccccEEEccccccccccccHHHHHHHHHHHcEEccEEEccccEEEEEEEEccccccccEEccccEEEEEEEEEEEEEEEEccEEEEEEEccccEEEEccccccccEEEcccccEEEcccccEEccccEEEEEEEEEEEccccccccccEEEEEEcccccc
Secondary Structure Prediction (SSPRO)
cEEEEEEccEEEEcHHHcccccccHHHHHHHHHHHHHHHHcccccccEEEEEEEEEEccccccEEEccccEEEEEEEEEEEEEEccccEEEEEEcccHHHEEEccccccccEEcccccccEEcccccEEEccEEEEEEEEEEEEcccccHHHHHHEEHEEcccccc
Coil and Loop (DISEMBL)
MFFEVELLRDIavpaksvdrnelrvpqrytvprllegwinqkackdhgyflsvtksksidkegptvngpgvvsfpVIFMCRtflpvkgeilhgvcgpmkyalmsprrmptyrhvsgkksffsndqqpkigngVVVQFLVTAVRWsgegrnlkrEYLVFGRAKGESI
Flexible Loop (DISEMBL)
mffevellrdiavpaksvdrnelrvpqrytvprllegwinqkACKDHGYFLSVTKsksidkegptvngpGVVSFPVIFMCRTFLPVKGEILHGVCGPMKYALMSPRRMPTYRHVSGKKSffsndqqpkignGVVVQFLVTAvrwsgegrnlkreylvfgrakgesi
Low Complexity Region (SEG)
MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGVCGPMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAKGESI
Disordered region (IsUnstruct)
**FEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID**GPTVNGPGVVSFPVIFMCRTFLPVKGEILHGVCGPMKYALMSPRRMPTYRHV*****FF*****PKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFG*******
Disordered Region (DISOPRED)
MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGVCGPMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAKGESI
Disordered Region (DISEMBL)
MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGVCGPMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAKGESI
Disordered Region (DISPRO)
MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGVCGPMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAKGESI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGVCGPMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAKGESI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	166	2.2.26 [Sep-21-2011]
P46279	176	DNA-directed RNA polymera	no	no	0.530	0.5	0.351	7e-05
P38421	176	DNA-directed RNA polymera	no	no	0.530	0.5	0.329	0.0003

>sp|P46279|RPB7_SOYBN DNA-directed RNA polymerase II subunit RPB7 OS=Glycine max PE=2 SV=1

 Score = 46.6 bits (109), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 51/94 (54%), Gaps = 6/94 (6%)

Query: 1  MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
          MFF + L R++ +  +   RN LR      + + +EG  + +    HG+ ++VT  ++I 
Sbjct: 1  MFFHIVLERNMQLHPRYFGRN-LRDNLVSKLMKDVEGTCSGR----HGFVVAVTGIENIG 55

Query: 61 KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV 94
          K G   +G G V+FPV + C  F P KGEIL  V
Sbjct: 56 K-GLIRDGTGFVTFPVKYQCVVFRPFKGEILEAV 88

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.
Glycine max (taxid: 3847)

>sp|P38421|RPB7_ARATH DNA-directed RNA polymerase II subunit RPB7 OS=Arabidopsis thaliana GN=RPB19 PE=1 SV=1

 Score = 44.7 bits (104), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 50/94 (53%), Gaps = 6/94 (6%)

Query: 1  MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
          MFF + L R++ +  +   RN L+      + + +EG  + +    HG+ +++T   +I 
Sbjct: 1  MFFHIVLERNMQLHPRFFGRN-LKENLVSKLMKDVEGTCSGR----HGFVVAITGIDTIG 55

Query: 61 KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV 94
          K G   +G G V+FPV + C  F P KGEIL  V
Sbjct: 56 K-GLIRDGTGFVTFPVKYQCVVFRPFKGEILEAV 88

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.

Arabidopsis thaliana (taxid: 3702)

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	166
449432628	190	PREDICTED: DNA-directed RNA polymerase I	0.981	0.857	0.446	3e-34
224107919	189	predicted protein [Populus trichocarpa]	0.987	0.867	0.438	2e-32
30682881	200	DNA-directed RNA polymerase II-like prot	0.963	0.8	0.349	4e-22
225432916	177	PREDICTED: DNA-directed RNA polymerase I	0.903	0.847	0.371	1e-20
297737162	242	unnamed protein product [Vitis vinifera]	0.903	0.619	0.371	2e-20
449465372	175	PREDICTED: DNA-directed RNA polymerase I	0.897	0.851	0.390	2e-19
2244808	194	hypothetical protein [Arabidopsis thalia	0.933	0.798	0.331	2e-19
224102153	176	predicted protein [Populus trichocarpa]	0.903	0.852	0.365	9e-19
297804848	194	hypothetical protein ARALYDRAFT_493454 [	0.903	0.773	0.335	1e-18
255563208	176	DNA-directed RNA polymerase II 19 kD pol	0.903	0.852	0.365	1e-18

>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 =  149 bits (377), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 79/177 (44%), Positives = 109/177 (61%), Gaps = 14/177 (7%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           MF+EVEL+RD+ +  +   R+     QRY +  LLE  + +KA KDHGYFLSVT  +SI 
Sbjct: 1   MFYEVELVRDVEITVEKEKRDAHNF-QRYIITCLLENLLKEKANKDHGYFLSVTSLRSIG 59

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
           K G   N    VSFP+ F+CRTFLP +GEILHGV            CGP+KY  +S R+M
Sbjct: 60  K-GIVKNESQCVSFPITFICRTFLPFEGEILHGVVRHIFQRGLLLKCGPIKYVFLSARKM 118

Query: 109 PTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAKGES 165
           PTY++V G+   FS+ +   IGN VVV+F V  VRW  +   +K+E+++    +G +
Sbjct: 119 PTYQYVGGENPVFSSKEFATIGNDVVVRFSVLGVRWIEKRGCIKKEFVMLASLEGNN 175

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 78/178 (43%), Positives = 110/178 (61%), Gaps = 14/178 (7%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           MF EVE+   + + A+++DRN L VPQR  V  LL+  ++ KA KDHGYFL+VT  KSI 
Sbjct: 1   MFGEVEVCSTVRIIAENLDRNGL-VPQRSIVTHLLKDLLSMKASKDHGYFLAVTNLKSIG 59

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
           K G  VN  G V F V F CRTF+P+KGEIL GV            CGP+KY  +S R+M
Sbjct: 60  K-GEVVNKSGDVLFHVEFKCRTFMPMKGEILQGVVHRTFRHGVLLRCGPVKYIFLSARKM 118

Query: 109 PTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAKGESI 166
           P Y++ S +   F ND+  +I N V+V+F V  VRW  +  +++R++++     G+S+
Sbjct: 119 PNYQYTSEENPVFLNDELARIENNVLVRFSVLDVRWIEKMWDMRRDFMMLASLVGDSL 176

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 65/186 (34%), Positives = 99/186 (53%), Gaps = 26/186 (13%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSI- 59
           MF EVE+ RD+A+ AK ++      P +  + RLL+  I++KAC++HG++L +T  KSI 
Sbjct: 1   MFSEVEMARDVAICAKHLNGQS---PHQPILCRLLQDLIHEKACREHGFYLGITALKSIG 57

Query: 60  -----DKEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYAL 102
                + +    +   +++FPV F CRTFLP +G+IL G              GP++YA 
Sbjct: 58  NNKNNNIDNENNHQAKILTFPVSFTCRTFLPARGDILQGTVKKVLWNGAFIRSGPLRYAY 117

Query: 103 MSPRRMPTYRHVSG-----KKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLV 157
           +S  +MP Y +V       +K  F  D   KI  GVVV+F V AVR+       + +Y V
Sbjct: 118 LSLLKMPHYHYVHSPLSEDEKPHFQKDDLSKIAVGVVVRFQVLAVRFKERPHKRRNDYYV 177

Query: 158 FGRAKG 163
               +G
Sbjct: 178 LATLEG 183

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  104 bits (259), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 61/164 (37%), Positives = 93/164 (56%), Gaps = 14/164 (8%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           MF +V+L  ++ +PA+ +D   L + QR  + RLL+ + N+KA ++ GYFL+VT  ++I 
Sbjct: 1   MFLKVQLPWNVIIPAECLDAKGLML-QRSIIIRLLDAFSNKKATQELGYFLAVTTLENIG 59

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
            EG      G V FPV+F C TF   +GEIL GV            CGP++   +S ++M
Sbjct: 60  -EGKVRQHSGDVLFPVVFSCVTFKLFRGEILDGVVHKVLKHGVILRCGPVENIYLSCQKM 118

Query: 109 PTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLK 152
           P YR+V G+   F N++  KI   VVV+F+V   +W    R  +
Sbjct: 119 PDYRYVPGENPVFLNEKLSKIEKDVVVRFIVMGTKWLEAEREFQ 162

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 61/164 (37%), Positives = 93/164 (56%), Gaps = 14/164 (8%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           MF +V+L  ++ +PA+ +D   L + QR  + RLL+ + N+KA ++ GYFL+VT  ++I 
Sbjct: 66  MFLKVQLPWNVIIPAECLDAKGLML-QRSIIIRLLDAFSNKKATQELGYFLAVTTLENIG 124

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
            EG      G V FPV+F C TF   +GEIL GV            CGP++   +S ++M
Sbjct: 125 -EGKVRQHSGDVLFPVVFSCVTFKLFRGEILDGVVHKVLKHGVILRCGPVENIYLSCQKM 183

Query: 109 PTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLK 152
           P YR+V G+   F N++  KI   VVV+F+V   +W    R  +
Sbjct: 184 PDYRYVPGENPVFLNEKLSKIEKDVVVRFIVMGTKWLEAEREFQ 227

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 =  100 bits (248), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 64/164 (39%), Positives = 92/164 (56%), Gaps = 15/164 (9%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           MF +V+L  ++ +PA+++D   L + QR  + RLL+ +  +KA KD GYFL+VT  ++I 
Sbjct: 1   MFLKVQLPWNVIIPAENLDAKGLML-QRSIIIRLLDEFATKKATKDLGYFLAVTTLENIG 59

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
            EG  V   G V FPVIF   TF   +GEIL GV            CGP++   +S  +M
Sbjct: 60  -EG-KVRQTGDVLFPVIFSGITFKLYRGEILEGVVHKVLKHGVFLRCGPVENIYLSYLKM 117

Query: 109 PTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLK 152
           P YR+V G+   F ND+  KI   VVV+F+V   +W    R  +
Sbjct: 118 PDYRYVPGENPVFLNDKLSKIEKDVVVRFIVIGTKWLEAEREFQ 161

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  100 bits (248), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 60/181 (33%), Positives = 94/181 (51%), Gaps = 26/181 (14%)

Query: 7   LLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSI------D 60
           + RD+A+ AK ++      P +  + RLL+  I++KAC++HG++L +T  KSI      +
Sbjct: 1   MARDVAICAKHLNGQS---PHQPILCRLLQDLIHEKACREHGFYLGITALKSIGNNKNNN 57

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
            +    +   +++FPV F CRTFLP +G+IL G              GP++YA +S  +M
Sbjct: 58  IDNENNHQAKILTFPVSFTCRTFLPARGDILQGTVKKVLWNGAFIRSGPLRYAYLSLLKM 117

Query: 109 PTYRHVSG-----KKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAKG 163
           P Y +V       +K  F  D   KI  GVVV+F V AVR+       + +Y V    +G
Sbjct: 118 PHYHYVHSPLSEDEKPHFQKDDLSKIAVGVVVRFQVLAVRFKERPHKRRNDYYVLATLEG 177

Query: 164 E 164
            
Sbjct: 178 N 178

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224102153|ref|XP_002312568.1| predicted protein [Populus trichocarpa] gi|222852388|gb|EEE89935.1| predicted protein [Populus trichocarpa]

 Score = 98.2 bits (243), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 60/164 (36%), Positives = 90/164 (54%), Gaps = 14/164 (8%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           MF +V+L  ++ +PA+++D   L + QR  V RLL+ +  + A KD GY+L+V+  +SI 
Sbjct: 1   MFLKVQLPWNVIIPAENLDAKGLML-QRSIVVRLLDDFAKKGATKDLGYYLAVSTLESIG 59

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
            EG      G V FPV+F   TF   +GEIL G+            CGP++   +S  +M
Sbjct: 60  -EGKVRQHTGDVLFPVVFSGITFKIFRGEILDGIVHKVLKHGVLLRCGPIENIYLSCMKM 118

Query: 109 PTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLK 152
           P YR+V G+   F ND+  KI   VVV+F+V   +W    R  +
Sbjct: 119 PDYRYVPGENPVFLNDKTSKIEKDVVVRFVVLGTKWLEAEREFQ 162

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 59/176 (33%), Positives = 93/176 (52%), Gaps = 26/176 (14%)

Query: 7   LLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSI------D 60
           + RD+A+ A  ++    + P    + RLL+  I++KAC++HG++L +T  KSI      +
Sbjct: 1   MARDVAICANHLNG---QAPHHQILGRLLKDLIHEKACREHGFYLGITALKSIGNNKNNN 57

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
            E    +   +++FPV F CRTFLP +G+IL G              GP++YA +S  +M
Sbjct: 58  DENKDNHQAHLLTFPVSFTCRTFLPARGDILQGTVKKVLWNGAFIRSGPLRYAYLSFLKM 117

Query: 109 PTYRHVSG-----KKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFG 159
           P Y +V       +K +F  D   KI  GVVV+F V AVR+  +    + +Y V  
Sbjct: 118 PDYHYVHSPLLEDEKPYFQKDDLSKIAVGVVVRFGVLAVRFKEKPHKRRNDYYVLA 173

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 60/164 (36%), Positives = 89/164 (54%), Gaps = 14/164 (8%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           M+ +V+L  ++ + A+ +D   L + QR  + RLLE + ++KA KD GY+L+VT  +SI 
Sbjct: 1   MYLKVQLPWNVIISAEHLDAKGLML-QRSIIIRLLEDFASKKATKDLGYYLAVTTLESIG 59

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
            EG      G V FPV+F   TF   +GEIL GV            CGP++   +S  +M
Sbjct: 60  -EGKVREHTGDVLFPVVFNGITFKIFRGEILEGVVHKVLKHGVFIRCGPIENIYLSCMKM 118

Query: 109 PTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLK 152
           P Y +V G+   F ND+  KI   VVV+F+V   +W    R  +
Sbjct: 119 PDYHYVPGENPVFLNDKTSKIEKDVVVRFIVIGTKWLEAEREFQ 162

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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	166
TAIR|locus:2130060	178	NRPE7 [Arabidopsis thaliana (t	0.951	0.887	0.306	9.5e-18
TAIR|locus:2084573	174	NRPD7 [Arabidopsis thaliana (t	0.957	0.913	0.314	5.3e-17
TAIR|locus:2168514	176	NRPB7 [Arabidopsis thaliana (t	0.530	0.5	0.329	6.1e-05

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

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 54/176 (30%), Positives = 94/176 (53%)

Query:     1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
             MF +V+L  ++ +PA+++D   L + +R  +  LLE + ++KA K+ GY+++VT    I 
Sbjct:     1 MFLKVQLPWNVMIPAENMDAKGLML-KRAILVELLEAFASKKATKELGYYVAVTTLDKIG 59

Query:    61 KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
              EG      G V FPV+F   TF   KGEI+HGV            CGP++   +S  +M
Sbjct:    60 -EGKIREHTGEVLFPVMFSGMTFKIFKGEIIHGVVHKVLKHGVFMRCGPIENVYLSYTKM 118

Query:   109 PTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAKGE 164
             P Y+++ G+   F N++  +I     V+ +V  ++W      ++RE+      +G+
Sbjct:   119 PDYKYIPGENPIFMNEKTSRIQVETTVRVVVIGIKWM----EVEREFQALASLEGD 170

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:2084573 NRPD7 [Arabidopsis thaliana (taxid:3702)]

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 56/178 (31%), Positives = 88/178 (49%)

Query:     1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
             MF +V+L  D+ +PA+ +D   +   QR  V RLLE +  +KA KD GY ++ T  ++I 
Sbjct:     1 MFIKVKLPWDVTIPAEDMDTGLML--QRAIVIRLLEAFSKEKATKDLGYLITPTILENIG 58

Query:    61 KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGVC------------GPMKYALMSPRRM 108
              EG      G + FPV+F    F   KGEI+HGV             GP +   +S  +M
Sbjct:    59 -EGKIKEQTGEIQFPVVFNGICFKMFKGEIVHGVVHKVHKTGVFLKSGPYEIIYLSHMKM 117

Query:   109 PTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAKGESI 166
             P Y  + G+  FF N    +I  G  V+F+V    W    R  +++++      G+++
Sbjct:   118 PGYEFIPGENPFFMNQYMSRIQIGARVRFVVLDTEW----REAEKDFMALASIDGDNL 171

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:2168514 NRPB7 [Arabidopsis thaliana (taxid:3702)]

 Score = 107 (42.7 bits), Expect = 6.1e-05, P = 6.1e-05
 Identities = 31/94 (32%), Positives = 49/94 (52%)

Query:     1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
             MFF + L R++ +  +   RN L+      V +L++  +       HG+ +++T   +I 
Sbjct:     1 MFFHIVLERNMQLHPRFFGRN-LK---ENLVSKLMKD-VEGTCSGRHGFVVAITGIDTIG 55

Query:    61 KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV 94
             K G   +G G V+FPV + C  F P KGEIL  V
Sbjct:    56 K-GLIRDGTGFVTFPVKYQCVVFRPFKGEILEAV 88


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        0.323   0.140   0.430    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      166       166   0.00097  107 3  11 22  0.36    32
                                                     30  0.46    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:  597 (63 KB)
  Total size of DFA:  153 KB (2092 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:  13.76u 0.18s 13.94t   Elapsed:  00:00:00
  Total cpu time:  13.76u 0.18s 13.94t   Elapsed:  00:00:00
  Start:  Tue May 21 03:05:48 2013   End:  Tue May 21 03:05:48 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

ID	Length	Definition	E-value
Query	166
PTZ00162	176	PTZ00162, PTZ00162, DNA-directed RNA polymerase II	7e-05
cd04329	80	cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-t	0.002

>gnl|CDD|240298 PTZ00162, PTZ00162, DNA-directed RNA polymerase II subunit 7; Provisional

 Score = 40.8 bits (96), Expect = 7e-05
 Identities = 36/164 (21%), Positives = 66/164 (40%), Gaps = 26/164 (15%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYT--VPRLLEGWINQKACKDHGYFLSVTKSKS 58
           MFF VEL +++++    +         RY   +  +L   +  +  + +GY + V +   
Sbjct: 1   MFFVVELWKNVSLKPSQLG-------PRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIH 53

Query: 59  IDKEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPR 106
            +  G   +G G++   V +    F P K E+L  +             GP+K A +S  
Sbjct: 54  NE-PGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFFAQAGPLK-AFVSRS 111

Query: 107 RMP---TYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE 147
            +P    Y   S    + S+D Q +I     V+  +  VR+   
Sbjct: 112 AIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDAS 155

Length = 176

>gnl|CDD|239821 cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 27/86 (31%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 2  FFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDK 61
          FF++EL  +I +       N     + Y   +LLE         D+GY ++VT    I  
Sbjct: 1  FFKIELEHNILLHPSYFGPNL----KEYLEQKLLEEVEGTCT-GDYGYIIAVTDIDDI-G 54

Query: 62 EGPTVNGPGVVSFPVIFMCRTFLPVK 87
          EG  + G G V FPV +    F P K
Sbjct: 55 EGKILPGTGSVEFPVKYKAIVFKPFK 80

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. Length = 80

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	166
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	100.0
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	100.0
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	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	99.97
cd00655	80	RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved	99.96
cd04330	80	RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-termin	99.96
cd04331	80	RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprot	99.96
PF03876	70	SHS2_Rpb7-N: SHS2 domain found in N terminus of Rp	99.82
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	99.78
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	99.76
cd04328	89	RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal r	99.71
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	97.36
KOG4134	253	consensus DNA-dependent RNA polymerase I [Transcri	97.09
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	96.72
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	96.22
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	92.01
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	91.86
PRK11642	813	exoribonuclease R; Provisional	89.77
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	89.5
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	88.95
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	86.74
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	86.65
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	86.31
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	85.04
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	84.77
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	84.75
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	84.74
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	83.92
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	81.58
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	81.03
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	80.87
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	80.84
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	80.07

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

Probab=100.00  E-value=5.7e-51  Score=324.74  Aligned_cols=153  Identities=22%  Similarity=0.357  Sum_probs=145.6

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||++++|+|+|+|||++|+++  +  ++++.++|+++|+|+ |.+++||||||+|++++++|+ |.||||++||+|+|||
T Consensus         1 MF~~~~l~d~v~i~P~~f~~~--~--~~~i~~~L~~~~egk-v~~~~GliV~v~di~~i~~G~-I~~gdG~~~~~V~Fra   74 (176)
T PTZ00162          1 MFFVVELWKNVSLKPSQLGPR--Y--QQIIEDMLRSQVEGQ-CTRKYGYVICVIRIIHNEPGR-VQDGTGMIVVNVKYQA   74 (176)
T ss_pred             CcEEEEEEEEEEECHHHcCcc--H--HHHHHHHHHHHHCCC-CcCcccEEEEEEEeeEecCCE-EEcCCCCEEEEEEEEE
Confidence            999999999999999999998  5  999999999999999 999999999999999999999 9999999999999999


Q ss_pred             EEEeeecCcEEEEE------------eCCcceEEecCCCCC-CceeeCCCceeEec--CCCCeecCCCEEEEEEEEEEEc
Q 042741           81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMP-TYRHVSGKKSFFSN--DQQPKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus        81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~-~~~~~~~~~~~~~~--~~~~~i~~g~~VR~RI~~~~~~  145 (166)
                      +|||||+|||++|+            +|||+ +|+|.+.|| ++.||+++++|.|.  +++.+|++|+.|||||++++|+
T Consensus        75 ivFrPf~gEVv~g~V~~v~~~G~~v~~Gp~~-ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~  153 (176)
T PTZ00162         75 IVFKPFKDEVLDAIVTDVNKLGFFAQAGPLK-AFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYD  153 (176)
T ss_pred             EEEecCCCCEEEEEEEEEecceEEEEeeCeE-EEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEec
Confidence            99999999999999            99999 999999996 57899999988774  5568999999999999999999


Q ss_pred             CCCcCccccEEEEEEecCCCC
Q 042741          146 GEGRNLKREYLVFGRAKGESI  166 (166)
Q Consensus       146 ~~~~~~~~~~~~igti~~d~l  166 (166)
                      ++    +  ++|+|||++|||
T Consensus       154 ~~----~--~~~i~T~~~~~L  168 (176)
T PTZ00162        154 AS----N--LFAIATINSDYL  168 (176)
T ss_pred             CC----C--cEEEEEecCCCc
Confidence            87    5  899999999998

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

Probab=100.00  E-value=5.7e-47  Score=301.37  Aligned_cols=157  Identities=21%  Similarity=0.268  Sum_probs=143.5

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||++++++|+|+|||++||++  +  ++++.++|+++|+|+ |++++|+||+|+|+++|++|+ |.||||++||+|+|+|
T Consensus         1 My~l~~~~d~VripP~~fg~~--~--~~~v~~~L~~k~eG~-~~~~~G~~v~V~~v~~igeG~-I~~GDG~~y~~V~f~a   74 (183)
T COG1095           1 MYKLVELEDTVRIPPSYFGED--L--EEAVKEELKEKYEGK-LDGDVGLVVLVLDVKEIGEGI-IVPGDGSTYHEVKFRA   74 (183)
T ss_pred             CcEEEEEeeEEEeCHHHcCcc--H--HHHHHHHHHHHhcce-EccccCEEEEEEEeeEeeccE-EecCCCcEEEEEEEEE
Confidence            999999999999999999999  5  999999999999999 999999999999999999999 9999999999999999


Q ss_pred             EEEeeecCcEEEEE------------eCCcceEEecCCCCCCce-eeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741           81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMPTYR-HVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus        81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~~~-~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      |+|+||+|||++|+            +||+|++.|.+|+|+|+. ||+....|..+++++.|++||.|||||++++++++
T Consensus        75 l~fkP~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~  154 (183)
T COG1095          75 LVFKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSR  154 (183)
T ss_pred             EEEEeccccEEEEEEEEEeecceEEEeccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccC
Confidence            99999999999999            999996666688888743 66666666777888999999999999999999876


Q ss_pred             CcCccccEEEEEEecCCCC
Q 042741          148 GRNLKREYLVFGRAKGESI  166 (166)
Q Consensus       148 ~~~~~~~~~~igti~~d~l  166 (166)
                       .  .++..+.+||+++||
T Consensus       155 -~--~~~~~I~lTmrq~~L  170 (183)
T COG1095         155 -R--PRESKIGLTMRQPGL  170 (183)
T ss_pred             -c--cccceEEEEeccccC
Confidence             1  145899999999997

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

Probab=100.00  E-value=1.9e-45  Score=286.62  Aligned_cols=153  Identities=28%  Similarity=0.490  Sum_probs=145.2

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||+...++.+|.+||++||++  +  ++.+.+.|.++.+|+ |++++||+|||+++++||+|+ |.+|+|.+.|+|+|+|
T Consensus         1 mff~~~l~~~i~l~p~~~gp~--~--~~~l~~~L~~~veg~-ctg~~Gyvi~vt~ld~Ig~g~-I~~~~G~v~FpVky~a   74 (170)
T KOG3298|consen    1 MFFHKDLDLNICLHPSYFGPN--L--QAILKRKLLAEVEGK-CTGKYGYVIAVTTLDNIGEGR-IRPGTGFVTFPVKYKA   74 (170)
T ss_pred             CcceeeeeeeeeecccccCch--H--HHHHHHHHHHHhhcc-ccccccEEEEEEEhhhccCCc-cccCCceEEEEEEEEE
Confidence            999999999999999999998  5  777788888889999 999999999999999999999 9999999999999999


Q ss_pred             EEEeeecCcEEEEE------------eCCcceEEecCCCC-CCceeeCCCc-eeEecCCCCeecCCCEEEEEEEEEEEcC
Q 042741           81 RTFLPVKGEILHGV------------CGPMKYALMSPRRM-PTYRHVSGKK-SFFSNDQQPKIGNGVVVQFLVTAVRWSG  146 (166)
Q Consensus        81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m-~~~~~~~~~~-~~~~~~~~~~i~~g~~VR~RI~~~~~~~  146 (166)
                      ++|||||||||+|+            +||++ +|+++|.+ |||.|++++| ++|.++++.+|++|+.||++|+|++|++
T Consensus        75 v~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~-~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~  153 (170)
T KOG3298|consen   75 VTFKPFKGEVVDGVVTKVNKMGVFARSGPLE-VFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDE  153 (170)
T ss_pred             EEEeecCCcEEEEEEEEEeeeeEEEeccceE-eeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEee
Confidence            99999999999999            99999 99999988 6899999988 8888877779999999999999999998


Q ss_pred             CCcCccccEEEEEEecCCCC
Q 042741          147 EGRNLKREYLVFGRAKGESI  166 (166)
Q Consensus       147 ~~~~~~~~~~~igti~~d~l  166 (166)
                      +    +  |+|+|||+||||
T Consensus       154 ~----~--i~algtl~~D~L  167 (170)
T KOG3298|consen  154 T----E--IFALGTLKGDYL  167 (170)
T ss_pred             e----e--EEEEEEecCccc
Confidence            8    5  999999999998

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

Probab=100.00  E-value=1.1e-45  Score=292.87  Aligned_cols=160  Identities=16%  Similarity=0.273  Sum_probs=147.5

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||++++|+|+|||||++|.++  +  +++|.++|++++.|| +.+|+||||||+||.++++|+ |.||||++|++|.||+
T Consensus         1 MF~Lsel~D~VrI~P~qf~~~--~--~~ai~~eL~~k~anK-vl~nvGLCI~vyDi~~v~e~~-v~pGDGas~~~V~FR~   74 (202)
T KOG3297|consen    1 MFYLSELEDTVRIPPSQFEKP--L--EDAIKEELNRKLANK-VLPNVGLCICVYDILEVEEGI-VLPGDGASYARVWFRV   74 (202)
T ss_pred             CeeehhcccceecChHHhCch--H--HHHHHHHHHHHHHhh-hcccccEEEEEeEeeeecceE-EecCCCceEEEEEEEE
Confidence            999999999999999999988  4  999999999999999 999999999999999999999 9999999999999999


Q ss_pred             EEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEec-C------CCCeecCCCEEEEEEE
Q 042741           81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSN-D------QQPKIGNGVVVQFLVT  140 (166)
Q Consensus        81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~-~------~~~~i~~g~~VR~RI~  140 (166)
                      +|||||.|||+.|+            +|+|||||||+..|++ +.|++++++|+|. +      ++.+++.|+.|||||.
T Consensus        75 vVFrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~  154 (202)
T KOG3297|consen   75 VVFRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVE  154 (202)
T ss_pred             EEEecccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEe
Confidence            99999999999999            8999999999999965 7799999999996 2      4568999999999999


Q ss_pred             EEEEcCCCcC-------------ccccEEEEEEecCCCC
Q 042741          141 AVRWSGEGRN-------------LKREYLVFGRAKGESI  166 (166)
Q Consensus       141 ~~~~~~~~~~-------------~~~~~~~igti~~d~l  166 (166)
                      ..+|.+.+.+             .+.+|..+|+|++|+|
T Consensus       155 ~e~f~d~~p~~~~~~~t~~e~~e~~~py~l~gs~~~~GL  193 (202)
T KOG3297|consen  155 DESFVDVSPEGNSTAITGAEDPEKESPYTLLGSMNEDGL  193 (202)
T ss_pred             eecccccCccccccccccccccccCCCeEEEEEecCCCC
Confidence            9999654332             2348999999999987

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

Probab=100.00  E-value=4.5e-45  Score=290.51  Aligned_cols=157  Identities=14%  Similarity=0.211  Sum_probs=145.9

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||++++|+|+|+|||++|+++  +  ++++.++|+++|+|| |.+++||||||+|++++++|+ |.||||+++|+|+|||
T Consensus         1 Mf~~~~l~d~v~i~P~~~~~~--~--~~~i~~~l~~~~~gk-~~~~~G~~i~v~di~~i~~g~-i~~gdG~~~~~V~f~~   74 (179)
T TIGR00448         1 MYILSKIADTVRIPPDQFGED--L--EEVITHQLNEKFEGR-LDKNVGLCITIYDIEDIGEGK-VIPGDGSAYHNVTFRA   74 (179)
T ss_pred             CeEEEEEeeEEEECHHHhCcc--H--HHHHHHHHHHHhcCc-CcCCcCEEEEEEEeEEecCCE-EECCCCCEEEEEEEEE
Confidence            999999999999999999988  5  999999999999999 999999999999999999999 9999999999999999


Q ss_pred             EEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741           81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus        81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ++||||+|||++|+            +||+++++++++++++ +.||++++.|+|++++.+++.||.|||||.++++++.
T Consensus        75 i~f~p~~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~  154 (179)
T TIGR00448        75 LVFKPELGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDR  154 (179)
T ss_pred             EEEeccCCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCC
Confidence            99999999999999            8999999999999976 5689999999998888999999999999999999754


Q ss_pred             CcCccccEEEEEEecCCCC
Q 042741          148 GRNLKREYLVFGRAKGESI  166 (166)
Q Consensus       148 ~~~~~~~~~~igti~~d~l  166 (166)
                      .. .  .-.+.+||+++||
T Consensus       155 ~~-~--~~~I~lt~k~~~L  170 (179)
T TIGR00448       155 RP-E--GSKIGLTMRQPLL  170 (179)
T ss_pred             CC-C--cceEEEEeccCcC
Confidence            11 1  1356999999998

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=4.2e-42  Score=274.37  Aligned_cols=156  Identities=19%  Similarity=0.231  Sum_probs=144.3

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||++++|+|+|+|||++|+++  +  ++++.++|+++|+|+ |.+++||||||+|++++++|+ |.||||+++|+|+|+|
T Consensus         1 MF~~~~l~d~v~i~P~~~~~~--~--~~~i~~~l~~~~~~k-~~~~~G~~v~v~di~~i~~g~-i~~gdg~~~~~v~f~~   74 (187)
T PRK08563          1 MYKLVKLEDVVRIPPEMFGED--L--EEAALEVLREKYEGR-IDKELGIIVAVLDVKVIGEGK-IVPGDGATYHEVEFDA   74 (187)
T ss_pred             CeEEEEEeEEEEECHHHcCcc--H--HHHHHHHHHHHhhCc-CcCCcCEEEEEEEeEEecccE-EecCCCCcEEEEEEEE
Confidence            999999999999999999988  5  999999999999999 999999999999999999999 9999999999999999


Q ss_pred             EEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741           81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus        81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      +||+||+|||++|+            +||+++++++++++++ +.||++++.|+|++.+..++.|+.|||||.++++++.
T Consensus        75 lvf~P~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~  154 (187)
T PRK08563         75 LVFKPELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKER  154 (187)
T ss_pred             EEEeccCCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccC
Confidence            99999999999999            8999999999888876 6699999999999888899999999999999999765


Q ss_pred             CcCcc-ccEEEEEEecCCCC
Q 042741          148 GRNLK-REYLVFGRAKGESI  166 (166)
Q Consensus       148 ~~~~~-~~~~~igti~~d~l  166 (166)
                          + +...+.+||+++||
T Consensus       155 ----~~~~~~I~ls~~~~~L  170 (187)
T PRK08563        155 ----RPRGSKIGLTMRQPGL  170 (187)
T ss_pred             ----CCCCCEEEEEecCCCC
Confidence                2 01366669999997

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

Probab=99.97  E-value=2.7e-30  Score=182.06  Aligned_cols=80  Identities=31%  Similarity=0.514  Sum_probs=78.1

Q ss_pred             eEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeEE
Q 042741            2 FFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCR   81 (166)
Q Consensus         2 F~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~al   81 (166)
                      |++++++|+|+|||++||++  +  ++++.++|+++++|+ |.+++||||||+|++++++|+ |.||||++||+|+|+|+
T Consensus         1 F~~~~l~d~v~i~P~~fg~~--l--~~~i~~~L~~~~egk-~~~~~G~iv~v~di~~i~~G~-I~~gdG~~~~~V~F~ai   74 (80)
T cd04329           1 FFKIELEHNILLHPSYFGPN--L--KEYLEQKLLEEVEGT-CTGDYGYIIAVTDIDDIGEGK-ILPGTGSVEFPVKYKAI   74 (80)
T ss_pred             CEEEEEEEEEEECHHHhCcc--H--HHHHHHHHHHHhCCc-CcCceeEEEEEEEeeEecCcE-EEcCCCCEEEEEEEEEE
Confidence            89999999999999999988  5  999999999999999 999999999999999999999 99999999999999999


Q ss_pred             EEeeec
Q 042741           82 TFLPVK   87 (166)
Q Consensus        82 vFrPf~   87 (166)
                      |||||+
T Consensus        75 vfrPf~   80 (80)
T cd04329          75 VFKPFK   80 (80)
T ss_pred             EEEccC
Confidence            999996

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.

>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=99.96  E-value=5.8e-30  Score=180.31  Aligned_cols=80  Identities=21%  Similarity=0.231  Sum_probs=78.0

Q ss_pred             eEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeEE
Q 042741            2 FFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCR   81 (166)
Q Consensus         2 F~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~al   81 (166)
                      |++++++|+|+|||++||++  +  ++++.++|+++|+|+ |.+++||||||+|++++++|+ |.||||++||+|+|||+
T Consensus         1 f~l~~l~d~v~i~P~~f~~~--~--~~~i~~~L~~k~~gk-v~~~~G~~v~v~di~~i~~G~-I~~gdG~~~~~V~F~~i   74 (80)
T cd00655           1 FQILEIADLVSVPPKYFGDD--C--KGVKKCLLQEKGEGD-RTPVVGIILAIKDTKDIPEGA-IRPGDGSAYVNVSFRAV   74 (80)
T ss_pred             CEEEEEEEEEEECHHHhCcc--H--HHHHHHHHHHHhCCe-EeCCccEEEEEEEeEEEcCCE-EECCCCCEEEEEEEEEE
Confidence            79999999999999999988  5  999999999999999 999999999999999999999 99999999999999999


Q ss_pred             EEeeec
Q 042741           82 TFLPVK   87 (166)
Q Consensus        82 vFrPf~   87 (166)
                      |||||+
T Consensus        75 vFrPf~   80 (80)
T cd00655          75 VFKPFS   80 (80)
T ss_pred             EEEcCC
Confidence            999996

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.

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

Probab=99.96  E-value=8e-30  Score=179.65  Aligned_cols=80  Identities=16%  Similarity=0.287  Sum_probs=78.0

Q ss_pred             eEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeEE
Q 042741            2 FFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCR   81 (166)
Q Consensus         2 F~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~al   81 (166)
                      |++++++|+|+|||++||++  +  ++++.++|+++|+|+ |.+++||||||+|++++++|+ |.||||++||+|+|||+
T Consensus         1 F~~~~l~d~v~i~P~~fg~~--~--~~~i~~~L~~ky~gk-v~~~~Gl~v~v~di~~i~eG~-I~~gdG~~~~~V~Fr~l   74 (80)
T cd04330           1 FILSEIEDTVRIPPSQFSRP--L--NDAIEDELNKKYANK-VIQNVGLCICLYDILEVEDGY-ILPGDGASHYKVTFRMV   74 (80)
T ss_pred             CEEEEEEEEEEECHHHcCcC--H--HHHHHHHHHHHhCCc-EeCCccEEEEEEEeEEEcCCE-EECCCCCEEEEEEEEEE
Confidence            88999999999999999988  5  999999999999999 999999999999999999999 99999999999999999


Q ss_pred             EEeeec
Q 042741           82 TFLPVK   87 (166)
Q Consensus        82 vFrPf~   87 (166)
                      |||||+
T Consensus        75 vFrPf~   80 (80)
T cd04330          75 VFRPFV   80 (80)
T ss_pred             EEECCC
Confidence            999996

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.

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

Probab=99.96  E-value=2.5e-29  Score=177.16  Aligned_cols=80  Identities=26%  Similarity=0.302  Sum_probs=77.4

Q ss_pred             eEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeEE
Q 042741            2 FFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCR   81 (166)
Q Consensus         2 F~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~al   81 (166)
                      |++++++|+|+|||++||++  +  ++++.++|+++|+|+ |++++||||||+|++++++|+ |.||||++||+|+|||+
T Consensus         1 f~~~~l~d~vri~P~~fg~~--~--~~~i~~~L~~~~egk-~~~~~G~iv~v~di~~i~eG~-I~~gdG~~~~~V~F~~i   74 (80)
T cd04331           1 YKLVELEDVVRVPPELFGED--L--EEAVLEILKEKYEGR-LDKDLGKIVSVLDVKDVGEGK-IVHGDGAVYHEVRFDAL   74 (80)
T ss_pred             CEEEEEEEeEEECHHHcCcC--H--HHHHHHHHHHHhcCc-CcCCCCEEEEEEEEEEecCCE-EEcCCCCEEEEEEEEEE
Confidence            78999999999999999988  5  999999999999999 999999999999999999999 99999999999999999


Q ss_pred             EEeeec
Q 042741           82 TFLPVK   87 (166)
Q Consensus        82 vFrPf~   87 (166)
                      ||||..
T Consensus        75 vFrP~~   80 (80)
T cd04331          75 VFKPEL   80 (80)
T ss_pred             EEecCC
Confidence            999963

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.

>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=99.82  E-value=4.7e-20  Score=125.61  Aligned_cols=70  Identities=21%  Similarity=0.339  Sum_probs=65.2

Q ss_pred             ceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeEEEE
Q 042741            8 LRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMCRTF   83 (166)
Q Consensus         8 ~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~alvF   83 (166)
                      +|+|+|||++|+++  +  ++.+.++|+++++|+ +.+++|+|||++|+..+++|+ |.+|||+++|+|+|+|+||
T Consensus         1 e~~v~l~P~~l~~~--~--~~~i~~~L~~~~~~k-~~~~~G~~i~v~~i~~~~~g~-I~~~~g~~~~~V~f~~lvF   70 (70)
T PF03876_consen    1 EDTVRLPPSYLGPD--L--KDGIKEQLLDKYEGK-YIPELGVVIAVTDIKEISEGK-IIPGDGFVYFKVTFRALVF   70 (70)
T ss_dssp             EEEEEE-GGGTTST--H--HHHHHHHHHHHHTTE-EETTTEEEEEEEEEEEESCEE-E-TTTSSEEEEEEEEEEEE
T ss_pred             CcEEEECHHHhCcC--H--HHHHHHHHHHHHhCc-CcCCceEEEEEeeeeEecCcE-EECCCCCEEEEEEEEEEEC
Confidence            68999999999977  4  899999999999999 999999999999999999999 9999999999999999998

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=99.78  E-value=8.6e-19  Score=125.38  Aligned_cols=74  Identities=14%  Similarity=0.226  Sum_probs=63.0

Q ss_pred             cCcEEEEE------------eCCcceEEecCCCCCCceeeCCCceeEec-CCCCeecCCCEEEEEEEEEEEcCCCcCccc
Q 042741           87 KGEILHGV------------CGPMKYALMSPRRMPTYRHVSGKKSFFSN-DQQPKIGNGVVVQFLVTAVRWSGEGRNLKR  153 (166)
Q Consensus        87 ~gEVv~G~------------~Gp~~~ifi~~~~m~~~~~~~~~~~~~~~-~~~~~i~~g~~VR~RI~~~~~~~~~~~~~~  153 (166)
                      +|||++|+            +||++.+|+..++++++.|++++++|.|. +++.+|++|+.|||||++++|+.+    + 
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~----~-   75 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT----D-   75 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC----c-
Confidence            69999999            99999555555555678899877888876 467899999999999999999766    4 


Q ss_pred             cEEEEEEecCCCC
Q 042741          154 EYLVFGRAKGESI  166 (166)
Q Consensus       154 ~~~~igti~~d~l  166 (166)
                       ++|+|||++|||
T Consensus        76 -~~~igt~~~~~L   87 (88)
T cd04462          76 -IFAIGTIKDDYL   87 (88)
T ss_pred             -eEEEEEccCCCC
Confidence             999999999998

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.

>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=99.76  E-value=3.3e-18  Score=129.35  Aligned_cols=82  Identities=20%  Similarity=0.348  Sum_probs=60.2

Q ss_pred             eecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEec---CCCCeecCCCEEEEEEEEEEEcCC-
Q 042741           85 PVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSN---DQQPKIGNGVVVQFLVTAVRWSGE-  147 (166)
Q Consensus        85 Pf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~---~~~~~i~~g~~VR~RI~~~~~~~~-  147 (166)
                      ||+||||.|+            +|||+|||||++.|++ +.||++++.|+|.   +++..++.|+.|||||.++.|.+. 
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            9999999999            8999999999999975 7799999999997   344689999999999999999432 


Q ss_pred             CcC-----------------ccccEEEEEEecCCCC
Q 042741          148 GRN-----------------LKREYLVFGRAKGESI  166 (166)
Q Consensus       148 ~~~-----------------~~~~~~~igti~~d~l  166 (166)
                      |..                 ..-+|.++|||++++|
T Consensus        81 p~~~~~~~~~~~~~~~~~~~~~~Py~I~gs~~~~GL  116 (122)
T PF08292_consen   81 PTPPPSAEASGEEEEEEEDEPKPPYQIIGSINEDGL  116 (122)
T ss_dssp             -----------------------SEEEEEEB-STT-
T ss_pred             CCCcccccccccccccccccCCCCeEEEEEecCCCC
Confidence            111                 1128999999999987

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

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

Probab=99.71  E-value=5.9e-17  Score=115.73  Aligned_cols=79  Identities=13%  Similarity=0.102  Sum_probs=74.2

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCe-eEEEEEEEecccCC--CcceecCCCceEEEEE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDH-GYFLSVTKSKSIDK--EGPTVNGPGVVSFPVI   77 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~-GliI~V~di~~i~~--G~~I~~gdG~~~~~V~   77 (166)
                      ||.+++++++|+|+|++|+++     .+++.++|++.+. + +..++ |+|+|.+|+..+++  |+ |.+++|.++++|+
T Consensus         8 ~f~~~~~~~~v~l~P~~~~~~-----~~~i~~~l~~~l~-k-y~~~l~Gv~l~~~di~~~~~~~~~-i~~~~~~~~~~V~   79 (89)
T cd04328           8 CFETLTVSLYVSLAPKYLGNP-----LTGIKAQLLNPLL-K-YSPKLKGVVLAYSNIKLLEGELAK-IVDDSPFIFVWIS   79 (89)
T ss_pred             cEEEEEEEEEEEECchhhcCH-----hHHHHHHHhhhHh-h-hcccCCeEEEEecceEecccccee-eeCCCcEEEEEEE
Confidence            899999999999999999987     4699999998888 7 99999 99999999999977  99 9999999999999


Q ss_pred             EeEEEEeeec
Q 042741           78 FMCRTFLPVK   87 (166)
Q Consensus        78 F~alvFrPf~   87 (166)
                      |+++|||||.
T Consensus        80 ~~~lVFrP~~   89 (89)
T cd04328          80 ADFLVFRPKI   89 (89)
T ss_pred             EEEEEEecCC
Confidence            9999999985

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=97.36  E-value=0.0009  Score=47.97  Aligned_cols=68  Identities=16%  Similarity=0.191  Sum_probs=44.4

Q ss_pred             eCCcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCCCcCccccEEEEE-EecCCCC
Q 042741           95 CGPMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNLKREYLVFG-RAKGESI  166 (166)
Q Consensus        95 ~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~~~~~~~~~~~ig-ti~~d~l  166 (166)
                      +++.+++.+.+++.++ +.|++....|...+.+..++.||.|+++|.++.....    ++.+..++ |+++++|
T Consensus        19 l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~----~~~~~~i~ls~k~~~~   88 (99)
T cd04460          19 IGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKER----RPRESKIGLTMRQPGL   88 (99)
T ss_pred             EcCeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHC----cCCCceEEEEEecCCC
Confidence            5555644444555555 4566665555555666889999999999999886543    11134555 9998876

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.

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

Probab=97.09  E-value=0.0037  Score=52.05  Aligned_cols=84  Identities=14%  Similarity=0.105  Sum_probs=68.3

Q ss_pred             EEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccC-CCcceecCCCceEEEEEEeEEEE
Q 042741            5 VELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID-KEGPTVNGPGVVSFPVIFMCRTF   83 (166)
Q Consensus         5 ~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~-~G~~I~~gdG~~~~~V~F~alvF   83 (166)
                      .+..-.+.+.|-++..+     ..++.++.+......+-.+=.|.+++.-+|+-.+ .++ |.+-|+..+..+.=..+||
T Consensus        30 ~t~dlhlalaP~yl~np-----l~~~i~ehld~~vl~y~~~l~GivLgydnIKvLg~~ak-i~~D~pf~hlwi~adfyVf  103 (253)
T KOG4134|consen   30 ITTDLHLALAPYYLANP-----LHALIEEHLDTKVLFYDSGLDGIVLGYDNIKVLGQTAK-IRADDPFMHLWINADFYVF  103 (253)
T ss_pred             eeeheeeeecchhhcch-----hHHHHHHHhhHHHhhhccCCCceEEeecceEeeccccc-eecCCCceEEEEeeeEEEE
Confidence            45566789999999887     4656666666666663445568888887788766 688 9999999999999999999


Q ss_pred             eeecCcEEEEE
Q 042741           84 LPVKGEILHGV   94 (166)
Q Consensus        84 rPf~gEVv~G~   94 (166)
                      +|-.|.+|+|.
T Consensus       104 ~Pk~Gd~LeG~  114 (253)
T KOG4134|consen  104 RPKAGDILEGV  114 (253)
T ss_pred             CCCCCCeeeee
Confidence            99999999999

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

Probab=96.72  E-value=0.008  Score=40.14  Aligned_cols=54  Identities=17%  Similarity=0.184  Sum_probs=39.1

Q ss_pred             eeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741           84 LPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus        84 rPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      +|..|++++|+            +| ..+ .|+|.+.+++.         +..+....+..|+.|+++|.++.-+..
T Consensus         1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~-g~ip~~~l~~~---------~~~~~~~~~~~G~~v~v~v~~vd~~~~   67 (74)
T PF00575_consen    1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIE-GFIPISELSDD---------RIDDPSEVYKIGQTVRVKVIKVDKEKG   67 (74)
T ss_dssp             -SSTTSEEEEEEEEEETTEEEEEESTSSE-EEEEGGGSSSS---------EESSSHGTCETTCEEEEEEEEEETTTT
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCcEE-EEEEeehhcCc---------cccccccccCCCCEEEEEEEEEECCCC
Confidence            57789999999            66 666 77776666432         223334578999999999999887655

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 ....

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

Probab=96.22  E-value=0.027  Score=38.09  Aligned_cols=57  Identities=18%  Similarity=0.239  Sum_probs=37.4

Q ss_pred             CcEEEEE------------eCC--cceEEecCCCC-CC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEc
Q 042741           88 GEILHGV------------CGP--MKYALMSPRRM-PT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus        88 gEVv~G~------------~Gp--~~~ifi~~~~m-~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~  145 (166)
                      |++.+|.            +++  .+ -+++.+.+ ++ +.|++.+..+..+.....++.||.|+++|.++...
T Consensus         2 g~~~~g~V~~v~~~G~fv~l~~~~~~-G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~   74 (83)
T cd04471           2 GEEFDGVISGVTSFGLFVELDNLTVE-GLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLD   74 (83)
T ss_pred             CCEEEEEEEeEEeeeEEEEecCCCEE-EEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccc
Confidence            5666666            665  44 35554555 44 45665554334445567899999999999998763

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.

>TIGR02063 RNase_R ribonuclease R

Probab=92.01  E-value=0.45  Score=45.32  Aligned_cols=70  Identities=11%  Similarity=0.008  Sum_probs=49.6

Q ss_pred             EeEEEEeeecCcEEEEE------------eCC--cceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEE
Q 042741           78 FMCRTFLPVKGEILHGV------------CGP--MKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAV  142 (166)
Q Consensus        78 F~alvFrPf~gEVv~G~------------~Gp--~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~  142 (166)
                      +.|.-.++..||+.+|+            +.+  .+++.|.+++-++ +.|++....+.....+..++.||.|+++|.++
T Consensus       618 ~~~~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~v  697 (709)
T TIGR02063       618 KKAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKA  697 (709)
T ss_pred             HHHHhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEE
Confidence            44445667788888888            333  5666666655555 45777666666666667899999999999999


Q ss_pred             EEcCC
Q 042741          143 RWSGE  147 (166)
Q Consensus       143 ~~~~~  147 (166)
                      .....
T Consensus       698 d~~~~  702 (709)
T TIGR02063       698 DLDTG  702 (709)
T ss_pred             ecccC
Confidence            87544

This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.

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

Probab=91.86  E-value=0.72  Score=29.18  Aligned_cols=21  Identities=19%  Similarity=0.039  Sum_probs=17.4

Q ss_pred             CeecCCCEEEEEEEEEEEcCC
Q 042741          127 PKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus       127 ~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ..++.|+.|+++|..+.....
T Consensus        45 ~~~~~G~~v~~~V~~~~~~~~   65 (72)
T smart00316       45 EVLKVGDEVKVKVLSVDEEKG   65 (72)
T ss_pred             HeecCCCEEEEEEEEEeCCCC
Confidence            468999999999999986533

>PRK11642 exoribonuclease R; Provisional

Probab=89.77  E-value=1.6  Score=42.57  Aligned_cols=70  Identities=17%  Similarity=0.191  Sum_probs=48.2

Q ss_pred             EeEEEEeeecCcEEEEE------------eC--CcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEE
Q 042741           78 FMCRTFLPVKGEILHGV------------CG--PMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAV  142 (166)
Q Consensus        78 F~alvFrPf~gEVv~G~------------~G--p~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~  142 (166)
                      +.|-......||+.+|+            +.  ..+++.+.+++-++ |.|++.........++..++.||.|+++|..+
T Consensus       634 ~~~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~v  713 (813)
T PRK11642        634 LKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAV  713 (813)
T ss_pred             HHHhhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEe
Confidence            33444566788998888            32  25544444444455 56776666666666678899999999999998


Q ss_pred             EEcCC
Q 042741          143 RWSGE  147 (166)
Q Consensus       143 ~~~~~  147 (166)
                      .....
T Consensus       714 D~~~r  718 (813)
T PRK11642        714 NMDER  718 (813)
T ss_pred             ecCCC
Confidence            87644

>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases

Probab=89.50  E-value=1.8  Score=41.11  Aligned_cols=70  Identities=16%  Similarity=0.142  Sum_probs=48.7

Q ss_pred             EeEEEEeeecCcEEEEE------------eC-C-cceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEE
Q 042741           78 FMCRTFLPVKGEILHGV------------CG-P-MKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAV  142 (166)
Q Consensus        78 F~alvFrPf~gEVv~G~------------~G-p-~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~  142 (166)
                      +.|.-++...||+.+|+            +. + .+++.+.+++-++ |.||+.........++..++.||.|++||.++
T Consensus       563 ~~~~yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~v  642 (654)
T TIGR00358       563 LKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEV  642 (654)
T ss_pred             HHHHhhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEE
Confidence            44555666778888888            22 2 4544444444444 66887777777666778999999999999998


Q ss_pred             EEcCC
Q 042741          143 RWSGE  147 (166)
Q Consensus       143 ~~~~~  147 (166)
                      .....
T Consensus       643 d~~~~  647 (654)
T TIGR00358       643 NMETR  647 (654)
T ss_pred             ecccC
Confidence            76554

This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=88.95  E-value=0.16  Score=48.39  Aligned_cols=80  Identities=11%  Similarity=-0.002  Sum_probs=54.4

Q ss_pred             EEecccCCCcceecCCCceEEEE--EEeEEEEeeecCcEEEEE------------e-CCcceEEecCCCCCCceeeCCCc
Q 042741           54 TKSKSIDKEGPTVNGPGVVSFPV--IFMCRTFLPVKGEILHGV------------C-GPMKYALMSPRRMPTYRHVSGKK  118 (166)
Q Consensus        54 ~di~~i~~G~~I~~gdG~~~~~V--~F~alvFrPf~gEVv~G~------------~-Gp~~~ifi~~~~m~~~~~~~~~~  118 (166)
                      +||.+-|..+ |...++.++.++  ..+.++..|..|++++|+            + +..+++.|.+++-++        
T Consensus       584 I~i~ddG~V~-i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~--------  654 (684)
T TIGR03591       584 IDIEDDGTVK-IAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANE--------  654 (684)
T ss_pred             EEEecCeEEE-EEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCC--------
Confidence            4555556666 667778777777  667778889999999999            2 234544444443221        


Q ss_pred             eeEecCCCCeecCCCEEEEEEEEEEE
Q 042741          119 SFFSNDQQPKIGNGVVVQFLVTAVRW  144 (166)
Q Consensus       119 ~~~~~~~~~~i~~g~~VR~RI~~~~~  144 (166)
                        ++++-...++.||.|++||.++..
T Consensus       655 --~v~~~~~~~kvGD~V~VkVi~id~  678 (684)
T TIGR03591       655 --RVEKVEDVLKEGDEVKVKVLEIDK  678 (684)
T ss_pred             --cccChhhccCCCCEEEEEEEEECC
Confidence              122334568999999999998764

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).

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=86.74  E-value=1.7  Score=36.02  Aligned_cols=55  Identities=20%  Similarity=0.262  Sum_probs=33.7

Q ss_pred             EeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEE
Q 042741           83 FLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVR  143 (166)
Q Consensus        83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~  143 (166)
                      |.|-.|++|.|+            ++ +++++++.++........+      ..+-...+++||.|++||..+.
T Consensus        59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d------~~~~~~~~~~GDlV~akV~~i~  126 (235)
T PRK04163         59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVE------GTDLRKYLDIGDYIIAKVKDVD  126 (235)
T ss_pred             ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccc------hhhhHhhCCCCCEEEEEEEEEC
Confidence            899999999999            44 5564433333321111000      0112245899999999999875

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

Probab=86.65  E-value=2.4  Score=28.26  Aligned_cols=20  Identities=15%  Similarity=0.028  Sum_probs=16.1

Q ss_pred             CCeecCCCEEEEEEEEEEEc
Q 042741          126 QPKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus       126 ~~~i~~g~~VR~RI~~~~~~  145 (166)
                      ...++.||.|+++|.++...
T Consensus        46 ~~~~~~Gd~v~vkv~~vd~~   65 (73)
T cd05686          46 SEVVDVGEKVWVKVIGREMK   65 (73)
T ss_pred             hhEECCCCEEEEEEEEECCC
Confidence            45689999999999887653

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.

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

Probab=86.31  E-value=0.98  Score=30.94  Aligned_cols=55  Identities=15%  Similarity=0.203  Sum_probs=33.4

Q ss_pred             EeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEE
Q 042741           83 FLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVR  143 (166)
Q Consensus        83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~  143 (166)
                      |.|-+|++++|+            ++ +++++.+.+++..+. +    +.+ ..+-...+++||.|++||..+.
T Consensus         2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~-~----~~~-~~~~~~~l~vGd~i~~~V~~~~   69 (86)
T cd05789           2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPR-T----DED-ELNMRSYLDEGDLIVAEVQSVD   69 (86)
T ss_pred             CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCC-C----ccc-hHHHHhhCCCCCEEEEEEEEEC
Confidence            678899999999            33 455444444443210 0    000 1122346899999999998874

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".

>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=85.04  E-value=2.9  Score=27.45  Aligned_cols=22  Identities=14%  Similarity=-0.013  Sum_probs=17.7

Q ss_pred             CCeecCCCEEEEEEEEEEEcCC
Q 042741          126 QPKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus       126 ~~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ...++.||.|++||..+.....
T Consensus        45 ~~~~~~Gd~v~v~i~~vd~~~~   66 (77)
T cd05708          45 SKLFRVGDKVRAKVLKIDAEKK   66 (77)
T ss_pred             hHeecCCCEEEEEEEEEeCCCC
Confidence            3568999999999999876543

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.

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

Probab=84.77  E-value=3.6  Score=26.71  Aligned_cols=21  Identities=19%  Similarity=0.162  Sum_probs=17.1

Q ss_pred             CeecCCCEEEEEEEEEEEcCC
Q 042741          127 PKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus       127 ~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ..++.||.|+++|..+.....
T Consensus        43 ~~~~~Gd~v~~~v~~~d~~~~   63 (73)
T cd05691          43 ERFKVGDEVEAKITNVDRKNR   63 (73)
T ss_pred             HccCCCCEEEEEEEEEeCCCC
Confidence            458999999999999876543

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.

>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=84.75  E-value=7.1  Score=25.56  Aligned_cols=21  Identities=19%  Similarity=0.132  Sum_probs=17.0

Q ss_pred             CeecCCCEEEEEEEEEEEcCC
Q 042741          127 PKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus       127 ~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ..+..||.|+++|..+.....
T Consensus        46 ~~~~~Gd~v~~~V~~~d~~~~   66 (73)
T cd05706          46 YKFKKNDIVRACVLSVDVPNK   66 (73)
T ss_pred             cccCCCCEEEEEEEEEeCCCC
Confidence            568999999999998776533

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.

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

Probab=84.74  E-value=2.7  Score=28.50  Aligned_cols=52  Identities=15%  Similarity=0.165  Sum_probs=31.9

Q ss_pred             EeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEE
Q 042741           83 FLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRW  144 (166)
Q Consensus        83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~  144 (166)
                      |.|-.|.++.|+            +| .++ .++|...+...         ...+....+++||.|++||..+.-
T Consensus         2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~-g~l~~~~~~~~---------~~~~~~~~~~~GD~i~~~V~~~~~   66 (82)
T cd04454           2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGT-ARLEDSSATEK---------DKKEIRKSLQPGDLILAKVISLGD   66 (82)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEeCCCce-EEeechhccCc---------chHHHHhcCCCCCEEEEEEEEeCC
Confidence            679999999999            32 344 33333322110         011222458999999999998644

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".

>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=83.92  E-value=3  Score=27.13  Aligned_cols=19  Identities=21%  Similarity=0.132  Sum_probs=15.8

Q ss_pred             CeecCCCEEEEEEEEEEEc
Q 042741          127 PKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus       127 ~~i~~g~~VR~RI~~~~~~  145 (166)
                      ..+++|+.|++||.++.-.
T Consensus        43 ~~~~~G~~i~v~v~~~d~~   61 (70)
T cd05698          43 EHFRVGQVVKVKVLSCDPE   61 (70)
T ss_pred             HcccCCCEEEEEEEEEcCC
Confidence            4588999999999887654

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.

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

Probab=81.58  E-value=1.4  Score=31.37  Aligned_cols=17  Identities=18%  Similarity=0.153  Sum_probs=14.1

Q ss_pred             CeecCCCEEEEEEEEEE
Q 042741          127 PKIGNGVVVQFLVTAVR  143 (166)
Q Consensus       127 ~~i~~g~~VR~RI~~~~  143 (166)
                      ..+++||.||+||.+..
T Consensus        59 ~~f~~GDiV~AkVis~~   75 (92)
T cd05791          59 KCFRPGDIVRAKVISLG   75 (92)
T ss_pred             hhcCCCCEEEEEEEEcC
Confidence            34799999999998754

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".

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

Probab=81.03  E-value=7.3  Score=25.54  Aligned_cols=21  Identities=14%  Similarity=-0.081  Sum_probs=16.7

Q ss_pred             CeecCCCEEEEEEEEEEEcCC
Q 042741          127 PKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus       127 ~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ..++.||.|++||..+.....
T Consensus        48 ~~~~~Gd~v~vkv~~~d~~~~   68 (76)
T cd04452          48 KLVKVGRKEVVKVIRVDKEKG   68 (76)
T ss_pred             HeeCCCCEEEEEEEEEECCCC
Confidence            458999999999998766433

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

>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=80.87  E-value=3.7  Score=26.76  Aligned_cols=22  Identities=23%  Similarity=0.218  Sum_probs=17.8

Q ss_pred             CCeecCCCEEEEEEEEEEEcCC
Q 042741          126 QPKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus       126 ~~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ...++.|+.+.+||.++.....
T Consensus        42 ~~~~~~Gd~i~~~V~~id~~~~   63 (69)
T cd05697          42 EKKFKPGLKVKCRVLSVEPERK   63 (69)
T ss_pred             HHcCCCCCEEEEEEEEEECCCC
Confidence            3569999999999998876544

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.

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

Probab=80.84  E-value=6.4  Score=25.57  Aligned_cols=17  Identities=24%  Similarity=0.249  Sum_probs=14.9

Q ss_pred             CeecCCCEEEEEEEEEE
Q 042741          127 PKIGNGVVVQFLVTAVR  143 (166)
Q Consensus       127 ~~i~~g~~VR~RI~~~~  143 (166)
                      ..+++||.++++|.++.
T Consensus        43 ~~~~~Gd~i~~~i~~~~   59 (70)
T cd05687          43 DEVKVGDEVEVYVLRVE   59 (70)
T ss_pred             HcCCCCCEEEEEEEEEE
Confidence            45899999999999886

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.

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

Probab=80.07  E-value=5.7  Score=25.15  Aligned_cols=19  Identities=16%  Similarity=0.094  Sum_probs=16.2

Q ss_pred             CeecCCCEEEEEEEEEEEc
Q 042741          127 PKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus       127 ~~i~~g~~VR~RI~~~~~~  145 (166)
                      ..++.||.|+++|..+...
T Consensus        43 ~~~~~Gd~v~v~i~~vd~~   61 (68)
T cd05688          43 EVVNVGDEVEVKVLKIDKE   61 (68)
T ss_pred             HEECCCCEEEEEEEEEECC
Confidence            5689999999999998654

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.

---

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	166
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	4e-11
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	4e-11
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	5e-11
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	3e-10
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	4e-10
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	5e-10
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	5e-08

>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 = 57.6 bits (139), Expect = 4e-11
 Identities = 32/159 (20%), Positives = 57/159 (35%), Gaps = 22/159 (13%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           MF+ + L  +I +                TV + L   +       +G+ ++VT   +I 
Sbjct: 1   MFYHISLEHEILLHP-----RYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIG 55

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
             G    G G V +PV +    F P KGE++  V             GPM    +S   +
Sbjct: 56  -AGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMS-CFISRHSI 113

Query: 109 PT---YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRW 144
           P+   +   S    + + D+   I     ++  +   R 
Sbjct: 114 PSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV 152

>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 = 57.2 bits (138), Expect = 4e-11
 Identities = 28/156 (17%), Positives = 47/156 (30%), Gaps = 18/156 (11%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           MFF  +L  +I +       +      +  +   L   +        GY L V    +ID
Sbjct: 1   MFFIKDLSLNITLHP-----SFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNID 55

Query: 61  -KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRR 107
            + G  +   G   F V +    F P KGE++ G              GPMK  +     
Sbjct: 56  IQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLM 115

Query: 108 MPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVR 143
                  +G         +  I     ++  +    
Sbjct: 116 PQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCI 151

>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 = 57.8 bits (139), Expect = 5e-11
 Identities = 28/156 (17%), Positives = 47/156 (30%), Gaps = 18/156 (11%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           MFF  +L  +I +       +      +  +   L   +        GY L V    +ID
Sbjct: 1   MFFIKDLSLNITLHP-----SFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNID 55

Query: 61  -KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRR 107
            + G  +   G   F V +    F P KGE++ G              GPMK  +     
Sbjct: 56  IQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLM 115

Query: 108 MPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVR 143
                  +G         +  I     ++  +    
Sbjct: 116 PQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCI 151

>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 = 55.5 bits (133), Expect = 3e-10
 Identities = 21/162 (12%), Positives = 49/162 (30%), Gaps = 23/162 (14%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           MF   ++   + +P      ++        +   L      K   + G  +++    +++
Sbjct: 1   MFILSKIADLVRIPP-----DQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVE 55

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGVC-------------GPMKYALMSPRR 107
            EG    G G     V F    F P  GEI+ G               G      +    
Sbjct: 56  -EGQLKPGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNM 114

Query: 108 MPTYRHVSGKKSFF----SNDQQPKIGNGVVVQFLVTAVRWS 145
           +    + + ++S +      + +        ++F +    + 
Sbjct: 115 LFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFV 156

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

 Score = 55.5 bits (133), Expect = 4e-10
 Identities = 21/166 (12%), Positives = 45/166 (27%), Gaps = 27/166 (16%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           MF        I++   +  +     P +  +   +      K  ++ G  + V     I 
Sbjct: 1   MFLLSRFSDIISIHPSNFWK-----PTKEALAEEIHKKYANKVIQNIGLAICVYDFLKIG 55

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
            EG    G G     V+F    F P +GE++ G                     +    +
Sbjct: 56  -EGIIKYGDGSSYMNVVFRLIIFRPFRGEVMLGKIKSCSEEGIRVTISFFDDIFIPKDML 114

Query: 109 PTYRHVSGKKSFF---------SNDQQPKIGNGVVVQFLVTAVRWS 145
                    +  +         S   +        ++F + +  + 
Sbjct: 115 FDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQIESEDFV 160

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

 Score = 54.2 bits (130), Expect = 5e-10
 Identities = 29/157 (18%), Positives = 52/157 (33%), Gaps = 18/157 (11%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
            FF  EL   I++       +      +  +   L   +       +GY + V  S +ID
Sbjct: 2   PFFLKELSLTISLHP-----SYFGPRMQDYLKAKLLADVEGTCSGQYGYIICVLDSNTID 56

Query: 61  -KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRR 107
             +G  V G G   F V +    + P +GE++  +             GP+   + S   
Sbjct: 57  IDKGRVVPGQGFAEFEVKYRAVLWRPFRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLV 116

Query: 108 MPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRW 144
            P  +          + +   I  G  V+  +   R 
Sbjct: 117 PPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRT 153

>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 = 49.2 bits (117), Expect = 5e-08
 Identities = 31/161 (19%), Positives = 62/161 (38%), Gaps = 21/161 (13%)

Query: 1   MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
           M+  +E+   + VP +   ++         V ++L      +  KD G+ LS+   K I 
Sbjct: 1   MYKILEIADVVKVPPEEFGKDLKET-----VKKILMEKYEGRLDKDVGFVLSIVDVKDIG 55

Query: 61  KEGPTVNGPGVVSFPVIFMCRTFLPVKGEILHGV------------CGPMKYALMSPRRM 108
            EG  V+G G    PV+F    ++P   E++ G              GP+   L+   ++
Sbjct: 56  -EGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVDVVEFGSFVRLGPLD-GLIHVSQI 113

Query: 109 P--TYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE 147
                 +   +++    +    +  G  V+  + A+    E
Sbjct: 114 MDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAE 154

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	166
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	100.0
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	100.0
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	100.0
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	100.0
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	100.0
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	100.0
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	100.0
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	100.0
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	99.97
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	94.68
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	93.05
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	93.01
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	92.58
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	92.0
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	91.61
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	90.87
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	90.7
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	90.46
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	89.8
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	88.62
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	88.27
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	88.25
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	88.01
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	87.73
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	87.35
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	86.64
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	85.14
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	82.23

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

Probab=100.00  E-value=2.7e-44  Score=290.13  Aligned_cols=160  Identities=11%  Similarity=0.178  Sum_probs=146.4

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||++++|+|+|+|||++|+++  +  .+++.++|+++|+|+ |.+++||||||+|+.++++|+ |.||||+++|+|+|+|
T Consensus         1 MF~l~~l~d~V~i~P~~f~~~--~--~~~i~~~L~~~~egk-v~~~~Gl~I~v~di~~i~~g~-I~~GdG~~~~~V~fk~   74 (203)
T 3ayh_B            1 MFLLSRFSDIISIHPSNFWKP--T--KEALAEEIHKKYANK-VIQNIGLAICVYDFLKIGEGI-IKYGDGSSYMNVVFRL   74 (203)
T ss_dssp             CEEEEEEEEEEEECGGGTTSC--H--HHHHHHHHHHHHTTE-EETTTEEEEEEEEEEEECCCE-ECTTTCCEEEEEEEEE
T ss_pred             CeEEEEEEEEEEECHHHcCCh--H--HHHHHHHhhhhhCCE-EeCCccEEEEEEEeeEecccE-EeCCCCCEEEEEEEEE
Confidence            999999999999999999987  4  999999999999999 999999999999999999999 9999999999999999


Q ss_pred             EEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEe--------cCCCCeecCCCEEEEEE
Q 042741           81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFS--------NDQQPKIGNGVVVQFLV  139 (166)
Q Consensus        81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~--------~~~~~~i~~g~~VR~RI  139 (166)
                      ++||||+||+++|+            +||+++++||++++++ +.||+++++|+|        ++++..++.||.|||||
T Consensus        75 ~~f~p~~GEv~~G~Vs~vt~~GifV~lg~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV  154 (203)
T 3ayh_B           75 IIFRPFRGEVMLGKIKSCSEEGIRVTISFFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQI  154 (203)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEECSSCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEE
T ss_pred             EEEccCCCCEEEEEEEEEeccEEEEEEeCceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEE
Confidence            99999999999999            8999999999999976 679999999999        55667899999999999


Q ss_pred             EEEEEcCC-Cc--------------CccccEEEEEEecCCCC
Q 042741          140 TAVRWSGE-GR--------------NLKREYLVFGRAKGESI  166 (166)
Q Consensus       140 ~~~~~~~~-~~--------------~~~~~~~~igti~~d~l  166 (166)
                      .++++.+. |.              +...+|+++|||++|||
T Consensus       155 ~~v~~~~~~p~~~~~~~~~~~~~~~~~~~~~~i~gs~~~~gL  196 (203)
T 3ayh_B          155 ESEDFVDISPKRNKNATAITGTEALESVSPYTLIASCSRDGL  196 (203)
T ss_dssp             EEEEECC--------------------CCSEEEEEEBCSTTC
T ss_pred             EEEEccccCCCCccccccccccccccCCCCeEEEEEecCCCC
Confidence            99999652 11              01236999999999998

>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=6.4e-43  Score=285.41  Aligned_cols=160  Identities=13%  Similarity=0.242  Sum_probs=146.1

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||++++|+|+|+|||++|+++  +  +++|.++|+++|+|+ |.+++||||||+|+.++++|+ |.||||+++|+|+|+|
T Consensus         1 MF~l~~l~d~V~I~P~~f~~~--l--~~~i~~~L~~kyegk-v~~~~Gl~I~v~di~~i~eG~-I~~GdG~~~~~V~fk~   74 (218)
T 2ckz_B            1 MFILSKIADLVRIPPDQFHRD--T--ISAITHQLNNKFANK-IIPNVGLCITIYDLLTVEEGQ-LKPGDGSSYINVTFRA   74 (218)
T ss_dssp             CEEEEEEEEEEEECGGGTTSC--H--HHHHHHHHHHHHTTE-EETTTEEEEEEEEEEEECCCE-ECSSSSCEEEEEEEEE
T ss_pred             CeEEEEEEEEEEECHHHcCch--H--HHHHHHHHHHHhcCc-CcCCccEEEEEEEeeeccCcE-EeCCCCCEEEEEEEEE
Confidence            999999999999999999988  4  999999999999999 999999999999999999999 9999999999999999


Q ss_pred             EEEeeecCcEEEEE------------e-CCcceEEecCCCCCC-ceeeCCCceeEe---cCCCCeecCCCEEEEEEEEEE
Q 042741           81 RTFLPVKGEILHGV------------C-GPMKYALMSPRRMPT-YRHVSGKKSFFS---NDQQPKIGNGVVVQFLVTAVR  143 (166)
Q Consensus        81 lvFrPf~gEVv~G~------------~-Gp~~~ifi~~~~m~~-~~~~~~~~~~~~---~~~~~~i~~g~~VR~RI~~~~  143 (166)
                      ++||||+||+++|+            + ||+++++|+++++++ +.||+++++|+|   ++++.+++.||.|||||++++
T Consensus        75 ~~f~p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~  154 (218)
T 2ckz_B           75 VVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREV  154 (218)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEE
T ss_pred             EEecCCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEE
Confidence            99999999999999            6 999999999999976 679999999999   566789999999999999999


Q ss_pred             EcCC-Cc-----C----------------------ccccEEEEEEecCCCC
Q 042741          144 WSGE-GR-----N----------------------LKREYLVFGRAKGESI  166 (166)
Q Consensus       144 ~~~~-~~-----~----------------------~~~~~~~igti~~d~l  166 (166)
                      +++. |.     +                      ..-+|.++|||++|.|
T Consensus       155 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~i~gs~~~~GL  205 (218)
T 2ckz_B          155 FVDVKPKSPKERELEERAQLENEIEGKNEETPQNEKPPAYALLGSCQTDGM  205 (218)
T ss_dssp             ECCCCC-------------------------------CSEEEEEECCSTTC
T ss_pred             cccCCCCCccccccccccccccccccccccccccCCCCCeEEEEEecCCCC
Confidence            9764 21     1                      1128999999999987

>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=100.00  E-value=1.2e-41  Score=268.79  Aligned_cols=156  Identities=18%  Similarity=0.214  Sum_probs=142.5

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||++++++|+|+|||++|+++  +  .+++.++|+++++|+ |.+++|+|||++|+.++++|+ |.+|||+++++|+|+|
T Consensus         1 Mf~l~~l~d~V~IpP~~f~~~--~--~~~i~~~L~~k~~~k-v~~~~G~~I~v~di~~~~~g~-I~~gdg~~~~~v~~~~   74 (180)
T 4ayb_E            1 MYKLIKARSIVRIPPNEFGKP--L--NEIALNELRQQYQEK-ILKDLGLVLAILNVKTSEEGM-LVFGDGATYHEVEFDM   74 (180)
T ss_dssp             CEEEEEEEEEEEECGGGTTSC--H--HHHHHHHHHHHTTTC-BCSSSCEEEEEEEEEEEEEEE-ECSSCSSEEEEEEEEE
T ss_pred             CeEEEEEEEEEEECHHHhCcc--H--HHHHHHHHHHHhcCe-EcCCCcEEEEeeeEeecCcee-EccCchHHHHHHhhhe
Confidence            999999999999999999988  4  999999999999999 999999999999999999999 9999999999999999


Q ss_pred             EEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741           81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus        81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ++||||+|||++|+            +||+++++|+++++++ +.|+++++.|+|++++..++.||.||+||++++.+..
T Consensus        75 iv~~p~~Gev~~G~V~~v~~~G~fv~l~~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~~  154 (180)
T 4ayb_E           75 ITYVPVVQEVVEGEVLQVDNYGVFVNLGPMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVT  154 (180)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC---
T ss_pred             eeeeccCCCEEEEEEeeeccceEEEEECCccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCCCC
Confidence            99999999999999            8999999999999987 5588888899999888999999999999999987655


Q ss_pred             CcCccccEEEEEEecCCCC
Q 042741          148 GRNLKREYLVFGRAKGESI  166 (166)
Q Consensus       148 ~~~~~~~~~~igti~~d~l  166 (166)
                          .+...+.+|||++||
T Consensus       155 ----~~~~rI~ls~k~~gL  169 (180)
T 4ayb_E          155 ----GRLPRIALTMRQPYL  169 (180)
T ss_dssp             --------CEEEECCSTTC
T ss_pred             ----cccCcEEEEcCCCCC
Confidence                333578889999997

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

Probab=100.00  E-value=1.5e-40  Score=261.83  Aligned_cols=153  Identities=20%  Similarity=0.346  Sum_probs=139.5

Q ss_pred             CeEEEEece-eeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEE--EecccCCCcceecCCCceEEEEE
Q 042741            1 MFFEVELLR-DIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVT--KSKSIDKEGPTVNGPGVVSFPVI   77 (166)
Q Consensus         1 MF~l~~l~d-~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~--di~~i~~G~~I~~gdG~~~~~V~   77 (166)
                      ||++.+++| +|++||++|+++  +  .+++..+|+++++|+ |.++.|+||||+  |++++++|+ |.||||+++|+|+
T Consensus         1 Mf~l~~l~d~~i~ipp~~~~~~--~--~~~i~~~l~~~~~g~-vi~~~G~~I~i~~idi~~i~~G~-I~~gdg~~~~~v~   74 (172)
T 3h0g_G            1 MPFFLKELSLTISLHPSYFGPR--M--QDYLKAKLLADVEGT-CSGQYGYIICVLDSNTIDIDKGR-VVPGQGFAEFEVK   74 (172)
T ss_dssp             --CEEEEEEEEEECCGGGCTTT--H--HHHHHHHHHHHHTTC-EETTTEEEEEECTTTSEEECCCE-ECTTTCCEEEEEE
T ss_pred             CeEEEEEecCeEEeCHHHhCcc--H--HHHHHHHHHHHhCCc-CcCCccEEEEEEeeeeeEeeCCE-EECCCCcEEEEEE
Confidence            999999999 999999999988  4  999999999999999 999999999999  999999999 9999999999999


Q ss_pred             EeEEEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEE
Q 042741           78 FMCRTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRW  144 (166)
Q Consensus        78 F~alvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~  144 (166)
                      |+|++|+||+||+++|+            +||++ .|+|.+.|++ +.||++++.|.|++++..++.||.||+||+++++
T Consensus        75 f~~ivf~p~~Gev~~G~V~~v~~fG~FV~l~~~~-glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~  153 (172)
T 3h0g_G           75 YRAVLWRPFRGEVVDAIVTTVNKMGFFANIGPLN-VFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRT  153 (172)
T ss_dssp             EEEEEECCCTTCEEECCCCEEETTEEECCBTTBC-CEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEE
T ss_pred             EEEeeeccCCCCEEEEEEEEEEcceEEEEeCCeE-EEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEEC
Confidence            99999999999999999            89999 6666666764 7799876667667777899999999999999999


Q ss_pred             cCCCcCccccEEEEEEecCCCC
Q 042741          145 SGEGRNLKREYLVFGRAKGESI  166 (166)
Q Consensus       145 ~~~~~~~~~~~~~igti~~d~l  166 (166)
                      +..    +  +++||||++|||
T Consensus       154 ~~~----~--~~~Igtm~~~~L  169 (172)
T 3h0g_G          154 DAT----E--IFAIATMKEDYL  169 (172)
T ss_dssp             SSS----C--EEEEEECCSTTC
T ss_pred             CCC----C--ceEEEEcCCCCC
Confidence            876    4  999999999998

>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=100.00  E-value=6.2e-34  Score=223.28  Aligned_cols=153  Identities=20%  Similarity=0.350  Sum_probs=139.9

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||++.+++++|++||++|+++  +  .+++..+|.++++|+ |.++.|+||+++|+.++++|. |.||||++++++.|+|
T Consensus         1 mfil~~m~~~I~~~p~~~~~~--~--~~~i~~~l~~~~~~~-vi~~~G~~I~~~di~~i~~g~-i~~~d~~~~~~~~~~~   74 (172)
T 2c35_B            1 MFYHISLEHEILLHPRYFGPN--L--LNTVKQKLFTEVEGT-CTGKYGFVIAVTTIDNIGAGV-IQPGRGFVLYPVKYKA   74 (172)
T ss_dssp             CEEEEEEEEEEEECGGGCCSC--H--HHHHHHHHHHHHTTC-EETTTEEEEEEEEEEEECCCB-CCTTCSSEEEEEEEEE
T ss_pred             CcEEEEEeEEEEECHHHhCCh--H--HHHHHHHHHHHHcCc-CcCCceEEEEEEEeeecCCeE-EeCCCCCEEEEEEEEE
Confidence            999999999999999999987  4  899999999999999 999999999999999999999 9999999999999999


Q ss_pred             EEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEec--CCCCeecCCCEEEEEEEEEEEc
Q 042741           81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSN--DQQPKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus        81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~--~~~~~i~~g~~VR~RI~~~~~~  145 (166)
                      ++|+|+.||+++|+            +||++ .++|.+.|++ +.|++.+++|.|.  +++..++.||.||+||.++.++
T Consensus        75 ~~~~~~~Gev~~G~V~~v~~fG~fV~l~~~~-glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~  153 (172)
T 2c35_B           75 IVFRPFKGEVVDAVVTQVNKVGLFTEIGPMS-CFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVD  153 (172)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEEETTEE-EEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEE
T ss_pred             EEeeCCCCCEEEEEEEEEeCCEEEEEECCEE-EEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcC
Confidence            99999999999999            89999 6666667765 6899988766554  5577899999999999999998


Q ss_pred             CCCcCccccEEEEEEecCCCC
Q 042741          146 GEGRNLKREYLVFGRAKGESI  166 (166)
Q Consensus       146 ~~~~~~~~~~~~igti~~d~l  166 (166)
                      ..    .  +.++|||++|||
T Consensus       154 ~~----~--~~~igsm~~~~L  168 (172)
T 2c35_B          154 KN----D--IFAIGSLMDDYL  168 (172)
T ss_dssp             TT----E--EEEEEECCSTTC
T ss_pred             CC----C--cEEEEEecCCCC
Confidence            65    3  899999999998

>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=100.00  E-value=2.3e-33  Score=222.33  Aligned_cols=157  Identities=20%  Similarity=0.308  Sum_probs=139.6

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||++++++++|+|||++|++.  +  .++|.+.|.++++|+ |.+++|+|||++|+.++++|+ |.+|||++++++.|++
T Consensus         1 Mf~~~~l~~~i~I~P~~~~~~--i--~~~I~~~L~~~~~gk-~~~~~G~~i~~idi~~~g~~~-I~~~d~~~~~~~~~~~   74 (187)
T 1go3_E            1 MYKILEIADVVKVPPEEFGKD--L--KETVKKILMEKYEGR-LDKDVGFVLSIVDVKDIGEGK-VVHGDGSAYHPVVFET   74 (187)
T ss_dssp             CEEEEEEEEEEEECGGGTTSC--H--HHHHHHHHHHHHTTC-EETTTEEEEEEEEEEEECCCB-CCTTCCSEEEEEEEEE
T ss_pred             CcEEEEEEEEEEECHHHhCcc--H--HHHHHHHHHHHhCCe-EcCCccEEEEEEEEeeccCCE-EeCCCccEEEEEEEEE
Confidence            999999999999999999987  4  788887789999999 999999999999999999999 9999999999999999


Q ss_pred             EEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCC
Q 042741           81 RTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus        81 lvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ++|+|+.||+++|+            +||+++++|+++++++ +.|+++++.|.|++.+..++.||.||+||.++..+..
T Consensus        75 i~~~~~~Gev~~G~V~~v~~~G~fV~l~~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  154 (187)
T 1go3_E           75 LVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAE  154 (187)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC-
T ss_pred             EEEccCCCCEEEEEEEEEeCcEEEEEEcCccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccC
Confidence            99999999999999            8999999999999876 5599999999998777899999999999999998643


Q ss_pred             CcCccccEEEEEEecCCCC
Q 042741          148 GRNLKREYLVFGRAKGESI  166 (166)
Q Consensus       148 ~~~~~~~~~~igti~~d~l  166 (166)
                      .   .+..++..||++++|
T Consensus       155 ~---p~~~~I~lS~k~~~L  170 (187)
T 1go3_E          155 R---KRGSKIALTMRQPYL  170 (187)
T ss_dssp             -------CEEEEECCSTTC
T ss_pred             C---CCccEEEEEEcCCCC
Confidence            0   012578889999987

>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=100.00  E-value=8.5e-34  Score=222.68  Aligned_cols=153  Identities=20%  Similarity=0.311  Sum_probs=123.8

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEec--ccCCCcceecCCCceEEEEEE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSK--SIDKEGPTVNGPGVVSFPVIF   78 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~--~i~~G~~I~~gdG~~~~~V~F   78 (166)
                      ||+|.+++++|++||++|+++  +  .+++..+|..+++|+ |.++.|+||+++||.  ++++|+ |.+|||++++++.|
T Consensus         1 mfil~~m~~~i~~pp~~l~~~--~--p~~i~~~i~~~~i~~-vig~~G~~I~~~di~~~di~~g~-i~~~d~~~~~~~~~   74 (171)
T 1y14_B            1 MFFIKDLSLNITLHPSFFGPR--M--KQYLKTKLLEEVEGS-CTGKFGYILCVLDYDNIDIQRGR-ILPTDGSAEFNVKY   74 (171)
T ss_dssp             CEEEEEEEEECCCCTTSCSTT--H--HHHHHHHHHHHHTTE-EETTTEEEEEECCGGGCBCC-------------CEEEE
T ss_pred             CeEEEEEEEEEEECHHHhCCh--H--HHHHHHHHHHHHcCc-CcCCceEEEEEEEecccccCccE-EeCCCCCEEEEEEE
Confidence            999999999999999999987  4  899999999999999 999999999999999  999999 99999999999999


Q ss_pred             eEEEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEc
Q 042741           79 MCRTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus        79 ~alvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~  145 (166)
                      ++++|+|+.||+++|+            +|| .+.|+|.+.|++ +.|++.+++|.|...+..++.||.||+||.++.++
T Consensus        75 ~~~~~~~~~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~  153 (171)
T 1y14_B           75 RAVVFKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQ  153 (171)
T ss_dssp             EEEEECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEE
T ss_pred             EEEEccCCCCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEEcC
Confidence            9999999999999999            899 557777777765 68999999887753336799999999999999998


Q ss_pred             CCCcCccccEEEEEEecCCCC
Q 042741          146 GEGRNLKREYLVFGRAKGESI  166 (166)
Q Consensus       146 ~~~~~~~~~~~~igti~~d~l  166 (166)
                      ..    +  +.++|||++|||
T Consensus       154 ~~----~--~~~igsm~~~~L  168 (171)
T 1y14_B          154 VS----S--IHAIGSIKEDYL  168 (171)
T ss_dssp             TT----E--EEEEEECCSTTC
T ss_pred             CC----C--cEEEEEcCCCCC
Confidence            65    4  999999999998

>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=100.00  E-value=3.6e-33  Score=227.41  Aligned_cols=153  Identities=20%  Similarity=0.311  Sum_probs=140.1

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEec--ccCCCcceecCCCceEEEEEE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSK--SIDKEGPTVNGPGVVSFPVIF   78 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~--~i~~G~~I~~gdG~~~~~V~F   78 (166)
                      ||+|.+|+++|++||++|+++  +  .+++..+|..+++|+ |.++.|+|||++||.  ++++|+ |.||||++++++.|
T Consensus         1 MfiL~~m~~~I~ipp~~~~~~--~--p~~i~~~I~~~~ig~-vIg~~G~vI~~~dI~~~di~dG~-I~~gdg~~~~~v~~   74 (215)
T 2b8k_G            1 MFFIKDLSLNITLHPSFFGPR--M--KQYLKTKLLEEVEGS-CTGKFGYILCVLDYDNIDIQRGR-ILPTDGSAEFNVKY   74 (215)
T ss_dssp             CEEEECCEEEEEECGGGCSSS--H--HHHHHHHHHHSSTTC-EETTTEEEEEECCSTTCBCCCEE-ECSSSCCEEEEEEC
T ss_pred             CEEeHHHHhhhhcCHHHHChh--H--hHHHHhcCCHHHCCe-EcCCCCEEEEEEEeeecccccce-EeCCCHHHHHHHHh
Confidence            999999999999999999987  4  899999999999999 999999999999999  999999 99999999999999


Q ss_pred             eEEEEeeecCcEEEEE------------eCCcceEEecCCCCCC-ceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEc
Q 042741           79 MCRTFLPVKGEILHGV------------CGPMKYALMSPRRMPT-YRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus        79 ~alvFrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~-~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~  145 (166)
                      ++++|+|+.||+++|+            +|| .+.|+|.+.|++ +.|++.+++|.|...+..++.||.||+||.++.++
T Consensus        75 ~~i~~~p~vGev~~G~V~~vt~fG~FVelg~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~  153 (215)
T 2b8k_G           75 RAVVFKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQ  153 (215)
T ss_dssp             CEEEECCCTTEEEEEEEEEEETTEEEEECTT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEE
T ss_pred             hhheeccCCCCEEEEEEEEEecceEEEEecC-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcC
Confidence            9999999999999999            899 457777667765 68999999887763337799999999999999998


Q ss_pred             CCCcCccccEEEEEEecCCCC
Q 042741          146 GEGRNLKREYLVFGRAKGESI  166 (166)
Q Consensus       146 ~~~~~~~~~~~~igti~~d~l  166 (166)
                      ..    +  +.++|||++|||
T Consensus       154 ~~----~--i~~IgSmk~~~L  168 (215)
T 2b8k_G          154 VS----S--IHAIGSIKEDYL  168 (215)
T ss_dssp             TT----E--EEEEEECCSTTC
T ss_pred             CC----c--cEEEEEcCCCCC
Confidence            65    4  999999999997

>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=99.97  E-value=2.3e-30  Score=210.47  Aligned_cols=145  Identities=13%  Similarity=0.136  Sum_probs=115.2

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCe-eEEEEEEEecccCC------------Ccceec
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDH-GYFLSVTKSKSIDK------------EGPTVN   67 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~-GliI~V~di~~i~~------------G~~I~~   67 (166)
                      ||++++++++|+|||++|+++     .+.+.++.++.+.++ .+.++ |+|+|++|+..+++            |+ |.+
T Consensus        37 mF~l~~~~~~V~L~P~~f~~~-----~~~i~~~~L~~ll~k-y~~~~~Gv~la~~di~~~~~~~~~~d~~~~~~g~-I~~  109 (214)
T 2rf4_A           37 CIVRVPIALYVSLAPMYLENP-----LQGVMKQHLNPLVMK-YNNKVGGVVLGYEGLKILDADPLSKEDTSEKLIK-ITP  109 (214)
T ss_dssp             CEEEEEEEEEEECCGGGTTCH-----HHHHHHHHHHHHBTS-EETTTTEEEEEEEEEETTSCCC----------------
T ss_pred             cEEEEEEEEEEEECHHHhCCh-----hHHHHHHHHHHHHhc-ccCCCCEEEEEEECeEeccCCCcCccccccceeE-EeC
Confidence            999999999999999999987     466666655567888 66665 89999999987775            79 999


Q ss_pred             CCCceEEEEEEeEEEEeeecCcEEEEE-------------eCCcceEEecCCCCC-CceeeCCC-----ceeEecCCCCe
Q 042741           68 GPGVVSFPVIFMCRTFLPVKGEILHGV-------------CGPMKYALMSPRRMP-TYRHVSGK-----KSFFSNDQQPK  128 (166)
Q Consensus        68 gdG~~~~~V~F~alvFrPf~gEVv~G~-------------~Gp~~~ifi~~~~m~-~~~~~~~~-----~~~~~~~~~~~  128 (166)
                      |+|.++++|+|+|+|||||+||||+|+             +|||+ +|||++.|| ++.|++++     +.|.|.++. .
T Consensus       110 ~~g~~~~~V~~~~iVFrPf~GevL~G~V~~~s~~~Ig~~~~G~Fn-~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~-~  187 (214)
T 2rf4_A          110 DTPFGFTWCHVNLYVWQPQVGDVLEGYIFIQSASHIGLLIHDAFN-ASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGE-P  187 (214)
T ss_dssp             --CCCEEEEEEEEEEECCCTTCEEEEEECCCCSSCEEEEETTTEE-EEECSTTSCSSCBCCCCSCC-CCCCCBCSSCC-B
T ss_pred             CCceEEEEEEEEEEEEecCCCCEEEEEEEEECCCcEEEEEeCCEE-EEEcHHHCCCcccccccccccCCCceEcCCCC-C
Confidence            999999999999999999999999999             59999 899999996 58898765     456555432 3


Q ss_pred             ecCCCEEEEEEEEEEEcCCCcCccccEEEEEEec
Q 042741          129 IGNGVVVQFLVTAVRWSGEGRNLKREYLVFGRAK  162 (166)
Q Consensus       129 i~~g~~VR~RI~~~~~~~~~~~~~~~~~~igti~  162 (166)
                        .|+.|||||.+++.+..    -  ..+-|||-
T Consensus       188 --ig~~IRFrV~~~~~~~~----~--lsI~Gsll  213 (214)
T 2rf4_A          188 --IDGKLRFTVRNVHTTGR----V--VSVDGTLI  213 (214)
T ss_dssp             --CCSEEEEEEEEEECCSS----S--CEEEEECC
T ss_pred             --CCCEEEEEEEEEEecCC----E--EEEEEEec
Confidence              49999999999998654    2  67888874

>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=94.68  E-value=0.068  Score=41.53  Aligned_cols=52  Identities=17%  Similarity=0.286  Sum_probs=36.5

Q ss_pred             EeeecCcEEEEE------------eCC--cceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEc
Q 042741           83 FLPVKGEILHGV------------CGP--MKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus        83 FrPf~gEVv~G~------------~Gp--~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~  145 (166)
                      |.|-.|++|.|+            +|+  ++++++.+ ..+     ...     ++....+++||.|++||.+++-+
T Consensus         3 Y~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s-~~~-----g~~-----k~~r~~l~~GDlV~ArV~~~~~~   68 (175)
T 2ja9_A            3 YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYM-AFP-----NAS-----KKNRPTLQVGDLVYARVCTAEKE   68 (175)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETT-SST-----TCC-----SSSCCCCCTTCEEEEEEEECCTT
T ss_pred             ccCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHH-HCC-----chh-----hhhhccCCCCCEEEEEEEEecCC
Confidence            789999999999            666  66444433 222     111     33456799999999999988754

>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=93.05  E-value=0.03  Score=40.67  Aligned_cols=59  Identities=10%  Similarity=-0.031  Sum_probs=38.4

Q ss_pred             EEeEEEEeeecCcEEEEE---eCCc-----------ceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEE
Q 042741           77 IFMCRTFLPVKGEILHGV---CGPM-----------KYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAV  142 (166)
Q Consensus        77 ~F~alvFrPf~gEVv~G~---~Gp~-----------~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~  142 (166)
                      .|+.+.+.|..|+++.|+   +-++           +++.|.+++.+++          ..+....++.||.|++||+.+
T Consensus        12 ~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~----------~~~~~~~~~~Gd~V~VkV~~v   81 (119)
T 2cqo_A           12 RPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCR----------VDKPSEIVDVGDKVWVKLIGR   81 (119)
T ss_dssp             CCCCSCCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSC----------CSCHHHHCCTTCEEEEEEEEE
T ss_pred             chhhhhcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCccc----------ccChhhcCCCCCEEEEEEEEE
Confidence            466778899999999999   3333           3333333322221          112234689999999999998


Q ss_pred             EEc
Q 042741          143 RWS  145 (166)
Q Consensus       143 ~~~  145 (166)
                      ...
T Consensus        82 d~~   84 (119)
T 2cqo_A           82 EMK   84 (119)
T ss_dssp             EEC
T ss_pred             ecc
Confidence            764

>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=93.01  E-value=0.14  Score=41.18  Aligned_cols=52  Identities=13%  Similarity=0.194  Sum_probs=35.7

Q ss_pred             EeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEE
Q 042741           83 FLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVR  143 (166)
Q Consensus        83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~  143 (166)
                      |.|-.|++|.|+            +| |++++.+.++....        .+ ..+-...+++||.|++||..+.
T Consensus        53 y~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~--------~~-~~~~~~~l~~GD~V~arVi~v~  117 (229)
T 2ba0_A           53 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEM--------KP-NKKPNEVLDIGDAIIAKVLNID  117 (229)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTC--------CT-TSCGGGTCCTTCEEEEEEEEEC
T ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHcccc--------cc-ccchhcccCCCCEEEEEEEEEC
Confidence            789999999999            44 66655555444410        00 1223356999999999999885

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

Probab=92.58  E-value=0.44  Score=31.59  Aligned_cols=21  Identities=14%  Similarity=0.075  Sum_probs=17.2

Q ss_pred             CeecCCCEEEEEEEEEEEcCC
Q 042741          127 PKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus       127 ~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ..++.||.|++||.++..+..
T Consensus        44 ~~~~~Gd~V~v~V~~vd~~~~   64 (80)
T 2k52_A           44 ENLNVGDEIIVQAIDVRPEKR   64 (80)
T ss_dssp             GGCCTTCEEEEEEEEEETTTT
T ss_pred             eeeCCCCEEEEEEEEEECCCC
Confidence            468999999999999876533

>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=92.00  E-value=0.15  Score=35.80  Aligned_cols=53  Identities=15%  Similarity=0.093  Sum_probs=34.1

Q ss_pred             EEeeecCcEEEEE------------eC----CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEE
Q 042741           82 TFLPVKGEILHGV------------CG----PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVR  143 (166)
Q Consensus        82 vFrPf~gEVv~G~------------~G----p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~  143 (166)
                      .+.|..|++++|+            ++    ..+++.|.+++.++..         ..+....++.||.|++||..+.
T Consensus         7 ~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~---------~~~~~~~~~~Gd~V~VkV~~vd   75 (103)
T 2eqs_A            7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGR---------VANVADVVSKGQRVKVKVLSFT   75 (103)
T ss_dssp             CSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSC---------CCCHHHHCCTTCEEEEEEEEEE
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcc---------cCCcccEeCCCCEEEEEEEEEE
Confidence            3567889999999            33    3454444444433321         1222346899999999999885

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

Probab=91.61  E-value=0.24  Score=35.34  Aligned_cols=62  Identities=15%  Similarity=0.102  Sum_probs=37.4

Q ss_pred             EEEeEEEEeeecCcEEEEE------------eCC-cceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEE
Q 042741           76 VIFMCRTFLPVKGEILHGV------------CGP-MKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAV  142 (166)
Q Consensus        76 V~F~alvFrPf~gEVv~G~------------~Gp-~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~  142 (166)
                      ..|..+..+|..|++++|+            +++ .+ .|++.+.|..   +  .   ...+....++.||.|++||.++
T Consensus        19 ~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~-Glvhisel~~---~--~---~~~~~~~~~~vGd~V~vkV~~v   89 (115)
T 2khi_A           19 SHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVE-GLVHVSEMDW---T--N---KNIHPSKVVNVGDVVEVMVLDI   89 (115)
T ss_dssp             --CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCE-EEEETTSSSC---S--S---TTCSSTTTCCTTCEEEEEEEEE
T ss_pred             CCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCE-EEEEHHHCCc---c--c---cccCcccEECCCCEEEEEEEEE
Confidence            4456666788999999999            322 33 2333222211   0  0   1123345799999999999998


Q ss_pred             EEcC
Q 042741          143 RWSG  146 (166)
Q Consensus       143 ~~~~  146 (166)
                      ....
T Consensus        90 d~~~   93 (115)
T 2khi_A           90 DEER   93 (115)
T ss_dssp             ETTT
T ss_pred             ECCC
Confidence            7643

>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=90.87  E-value=0.25  Score=40.33  Aligned_cols=55  Identities=18%  Similarity=0.198  Sum_probs=36.3

Q ss_pred             EEeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEE
Q 042741           82 TFLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVR  143 (166)
Q Consensus        82 vFrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~  143 (166)
                      .|.|-.|++|.|+            +| |++++++.++...... +.+      .+-...+++||.|++||..+.
T Consensus        69 ~y~p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei~~~~~-~~~------~~~~~~l~vGD~V~arVi~v~  136 (251)
T 2je6_I           69 FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSI-NVG------EDLRRYLDVGDYVIARIENFD  136 (251)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCC-CTT------CCCSSSCCTTCEEEEEEEEEE
T ss_pred             ccCCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCcc-ccc------cchhhcCCCCCEEEEEEEEEC
Confidence            3789999999999            44 5665555554443100 000      122346999999999999986

>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=90.70  E-value=0.14  Score=36.74  Aligned_cols=52  Identities=17%  Similarity=0.286  Sum_probs=32.1

Q ss_pred             eecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEe-cCCCCeecCCCEEEEEEEEEEEc
Q 042741           85 PVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFS-NDQQPKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus        85 Pf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~-~~~~~~i~~g~~VR~RI~~~~~~  145 (166)
                      +..|++++|+            +| +-.+.+|+++.+++         |+. ++.+..++.||.|++||..+..+
T Consensus        19 l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~---------~~~~~~~~~~~~~Gd~V~vkV~~vd~~   84 (119)
T 1wi5_A           19 LKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQE---------YIRQKNKGAKLKVGQYLNCIVEKVKGN   84 (119)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHH---------HHHHHSSSCCCCTTCEEEEEEEECCTT
T ss_pred             CCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccc---------cccccCccCEeCCCCEEEEEEEEEeCC
Confidence            5678999998            33 22334555444321         211 12245799999999999987543

>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=90.46  E-value=0.13  Score=41.40  Aligned_cols=55  Identities=18%  Similarity=0.265  Sum_probs=36.2

Q ss_pred             EeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEE
Q 042741           83 FLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVR  143 (166)
Q Consensus        83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~  143 (166)
                      |.|-.|++|.|+            +| +++++.+.++.... ..+    ++ ..+-...+++||.|++||+.+.
T Consensus        62 y~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~-~~~----~~-~~~~~~~l~~GD~V~a~Vi~v~  129 (235)
T 2z0s_A           62 YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGR-PFN----PA-VDDMQSLLKVGDYIKAKVVAFD  129 (235)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTS-CCC----TT-TTCCTTSSCTTCEEEEEEEEEC
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCC-ccc----cc-hhhHhhcCCCCCEEEEEEEEEC
Confidence            689999999999            44 56655555444431 000    11 1222356999999999999986

>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=89.80  E-value=0.58  Score=37.02  Aligned_cols=60  Identities=13%  Similarity=0.051  Sum_probs=32.5

Q ss_pred             EeeecCcEEEEE---eCCcceEEecCC-----CC----CCceeeCCCceeEec--CCCCeecCCCEEEEEEEEEE
Q 042741           83 FLPVKGEILHGV---CGPMKYALMSPR-----RM----PTYRHVSGKKSFFSN--DQQPKIGNGVVVQFLVTAVR  143 (166)
Q Consensus        83 FrPf~gEVv~G~---~Gp~~~ifi~~~-----~m----~~~~~~~~~~~~~~~--~~~~~i~~g~~VR~RI~~~~  143 (166)
                      |.|-.|+||.|+   +.++. .|+--.     .+    +....-.+-.....+  +-...+++||.|++||+++.
T Consensus        77 y~p~vGDvV~G~V~~v~~~~-a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~  150 (209)
T 2nn6_I           77 LLPDVGAIVTCKVSSINSRF-AKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLG  150 (209)
T ss_dssp             CCCCTTCEEEEEEEEECSSE-EEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEE
T ss_pred             CCCCCCCEEEEEEEEEECce-EEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEe
Confidence            689999999999   44544 443311     01    111110000000111  11235899999999999984

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

Probab=88.62  E-value=1.2  Score=32.32  Aligned_cols=51  Identities=18%  Similarity=0.070  Sum_probs=33.2

Q ss_pred             eeecCcEEEEE------------e-CCcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEE
Q 042741           84 LPVKGEILHGV------------C-GPMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRW  144 (166)
Q Consensus        84 rPf~gEVv~G~------------~-Gp~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~  144 (166)
                      .+-.|+++.|+            + +..+++.|.+++.+++.          .+-...++.||.|++||..+.-
T Consensus         4 ~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~----------~~~~~~~~vGd~V~vkV~~vd~   67 (130)
T 2k4k_A            4 KFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFV----------KDINEHLSVGDEVQVKVLAVDE   67 (130)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCC----------SCGGGTCCTTCEEEEEEEEEET
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccc----------cCccccCCCCCEEEEEEEEEeC
Confidence            35678888888            2 34555555554444322          1223569999999999999875

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

Probab=88.27  E-value=0.091  Score=49.06  Aligned_cols=88  Identities=11%  Similarity=-0.036  Sum_probs=0.0

Q ss_pred             ecCCeeEEEEEEEecccCCCcceecCCCceEEEE--EEeEEEEeeecCcEEEEE------------eCC-cceEEecCCC
Q 042741           43 ACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPV--IFMCRTFLPVKGEILHGV------------CGP-MKYALMSPRR  107 (166)
Q Consensus        43 ~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V--~F~alvFrPf~gEVv~G~------------~Gp-~~~ifi~~~~  107 (166)
                      +..+.|..   +||.+-+.-. |...|+....+.  .++.++..|..|++++|+            ++| .+++.|.+++
T Consensus       585 I~~~~G~~---IdI~~dg~v~-I~~~~~~~~~~a~~~i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel  660 (723)
T 3cdi_A          585 LTEETGTT---IEIEDDGTVK-IAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQI  660 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             eehhhCce---EEecCCccEE-EecCCHHHHHHHHHHHHHHhhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHc
Confidence            44566744   3666655555 555666665444  578889999999999999            222 4444444444


Q ss_pred             CCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEE
Q 042741          108 MPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRW  144 (166)
Q Consensus       108 m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~  144 (166)
                      ..++          .++.+..++.||.|++||.++.-
T Consensus       661 ~~~~----------v~~~~~~~~vGd~V~VkVi~vd~  687 (723)
T 3cdi_A          661 ADKR----------VEKVTDYLQMGQEVPVKVLEVDR  687 (723)
T ss_dssp             -------------------------------------
T ss_pred             CCcc----------ccCcccccCCCCEEEEEEEEECC
Confidence            3221          12334569999999999999864

>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=88.25  E-value=1.8  Score=33.24  Aligned_cols=52  Identities=13%  Similarity=-0.024  Sum_probs=31.4

Q ss_pred             eecCcEEEEE------------e---CCcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcC
Q 042741           85 PVKGEILHGV------------C---GPMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSG  146 (166)
Q Consensus        85 Pf~gEVv~G~------------~---Gp~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~  146 (166)
                      |-.|+++.|+            +   +..+++.|.+++..++          ..+-...++.||.|++||..+.-..
T Consensus        13 p~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~----------v~~~~~~~~vGd~V~vkVl~vd~~~   79 (175)
T 2a19_A           13 PEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRR----------IRSIQKLIRVGKNDVAVVLRVDKEK   79 (175)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC------------------CCCCCCCTTSEEEEEEEEEETTT
T ss_pred             CCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcc----------cCCHHHcCCCCCEEEEEEEEEECCC
Confidence            5579999999            4   3455444444433221          1233457999999999999986543

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

Probab=88.01  E-value=0.027  Score=52.69  Aligned_cols=80  Identities=10%  Similarity=-0.034  Sum_probs=8.1

Q ss_pred             EEecccCCCcceecCCCceEEE--EEEeEEEEeeecCcEEEEE------------e-CCcceEEecCCCCCCceeeCCCc
Q 042741           54 TKSKSIDKEGPTVNGPGVVSFP--VIFMCRTFLPVKGEILHGV------------C-GPMKYALMSPRRMPTYRHVSGKK  118 (166)
Q Consensus        54 ~di~~i~~G~~I~~gdG~~~~~--V~F~alvFrPf~gEVv~G~------------~-Gp~~~ifi~~~~m~~~~~~~~~~  118 (166)
                      +||.+-|.-+ |...|+.+...  ..++.++..|..|++++|+            + +..+++.|.+++..++       
T Consensus       603 idi~ddG~v~-I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~~r-------  674 (726)
T 4aid_A          603 VDINDDGVVK-VSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNER-------  674 (726)
T ss_dssp             ------------CCSCHHHHHHHHHC------------------------------------------------------
T ss_pred             eeEECCceEE-EEeCCHHHHHHHHHHHHHHhhhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCccc-------
Confidence            3566666666 77777776655  5688999999999999999            2 2245555555444321       


Q ss_pred             eeEecCCCCeecCCCEEEEEEEEEEE
Q 042741          119 SFFSNDQQPKIGNGVVVQFLVTAVRW  144 (166)
Q Consensus       119 ~~~~~~~~~~i~~g~~VR~RI~~~~~  144 (166)
                         .++-+..++.||.|++||.++.-
T Consensus       675 ---v~~~~d~~kvGD~V~VkVi~iD~  697 (726)
T 4aid_A          675 ---VAKPSDVLKEGQMVKVKLLGFDD  697 (726)
T ss_dssp             --------------------------
T ss_pred             ---ccCccccCCCCCEEEEEEEEECC
Confidence               12334569999999999999864

>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=87.73  E-value=1.3  Score=34.26  Aligned_cols=51  Identities=10%  Similarity=-0.023  Sum_probs=29.1

Q ss_pred             eecCcEEEEE------------e---CCcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEc
Q 042741           85 PVKGEILHGV------------C---GPMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus        85 Pf~gEVv~G~------------~---Gp~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~  145 (166)
                      |-.|++++|+            +   +..+++.|.+++..++          ..+-...++.||.|+++|..+.-.
T Consensus        13 p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~----------v~~~~~~~~vGd~V~VkVl~vD~~   78 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRR----------IRSINKLIRIGRNECVVVIRVDKE   78 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC----------------------CTTCEEEEEEEEEETT
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcc----------cCCHHHhcCCCCEEEEEEEEEECC
Confidence            6789999999            3   3455444444433221          122345799999999999998653

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

Probab=87.35  E-value=1.9  Score=30.13  Aligned_cols=62  Identities=21%  Similarity=0.147  Sum_probs=33.3

Q ss_pred             eeecCcEEEEE---eCCcceEEecCC-CCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcC
Q 042741           84 LPVKGEILHGV---CGPMKYALMSPR-RMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSG  146 (166)
Q Consensus        84 rPf~gEVv~G~---~Gp~~~ifi~~~-~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~  146 (166)
                      .+..|+++.|+   +-++- +|+--. ..+....-.+-...+..+....++.||.|++||..+..+.
T Consensus        28 ~~~~G~iv~G~V~~v~~~G-~fV~l~~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~~~   93 (109)
T 2khj_A           28 LNKKGAIVTGKVTAVDAKG-ATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDRKN   93 (109)
T ss_dssp             TCCSSSEEEEEEEEECSSC-EEEECSTTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEETTT
T ss_pred             cCCCCCEEEEEEEEEECCe-EEEEECCCCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEECCC
Confidence            45679999999   44443 554321 1111111100000011223346999999999999987643

>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=86.64  E-value=0.26  Score=41.48  Aligned_cols=58  Identities=16%  Similarity=0.165  Sum_probs=34.9

Q ss_pred             EeeecCcEEEEE------------eC-CcceEEecCCCC-CCceeeCCCceeEec--CCCCeecCCCEEEEEEEEEE
Q 042741           83 FLPVKGEILHGV------------CG-PMKYALMSPRRM-PTYRHVSGKKSFFSN--DQQPKIGNGVVVQFLVTAVR  143 (166)
Q Consensus        83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m-~~~~~~~~~~~~~~~--~~~~~i~~g~~VR~RI~~~~  143 (166)
                      |.|-.|++|.|+            +| |.++..+.++.. +.....   +.-..+  +-...+++||.||+||.++.
T Consensus        91 Y~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR---~~~~~D~~~m~~~l~vGDlV~ArVisv~  164 (308)
T 2nn6_H           91 YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELR---RRSAEDELAMRGFLQEGDLISAEVQAVF  164 (308)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC----------------CHHHHHHSCSSCEECCEEEEEE
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhccccceee---cccchhhhhhhccCCCCCEEEEEEEEcC
Confidence            789999999999            55 667555545543 221110   000000  11246999999999999987

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

Probab=85.14  E-value=0.93  Score=34.83  Aligned_cols=15  Identities=13%  Similarity=0.120  Sum_probs=13.6

Q ss_pred             CeecCCCEEEEEEEE
Q 042741          127 PKIGNGVVVQFLVTA  141 (166)
Q Consensus       127 ~~i~~g~~VR~RI~~  141 (166)
                      ..++.||.|++||++
T Consensus       110 ~~~~~GD~V~akVi~  124 (179)
T 3m7n_A          110 EAVGYLDILKARVIG  124 (179)
T ss_dssp             GTCCTTCEEEEEEEE
T ss_pred             hcCCCCCEEEEEEEC
Confidence            468999999999997

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=82.23  E-value=0.038  Score=51.86  Aligned_cols=87  Identities=14%  Similarity=0.019  Sum_probs=28.7

Q ss_pred             cCCeeEEEEEEEecccCCCcceecCCCceEEEE--EEeEEE--EeeecCcEEEEE---eCC----------cceEEecCC
Q 042741           44 CKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPV--IFMCRT--FLPVKGEILHGV---CGP----------MKYALMSPR  106 (166)
Q Consensus        44 ~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V--~F~alv--FrPf~gEVv~G~---~Gp----------~~~ifi~~~  106 (166)
                      ..+.|..|   ||.+-+.-. |...++......  ..+.++  ..|..|++++|+   +-+          .+++.|.++
T Consensus       624 ~~~~G~~I---dI~~dG~v~-Is~~~~~~~~~a~~~i~~i~~p~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSe  699 (757)
T 1e3p_A          624 QEDTGAEI---TIEDDGTIY-IGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQ  699 (757)
T ss_dssp             CCCCCSCC-----------C-CCBSSHHHHCC---------------------CBEEECC-CSCEECCC---CCCCC---
T ss_pred             hHhhCCEE---EecCCceEE-EecCCHHHHHHHHHHHHHhcchhhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHH
Confidence            45778765   454433333 434454443333  456778  899999999999   223          333444444


Q ss_pred             C----CCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEE
Q 042741          107 R----MPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRW  144 (166)
Q Consensus       107 ~----m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~  144 (166)
                      +    ..+         + .++-...++.||.|++||.++.-
T Consensus       700 l~~~~s~~---------r-v~~~~~~~~vGd~V~VkVi~vd~  731 (757)
T 1e3p_A          700 IRKLAGGK---------R-VENVEDVLGVGQKVQVEIAEIDS  731 (757)
T ss_dssp             --------------------------CCSSCBCCCCCCCCCS
T ss_pred             hccccCCC---------c-ccCcccccCCCCEEEEEEEEECC
Confidence            3    111         1 12334568999999999988764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	166
d2c35b2	77	d.230.1.1 (B:1-77) N-terminal, heterodimerisation	7e-05
d1go3e2	78	d.230.1.1 (E:1-78) N-terminal, heterodimerisation	2e-04

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

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]

 Score = 37.3 bits (87), Expect = 7e-05
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 1  MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
          MF+ + L  +I +  +    N        TV + L   +       +G+ ++VT   +I 
Sbjct: 1  MFYHISLEHEILLHPRYFGPN-----LLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIG 55

Query: 61 KEGPTVNGPGVVSFPVIFMCRTF 83
            G    G G V +PV +    F
Sbjct: 56 -AGVIQPGRGFVLYPVKYKAIVF 77

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

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]

 Score = 36.5 bits (85), Expect = 2e-04
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 6/84 (7%)

Query: 1  MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSID 60
          M+  +E+   + VP +   +       + TV ++L      +  KD G+ LS+   K I 
Sbjct: 1  MYKILEIADVVKVPPEEFGK-----DLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIG 55

Query: 61 KEGPTVNGPGVVSFPVIFMCRTFL 84
           EG  V+G G    PV+F    ++
Sbjct: 56 -EGKVVHGDGSAYHPVVFETLVYI 78

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	166
d1go3e2	78	N-terminal, heterodimerisation domain of RBP7 (Rpo	99.95
d1y14b2	80	N-terminal, heterodimerisation domain of RBP7 (Rpo	99.94
d2c35b2	77	N-terminal, heterodimerisation domain of RBP7 (Rpo	99.94
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	99.82
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	99.78
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	98.63
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	95.61
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	95.34
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	94.95
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	93.81
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	90.25
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	86.46
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	86.27
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	84.98
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	83.42
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	83.21
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	81.17

>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=99.95  E-value=8.8e-29  Score=170.80  Aligned_cols=77  Identities=25%  Similarity=0.427  Sum_probs=75.6

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||++++++|+|+|||++||++  +  ++++.++|+++|+|+ |.+++||||||+|+.++++|+ |.||||++||+|+|||
T Consensus         1 MF~~~~l~d~v~i~P~~~g~~--~--~~~i~~~L~~~~egk-v~~~~G~ii~v~di~~i~eG~-I~~gdG~~~~~V~F~~   74 (78)
T d1go3e2           1 MYKILEIADVVKVPPEEFGKD--L--KETVKKILMEKYEGR-LDKDVGFVLSIVDVKDIGEGK-VVHGDGSAYHPVVFET   74 (78)
T ss_dssp             CEEEEEEEEEEEECGGGTTSC--H--HHHHHHHHHHHHTTC-EETTTEEEEEEEEEEEECCCB-CCTTCCSEEEEEEEEE
T ss_pred             CcEEEEEEEEEEECHHHhCcC--H--HHHHHHHHHHHhCCc-CcCCcCEEEEEEEeeEecCCE-EEcCCCCEEEEEEEEE
Confidence            999999999999999999988  4  999999999999999 999999999999999999999 9999999999999999


Q ss_pred             EEE
Q 042741           81 RTF   83 (166)
Q Consensus        81 lvF   83 (166)
                      +||
T Consensus        75 lvF   77 (78)
T d1go3e2          75 LVY   77 (78)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            999

>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=99.94  E-value=3.4e-28  Score=168.51  Aligned_cols=78  Identities=23%  Similarity=0.336  Sum_probs=62.9

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEe--cccCCCcceecCCCceEEEEEE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKS--KSIDKEGPTVNGPGVVSFPVIF   78 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di--~~i~~G~~I~~gdG~~~~~V~F   78 (166)
                      ||++++++|+|+|||++||++  +  ++++.++|+++++|+ |.+++|+||||+++  .++++|+ |.||||+++|+|+|
T Consensus         1 MF~~~~l~d~I~I~P~~~g~~--~--~~~i~~~L~~~~egk-v~~~~G~vi~V~~~~~~~i~~G~-I~~gdG~~~~~V~F   74 (80)
T d1y14b2           1 MFFIKDLSLNITLHPSFFGPR--M--KQYLKTKLLEEVEGS-CTGKFGYILCVLDYDNIDIQRGR-ILPTDGSAEFNVKY   74 (80)
T ss_dssp             CEEEEEEEEECCCCTTSCSTT--H--HHHHHHHHHHHHTTE-EETTTEEEEEECCGGGCBCC-------------CEEEE
T ss_pred             CeEEEEEEEEEEECHHHhCch--H--HHHHHHHHHHHhCCc-CcCCcCEEEEEEEEeeeeccCCE-EECCCCCEEEEEEE
Confidence            999999999999999999998  5  999999999999999 99999999999776  5899999 99999999999999


Q ss_pred             eEEEEe
Q 042741           79 MCRTFL   84 (166)
Q Consensus        79 ~alvFr   84 (166)
                      +|+|||
T Consensus        75 ~alvFr   80 (80)
T d1y14b2          75 RAVVFK   80 (80)
T ss_dssp             EEEEEC
T ss_pred             EEEEEC
Confidence            999998

>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=99.94  E-value=1.7e-27  Score=163.48  Aligned_cols=77  Identities=21%  Similarity=0.346  Sum_probs=75.6

Q ss_pred             CeEEEEeceeeEEcCCCCCCCCCCCchhhHHHHHHhhhhcceecCCeeEEEEEEEecccCCCcceecCCCceEEEEEEeE
Q 042741            1 MFFEVELLRDIAVPAKSVDRNELRVPQRYTVPRLLEGWINQKACKDHGYFLSVTKSKSIDKEGPTVNGPGVVSFPVIFMC   80 (166)
Q Consensus         1 MF~l~~l~d~V~I~P~~fg~~~~l~~~~~i~~~L~~~~~~~k~~~~~GliI~V~di~~i~~G~~I~~gdG~~~~~V~F~a   80 (166)
                      ||++++|+|+|+|||++||++  +  ++++.++|+++++|+ |.+++|+|++++|++++++|+ |.||||+++|+|+|+|
T Consensus         1 MF~~~~l~d~v~i~P~~~~~~--~--~~~i~~~L~~~~egk-~~~~~G~~i~v~~i~~i~~G~-I~~gdG~~~~~V~F~~   74 (77)
T d2c35b2           1 MFYHISLEHEILLHPRYFGPN--L--LNTVKQKLFTEVEGT-CTGKYGFVIAVTTIDNIGAGV-IQPGRGFVLYPVKYKA   74 (77)
T ss_dssp             CEEEEEEEEEEEECGGGCCSC--H--HHHHHHHHHHHHTTC-EETTTEEEEEEEEEEEECCCB-CCTTCSSEEEEEEEEE
T ss_pred             CcEEEEEEEEEEECHHHhCcc--H--HHHHHHHHHHHhCCE-EeCCCCEEEEEEEEEEecCCE-EEcCCCCEEEEEEEEE
Confidence            999999999999999999998  5  999999999999999 999999999999999999999 9999999999999999


Q ss_pred             EEE
Q 042741           81 RTF   83 (166)
Q Consensus        81 lvF   83 (166)
                      +||
T Consensus        75 lvF   77 (77)
T d2c35b2          75 IVF   77 (77)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            998

>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=99.82  E-value=2.6e-20  Score=131.30  Aligned_cols=76  Identities=17%  Similarity=0.302  Sum_probs=66.2

Q ss_pred             eeecCcEEEEE------------eCCcceEEecCCCC-CCceeeCCCceeEe--cCCCCeecCCCEEEEEEEEEEEcCCC
Q 042741           84 LPVKGEILHGV------------CGPMKYALMSPRRM-PTYRHVSGKKSFFS--NDQQPKIGNGVVVQFLVTAVRWSGEG  148 (166)
Q Consensus        84 rPf~gEVv~G~------------~Gp~~~ifi~~~~m-~~~~~~~~~~~~~~--~~~~~~i~~g~~VR~RI~~~~~~~~~  148 (166)
                      |||+|||++|+            +||++ .|+|.+.| +++.|+.+++.|.|  ++++..++.||.||+||++++++.. 
T Consensus         1 rPf~Gev~~g~V~~v~~~G~fv~lg~~~-~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~-   78 (94)
T d2c35b1           1 RPFKGEVVDAVVTQVNKVGLFTEIGPMS-CFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKN-   78 (94)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTEE-EEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETT-
T ss_pred             CCCCCCEEEEEEEEEEeeEEEEEecCce-EEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcC-
Confidence            89999999999            99997 66666666 67788888887766  4777899999999999999999877 


Q ss_pred             cCccccEEEEEEecCCCC
Q 042741          149 RNLKREYLVFGRAKGESI  166 (166)
Q Consensus       149 ~~~~~~~~~igti~~d~l  166 (166)
                         +  |+|+|||++|||
T Consensus        79 ---~--I~~igt~~~d~L   91 (94)
T d2c35b1          79 ---D--IFAIGSLMDDYL   91 (94)
T ss_dssp             ---E--EEEEEECCSTTC
T ss_pred             ---c--ceEEEEccCCCc
Confidence               5  999999999998

>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=99.78  E-value=2.9e-19  Score=124.91  Aligned_cols=75  Identities=19%  Similarity=0.287  Sum_probs=64.2

Q ss_pred             eecCcEEEEE------------eCCcceEEecCCCC-CCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCCCcCc
Q 042741           85 PVKGEILHGV------------CGPMKYALMSPRRM-PTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNL  151 (166)
Q Consensus        85 Pf~gEVv~G~------------~Gp~~~ifi~~~~m-~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~~~~~  151 (166)
                      ||+|||++|+            +||++ .|+|.+.| +++.|+++++.|.|.+++..++.|+.||+||++++++..    
T Consensus         1 Pf~Gev~~g~I~~v~~~G~fv~lg~~e-g~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~----   75 (91)
T d1y14b1           1 PFKGEVVDGTVVSCSQHGFEVQVGPMK-VFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVS----   75 (91)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTEE-EEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETT----
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEEcCeE-EEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccC----
Confidence            9999999999            99997 78887777 578899999999999888999999999999999999876    


Q ss_pred             cccEEEEEEecCCCC
Q 042741          152 KREYLVFGRAKGESI  166 (166)
Q Consensus       152 ~~~~~~igti~~d~l  166 (166)
                      +  |+|+|||++|||
T Consensus        76 ~--i~~ig~~~~d~L   88 (91)
T d1y14b1          76 S--IHAIGSIKEDYL   88 (91)
T ss_dssp             E--EEEEEECCSTTC
T ss_pred             c--cEEEEEccCCCC
Confidence            4  999999999998

>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=98.63  E-value=9.5e-08  Score=67.39  Aligned_cols=78  Identities=14%  Similarity=0.229  Sum_probs=55.5

Q ss_pred             eecCcEEEEE------------eCCcceEEecCCCCCCc-eeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCCCcCc
Q 042741           85 PVKGEILHGV------------CGPMKYALMSPRRMPTY-RHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGRNL  151 (166)
Q Consensus        85 Pf~gEVv~G~------------~Gp~~~ifi~~~~m~~~-~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~~~~~  151 (166)
                      |-.|||++|+            +++++++.|.+++-+++ .|++....+...+.+..++.||.|++||+++..+..    
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~~~----   76 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAE----   76 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC-----
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEeeCeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchhhc----
Confidence            7889999999            88888444444444564 477777777777788999999999999999998765    


Q ss_pred             cccEEEEE-EecCCCC
Q 042741          152 KREYLVFG-RAKGESI  166 (166)
Q Consensus       152 ~~~~~~ig-ti~~d~l  166 (166)
                      .-+...++ |++.+++
T Consensus        77 ~~~~~~i~ls~K~~~~   92 (106)
T d1go3e1          77 RKRGSKIALTMRQPYL   92 (106)
T ss_dssp             ----CEEEEECCSTTC
T ss_pred             cccCceeecccccCCC
Confidence            21234455 8888764

>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=95.61  E-value=0.005  Score=40.55  Aligned_cols=55  Identities=20%  Similarity=0.314  Sum_probs=34.0

Q ss_pred             EEeeecCcEEEEE------------eC-CcceEEecCCCC-CCceeeCCCceeEecCCCCeecCCCEEEEEEEEEE
Q 042741           82 TFLPVKGEILHGV------------CG-PMKYALMSPRRM-PTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVR  143 (166)
Q Consensus        82 vFrPf~gEVv~G~------------~G-p~~~ifi~~~~m-~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~  143 (166)
                      +|.|-.|+++.|+            +| +.+ .|+|.+.+ ++..-.+.      .+....++.||.|.+||..+.
T Consensus         2 ~Y~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~-g~l~~se~~~~~~~~~~------~~~~~~~~vGd~V~~kV~~vd   70 (88)
T d2z0sa1           2 IYVPQAGDVVIGLIQSVGIMNWFVDINSPYV-AVLSVQDFLGRPFNPAV------DDMQSLLKVGDYIKAKVVAFD   70 (88)
T ss_dssp             CCCCCTTCCEEEEEEEECSSEEEEECSSSSC-EEEEHHHHHTSCCCTTT------TCCTTSSCTTCEEEEEEEEEC
T ss_pred             CcCCCCCCEEEEEEEEEECCeEEEEeCCCeE-EEEehHHhCcccccccc------cchhhhcccCcEEEEEEEEEC
Confidence            5889999999999            33 233 33333222 22111000      122356899999999999986

>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=95.34  E-value=0.018  Score=37.16  Aligned_cols=66  Identities=14%  Similarity=0.100  Sum_probs=39.0

Q ss_pred             EeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCCCc
Q 042741           83 FLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEGR  149 (166)
Q Consensus        83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~~~  149 (166)
                      |.|-.|+++.|+            +| .++++++.+++.++         +...+-...+++||.|++||.++.  +.  
T Consensus         1 Y~Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~---------~~~~~~~~~~~vGd~V~~kV~~vd--~~--   67 (83)
T d2ba0a1           1 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEM---------KPNKKPNEVLDIGDAIIAKVLNID--PK--   67 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTC---------CTTSCGGGTCCTTCEEEEEEEEEC--TT--
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEecCCCeeEEEeccccccc---------ccccChhhhcccccEEEEEEEEEC--CC--
Confidence            579999999999            33 34433332332211         001122345899999999999975  23  


Q ss_pred             CccccEEEEEEecCCCC
Q 042741          150 NLKREYLVFGRAKGESI  166 (166)
Q Consensus       150 ~~~~~~~~igti~~d~l  166 (166)
                        .   .+.=||++..|
T Consensus        68 --~---~i~LS~k~~~~   79 (83)
T d2ba0a1          68 --M---KVTLTMKDRIC   79 (83)
T ss_dssp             --C---CEEEECCSSSC
T ss_pred             --C---CEEEEecCCCC
Confidence              2   34447777643

>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=94.95  E-value=0.027  Score=36.75  Aligned_cols=66  Identities=18%  Similarity=0.237  Sum_probs=38.8

Q ss_pred             EeeecCcEEEEE---eC----------CcceEEecCCCC-CCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEcCCC
Q 042741           83 FLPVKGEILHGV---CG----------PMKYALMSPRRM-PTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWSGEG  148 (166)
Q Consensus        83 FrPf~gEVv~G~---~G----------p~~~ifi~~~~m-~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~~~~  148 (166)
                      |.|-.|+++.|+   +.          +.+ .|+|.+.+ .+..-.       ..+-...++.||.|++||..+.  .. 
T Consensus         3 Y~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~-gll~~s~~~~~~~~~-------~~~~~~~~~~Gd~v~~kV~~vd--~~-   71 (87)
T d2je6i1           3 YYPKINDIVIGLVEDVEIYGWVVDIKAPYK-AYLPASNLLGRSINV-------GEDLRRYLDVGDYVIARIENFD--RS-   71 (87)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSC-EEEEHHHHHTSCCCT-------TCCCSSSCCTTCEEEEEEEEEE--TT-
T ss_pred             ccCCCCCEEEEEEEEEECCEEEEEeCCCEE-EEEehHHhCCceecc-------ccccchhhcccceEEEEEEEEC--CC-
Confidence            679999999999   33          333 33332222 111100       0122346899999999999875  23 


Q ss_pred             cCccccEEEEEEecCCC
Q 042741          149 RNLKREYLVFGRAKGES  165 (166)
Q Consensus       149 ~~~~~~~~~igti~~d~  165 (166)
                            -.+.=||++.-
T Consensus        72 ------~~i~LS~k~~~   82 (87)
T d2je6i1          72 ------IDPVLSVKGKD   82 (87)
T ss_dssp             ------EEEEEECCSTT
T ss_pred             ------CCEEEEEecCC
Confidence                  24555677654

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=93.81  E-value=0.049  Score=35.95  Aligned_cols=50  Identities=10%  Similarity=0.018  Sum_probs=34.5

Q ss_pred             CcceEEecCCCC-CC-ceeeCCCceeEe-cCCCCeecCCCEEEEEEEEEEEcCC
Q 042741           97 PMKYALMSPRRM-PT-YRHVSGKKSFFS-NDQQPKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus        97 p~~~ifi~~~~m-~~-~~~~~~~~~~~~-~~~~~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ..+ -|||.+.| +| +.|+.+...... .+++..++.||.|++||..+.....
T Consensus        27 ~~e-GlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r   79 (87)
T d2ix0a3          27 GAI-AFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETR   79 (87)
T ss_dssp             CCE-EEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTT
T ss_pred             CcE-EEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccC
Confidence            355 55555555 55 567766554443 3556789999999999999987654

>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=90.25  E-value=0.035  Score=36.99  Aligned_cols=62  Identities=13%  Similarity=0.020  Sum_probs=34.0

Q ss_pred             EeeecCcEEEEE------------eC-CcceEEecCCCCC-CceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEc
Q 042741           83 FLPVKGEILHGV------------CG-PMKYALMSPRRMP-TYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus        83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~-~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~  145 (166)
                      |.|-.|+++.|+            +| +.+++.|.+++.. ...+......+. .+-...++.||.|.+||.++.=+
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 YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDE-LAMRGFLQEGDLISAEVQAVFSD   79 (95)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------C-HHHHHHSCSSCEECCEEEEEETT
T ss_pred             ccCCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchhh-hhhhhhcccccEEEEEEEEECCC
Confidence            579999999999            54 3554444444432 222211111100 11123589999999999998643

>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=86.46  E-value=0.63  Score=30.45  Aligned_cols=53  Identities=19%  Similarity=0.261  Sum_probs=36.5

Q ss_pred             EeeecCcEEEEE------------eC-CcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEEc
Q 042741           83 FLPVKGEILHGV------------CG-PMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRWS  145 (166)
Q Consensus        83 FrPf~gEVv~G~------------~G-p~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~~  145 (166)
                      |.|-.|.++.|+            +| |.+++++++...+.     .     .++.+..++.||.|-+||..+.-+
T Consensus         3 Y~P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g-----~-----~k~~r~~l~~GDlV~arV~~v~~~   68 (90)
T d2ja9a1           3 YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPN-----A-----SKKNRPTLQVGDLVYARVCTAEKE   68 (90)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTT-----C-----CSSSCCCCCTTCEEEEEEEECCTT
T ss_pred             ccCCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCc-----c-----ccccCCccCCCCEEEEEEEEECCC
Confidence            579999999999            55 45655554444332     1     123345699999999999987644

>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=86.27  E-value=0.79  Score=29.15  Aligned_cols=22  Identities=18%  Similarity=-0.023  Sum_probs=14.9

Q ss_pred             CCeecCCCEEEEEEEEEEEcCC
Q 042741          126 QPKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus       126 ~~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ...+++|+.|++||+.+.-...
T Consensus        57 ~~~~~~Gd~v~~kV~~vd~~~~   78 (86)
T d1kl9a2          57 NKLIRIGRNECVVVIRVDKEKG   78 (86)
T ss_dssp             ----CTTCEEEEEEEEEETTTT
T ss_pred             eEEeecccEEEEEEEEEECCCC
Confidence            3558999999999998765443

>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=84.98  E-value=0.43  Score=30.25  Aligned_cols=61  Identities=16%  Similarity=0.068  Sum_probs=31.9

Q ss_pred             eecCcEEEEE---eCCcceEEecCCCCCCce-eeCCCc-eeEe-cCCCCeecCCCEEEEEEEEEEEcC
Q 042741           85 PVKGEILHGV---CGPMKYALMSPRRMPTYR-HVSGKK-SFFS-NDQQPKIGNGVVVQFLVTAVRWSG  146 (166)
Q Consensus        85 Pf~gEVv~G~---~Gp~~~ifi~~~~m~~~~-~~~~~~-~~~~-~~~~~~i~~g~~VR~RI~~~~~~~  146 (166)
                      |-.|+++.|+   +-++- +|+.-...++.. +-+.+. .|-+ .+-...+++|+.|++||+.+.-..
T Consensus         9 p~~G~iv~G~V~~v~~~G-~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~   75 (84)
T d2ahob2           9 PSEGEILIATVKQVFDYG-SYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRK   75 (84)
T ss_dssp             CCTTCCCEEEEEEEETTE-EEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTT
T ss_pred             CCCCCEEEEEEEEEECCE-EEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEEECCC
Confidence            6679999999   33433 554321111100 111111 1111 122345899999999999986543

>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=83.42  E-value=0.81  Score=29.74  Aligned_cols=52  Identities=19%  Similarity=0.273  Sum_probs=33.6

Q ss_pred             EeeecCcEEEEE------------eCCcceEEecCCCCCCceeeCCCceeEecCCCCeecCCCEEEEEEEEEEE
Q 042741           83 FLPVKGEILHGV------------CGPMKYALMSPRRMPTYRHVSGKKSFFSNDQQPKIGNGVVVQFLVTAVRW  144 (166)
Q Consensus        83 FrPf~gEVv~G~------------~Gp~~~ifi~~~~m~~~~~~~~~~~~~~~~~~~~i~~g~~VR~RI~~~~~  144 (166)
                      |.|-.|.++.|+            +|+-...++|.+..+          +..++....++.||.|.+||..+.-
T Consensus         2 Y~P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~----------g~~k~~r~~l~~GD~V~arV~~v~~   65 (88)
T d2nn6g1           2 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFE----------GATKRNRPNVQVGDLIYGQFVVANK   65 (88)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSS----------CCSSCSSSSSCTTCEEEEEEEECCT
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcC----------ccccccCcccCCCCEEEEEEEEeCC
Confidence            579999999999            443332334432222          1123344679999999999987753

>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=83.21  E-value=1.3  Score=30.49  Aligned_cols=18  Identities=17%  Similarity=0.045  Sum_probs=14.8

Q ss_pred             CeecCCCEEEEEEEEEEE
Q 042741          127 PKIGNGVVVQFLVTAVRW  144 (166)
Q Consensus       127 ~~i~~g~~VR~RI~~~~~  144 (166)
                      ..+++||.||+||+++.-
T Consensus        60 ~~fr~GDiV~A~Vis~~~   77 (125)
T d2nn6i1          60 KSFRPGDIVLAKVISLGD   77 (125)
T ss_dssp             GTCCSSSEEEEEEEEEET
T ss_pred             HhcCCCCEEEEEEEEccC
Confidence            347899999999998753

>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=81.17  E-value=3.3  Score=25.68  Aligned_cols=21  Identities=19%  Similarity=0.248  Sum_probs=17.1

Q ss_pred             CeecCCCEEEEEEEEEEEcCC
Q 042741          127 PKIGNGVVVQFLVTAVRWSGE  147 (166)
Q Consensus       127 ~~i~~g~~VR~RI~~~~~~~~  147 (166)
                      ..+++||.||+=|..++-.+.
T Consensus        44 E~~~~Gdrik~~i~~V~~~~k   64 (72)
T d1hh2p1          44 EEIKAGDLVKVYIIDVVKTTK   64 (72)
T ss_dssp             CCCCTTCEEEEEEEEEEEETT
T ss_pred             CCCCCCCEEEEEEEEEEEcCC
Confidence            458899999999999986543