Citrus Sinensis ID: 032315

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140---
Protein Sequence
MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARREVGKQRADKHPVEAM
Secondary Structure (PSIPRED)
cccEEEEEEccEEEEEEEEEEccccccEEEcccccEEEEEEEEEEEEEEccccEEEEEEEEEEccEEEEEEcccEEEEccccccccccccccEEEcccccEEEccccEEEEEEEEEEEcccHHHHHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEcccEEEEEEEEEEEEccccEEEccccEEEEEEEEEEEEEEccccEEEEEEEEEEcccEEEEEEccEEEEEEcccccccccccccccEcccccEEEEcccEEEEEEEEEEEccccHHHccccccHHHHcccccccc
Coil and Loop (DISEMBL)
mkdvegtcsgrHGFAVAITGAEsigkglirnGTVLVTFLVRCqcivfrpfkgeiLGAGVTMVNKMGFLAEAGAVQIFClipddmelqtgdlpsyttsdgsvkiQKDCELWLKIIGTQVDVTEIEKARREVGkqradkhpveam
Flexible Loop (DISEMBL)
mkdvegtcsgrhgFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIigtqvdvteIEKARrevgkqradkhpveam
Low Complexity Region (SEG)
MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARREVGKQRADKHPVEAM
Disordered region (IsUnstruct)
*********GRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI********************
Disordered Region (DISOPRED)
MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV***********************
Disordered Region (DISEMBL)
********SGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKAR****************
Disordered Region (DISPRO)
MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIE*********R*********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARREVGKQRADKHPVEAM
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	143	2.2.26 [Sep-21-2011]
P46279	176	DNA-directed RNA polymera	yes	no	0.860	0.698	0.777	2e-50
P38421	176	DNA-directed RNA polymera	yes	no	0.860	0.698	0.761	3e-49
Q54P04	172	DNA-directed RNA polymera	yes	no	0.846	0.703	0.472	1e-24
Q7ZW41	172	DNA-directed RNA polymera	yes	no	0.846	0.703	0.456	1e-23
P62489	172	DNA-directed RNA polymera	yes	no	0.846	0.703	0.448	2e-23
P62488	172	DNA-directed RNA polymera	yes	no	0.846	0.703	0.448	2e-23
P62487	172	DNA-directed RNA polymera	yes	no	0.846	0.703	0.448	2e-23
Q5E9B8	172	DNA-directed RNA polymera	yes	no	0.846	0.703	0.448	2e-23
O14459	172	DNA-directed RNA polymera	yes	no	0.846	0.703	0.395	2e-19
P34087	171	DNA-directed RNA polymera	yes	no	0.832	0.695	0.293	4e-10

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

 Score =  197 bits (500), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 98/126 (77%), Positives = 108/126 (85%), Gaps = 3/126 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
           MKDVEGTCSGRHGF VA+TG E+IGKGLIR+GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct: 31  MKDVEGTCSGRHGFVVAVTGIENIGKGLIRDGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
           MVNKMGF AEAG VQIF    LIPDDME Q+GD+P+YTTSDGSVKIQKD E+ LKIIGT+
Sbjct: 91  MVNKMGFFAEAGPVQIFVSNHLIPDDMEFQSGDMPNYTTSDGSVKIQKDSEVRLKIIGTR 150

Query: 118 VDVTEI 123
           VD TEI
Sbjct: 151 VDATEI 156

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 =  193 bits (490), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 96/126 (76%), Positives = 107/126 (84%), Gaps = 3/126 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
           MKDVEGTCSGRHGF VAITG ++IGKGLIR+GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct: 31  MKDVEGTCSGRHGFVVAITGIDTIGKGLIRDGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
           +VNKMGF AEAG VQIF    LIPDDME Q GD+P+YTTSDGSVKIQK+CE+ LKIIGT+
Sbjct: 91  LVNKMGFFAEAGPVQIFVSKHLIPDDMEFQAGDMPNYTTSDGSVKIQKECEVRLKIIGTR 150

Query: 118 VDVTEI 123
           VD T I
Sbjct: 151 VDATAI 156

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)

>sp|Q54P04|RPB7_DICDI DNA-directed RNA polymerase II subunit rpb7 OS=Dictyostelium discoideum GN=polr2g PE=3 SV=1

 Score =  112 bits (279), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 59/125 (47%), Positives = 80/125 (64%), Gaps = 4/125 (3%)

Query: 3   DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
           +VEGTC+GR+GF + IT  + + KG +   +  V F V+ + I+F+PFKGE+L A VT V
Sbjct: 33  EVEGTCTGRYGFIITITSVDFLSKGKVLESSGYVVFNVKYKAIIFKPFKGEVLDAIVTKV 92

Query: 63  NKMGFLAEAGAVQIFC---LIPDDMELQT-GDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
             +GF AEAG + IF    LIP DM       +P + + DGS KI KD E+ L+I GT+V
Sbjct: 93  TNLGFFAEAGPLSIFVSTQLIPSDMIFDAQSAVPCFVSEDGSSKISKDDEVRLQIKGTRV 152

Query: 119 DVTEI 123
           D TEI
Sbjct: 153 DATEI 157

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.

Dictyostelium discoideum (taxid: 44689)

>sp|Q7ZW41|RPB7_DANRE DNA-directed RNA polymerase II subunit RPB7 OS=Danio rerio GN=polr2g PE=2 SV=1

 Score =  108 bits (269), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/125 (45%), Positives = 81/125 (64%), Gaps = 4/125 (3%)

Query: 3   DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
           +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT V
Sbjct: 33  EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92

Query: 63  NKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
           NK+G   E G +  F     IP +ME     + P Y T D  V IQ+D E+ LKI+GT+V
Sbjct: 93  NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTVDEDVVIQQDDEIRLKIVGTRV 152

Query: 119 DVTEI 123
           D  +I
Sbjct: 153 DKNDI 157

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.

Danio rerio (taxid: 7955)

>sp|P62489|RPB7_RAT DNA-directed RNA polymerase II subunit RPB7 OS=Rattus norvegicus GN=Polr2g PE=2 SV=1

 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 56/125 (44%), Positives = 81/125 (64%), Gaps = 4/125 (3%)

Query: 3   DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
           +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT V
Sbjct: 33  EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92

Query: 63  NKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
           NK+G   E G +  F     IP +ME     + P Y T D  + IQ+D E+ LKI+GT+V
Sbjct: 93  NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV 152

Query: 119 DVTEI 123
           D  +I
Sbjct: 153 DKNDI 157

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. Binds RNA.

Rattus norvegicus (taxid: 10116)

>sp|P62488|RPB7_MOUSE DNA-directed RNA polymerase II subunit RPB7 OS=Mus musculus GN=Polr2g PE=2 SV=1

 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 56/125 (44%), Positives = 81/125 (64%), Gaps = 4/125 (3%)

Query: 3   DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
           +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT V
Sbjct: 33  EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92

Query: 63  NKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
           NK+G   E G +  F     IP +ME     + P Y T D  + IQ+D E+ LKI+GT+V
Sbjct: 93  NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV 152

Query: 119 DVTEI 123
           D  +I
Sbjct: 153 DKNDI 157

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. Binds RNA.

Mus musculus (taxid: 10090)

>sp|P62487|RPB7_HUMAN DNA-directed RNA polymerase II subunit RPB7 OS=Homo sapiens GN=POLR2G PE=1 SV=1

 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 56/125 (44%), Positives = 81/125 (64%), Gaps = 4/125 (3%)

Query: 3   DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
           +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT V
Sbjct: 33  EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92

Query: 63  NKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
           NK+G   E G +  F     IP +ME     + P Y T D  + IQ+D E+ LKI+GT+V
Sbjct: 93  NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV 152

Query: 119 DVTEI 123
           D  +I
Sbjct: 153 DKNDI 157

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 (By similarity). Binds RNA.

Homo sapiens (taxid: 9606)

>sp|Q5E9B8|RPB7_BOVIN DNA-directed RNA polymerase II subunit RPB7 OS=Bos taurus GN=POLR2G PE=2 SV=1

 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 56/125 (44%), Positives = 81/125 (64%), Gaps = 4/125 (3%)

Query: 3   DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
           +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT V
Sbjct: 33  EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92

Query: 63  NKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
           NK+G   E G +  F     IP +ME     + P Y T D  + IQ+D E+ LKI+GT+V
Sbjct: 93  NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV 152

Query: 119 DVTEI 123
           D  +I
Sbjct: 153 DKNDI 157

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. Binds RNA.

Bos taurus (taxid: 9913)

>sp|O14459|RPB7_SCHPO DNA-directed RNA polymerase II subunit rpb7 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb7 PE=1 SV=1

 Score = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 51/129 (39%), Positives = 79/129 (61%), Gaps = 8/129 (6%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIG--KGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAG 58
           + DVEGTCSG++G+ + +  + +I   KG +  G     F V+ + +++RPF+GE++ A 
Sbjct: 32  LADVEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLWRPFRGEVVDAI 91

Query: 59  VTMVNKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKII 114
           VT VNKMGF A  G + +F    L+P DM+   T + P+Y+  D    I+K   + LKI+
Sbjct: 92  VTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQV--IEKGSNVRLKIV 149

Query: 115 GTQVDVTEI 123
           GT+ D TEI
Sbjct: 150 GTRTDATEI 158

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.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P34087|RPB7_YEAST DNA-directed RNA polymerase II subunit RPB7 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB7 PE=1 SV=1

 Score = 63.2 bits (152), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 39/133 (29%), Positives = 74/133 (55%), Gaps = 14/133 (10%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVT-----FLVRCQCIVFRPFKGEIL 55
           +++VEG+C+G+ G+ + +   ++I    I+ G +L T     F V+ + +VF+PFKGE++
Sbjct: 31  LEEVEGSCTGKFGYILCVLDYDNID---IQRGRILPTDGSAEFNVKYRAVVFKPFKGEVV 87

Query: 56  GAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTG-DLPSYTTSDGSVKIQKDCELWL 111
              V   ++ GF  + G +++F    L+P D+    G + PSY +S+  + I+    + +
Sbjct: 88  DGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKS--RIRV 145

Query: 112 KIIGTQVDVTEIE 124
           KI G    V+ I 
Sbjct: 146 KIEGCISQVSSIH 158

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. The RPB4-RPB7 subcomplex recruits FCP1 to Pol II.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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	143
224056563	176	predicted protein [Populus trichocarpa]	0.860	0.698	0.793	5e-49
255558950	176	DNA-directed RNA polymerase II 19 kD pol	0.860	0.698	0.785	6e-49
297796859	176	DNA-directed RNA polymerase II [Arabidop	0.860	0.698	0.785	9e-49
449466050	176	PREDICTED: DNA-directed RNA polymerase I	0.860	0.698	0.785	1e-48
357476433	176	DNA-directed RNA polymerase II subunit R	0.860	0.698	0.777	1e-48
351722267	176	DNA-directed RNA polymerase II subunit R	0.860	0.698	0.777	2e-48
388502464	176	unknown [Lotus japonicus]	0.860	0.698	0.769	2e-48
225434800	176	PREDICTED: DNA-directed RNA polymerase I	0.860	0.698	0.769	7e-48
357133761	177	PREDICTED: DNA-directed RNA polymerase I	0.860	0.694	0.777	1e-47
326497319	177	predicted protein [Hordeum vulgare subsp	0.860	0.694	0.777	1e-47

>gi|224056563|ref|XP_002298912.1| predicted protein [Populus trichocarpa] gi|222846170|gb|EEE83717.1| predicted protein [Populus trichocarpa]

 Score =  199 bits (505), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 100/126 (79%), Positives = 108/126 (85%), Gaps = 3/126 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
           MKDVEGTCSGRHGF VAITG E+IGKGLIR+GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct: 31  MKDVEGTCSGRHGFVVAITGIENIGKGLIRDGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
           MVNKMGF AEAG VQIF    LIPDDME QTGD+P+YTTSDGSVKIQKD E+ LKIIGT+
Sbjct: 91  MVNKMGFFAEAGPVQIFVSNHLIPDDMEFQTGDMPNYTTSDGSVKIQKDSEVRLKIIGTR 150

Query: 118 VDVTEI 123
           VD TEI
Sbjct: 151 VDATEI 156

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255558950|ref|XP_002520498.1| DNA-directed RNA polymerase II 19 kD polypeptide rpb7, putative [Ricinus communis] gi|223540340|gb|EEF41911.1| DNA-directed RNA polymerase II 19 kD polypeptide rpb7, putative [Ricinus communis]

 Score =  198 bits (503), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 99/126 (78%), Positives = 108/126 (85%), Gaps = 3/126 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
           MKDVEGTCSGRHGF VAITG ES+GKGLIR+GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct: 31  MKDVEGTCSGRHGFVVAITGIESVGKGLIRDGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
           MVNKMGF AEAG VQIF    LIPDDME Q+GD+P+YTTSDGSVKIQKD E+ LKIIGT+
Sbjct: 91  MVNKMGFFAEAGPVQIFVSNHLIPDDMEFQSGDMPNYTTSDGSVKIQKDSEVRLKIIGTR 150

Query: 118 VDVTEI 123
           VD TEI
Sbjct: 151 VDATEI 156

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297796859|ref|XP_002866314.1| DNA-directed RNA polymerase II [Arabidopsis lyrata subsp. lyrata] gi|297312149|gb|EFH42573.1| DNA-directed RNA polymerase II [Arabidopsis lyrata subsp. lyrata]

 Score =  197 bits (502), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 99/126 (78%), Positives = 108/126 (85%), Gaps = 3/126 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
           MKDVEGTCSGRHGF VAITG ESIGKGLIR+GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct: 31  MKDVEGTCSGRHGFVVAITGIESIGKGLIRDGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
           +VNKMGF AEAG VQIF    LIPDDME Q GD+P+YTTSDGSVKIQK+CE+ LKIIGT+
Sbjct: 91  LVNKMGFFAEAGPVQIFVSKHLIPDDMEFQAGDMPNYTTSDGSVKIQKECEVRLKIIGTR 150

Query: 118 VDVTEI 123
           VD TEI
Sbjct: 151 VDATEI 156

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449466050|ref|XP_004150740.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Cucumis sativus] gi|449518487|ref|XP_004166273.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Cucumis sativus]

 Score =  197 bits (501), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 99/126 (78%), Positives = 108/126 (85%), Gaps = 3/126 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
           MKDVEGTCSGRHGF VAITG E+IGKGLIR+GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct: 31  MKDVEGTCSGRHGFVVAITGIENIGKGLIRDGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
           MVNKMGF AEAG VQIF    LIPDDME Q+GD+P+YTTSDGSVKIQKD E+ LKIIGT+
Sbjct: 91  MVNKMGFFAEAGPVQIFVSNHLIPDDMEFQSGDVPNYTTSDGSVKIQKDSEVRLKIIGTR 150

Query: 118 VDVTEI 123
           VD TEI
Sbjct: 151 VDATEI 156

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357476433|ref|XP_003608502.1| DNA-directed RNA polymerase II subunit RPB7 [Medicago truncatula] gi|217071674|gb|ACJ84197.1| unknown [Medicago truncatula] gi|355509557|gb|AES90699.1| DNA-directed RNA polymerase II subunit RPB7 [Medicago truncatula] gi|388514911|gb|AFK45517.1| unknown [Medicago truncatula]

 Score =  197 bits (500), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 98/126 (77%), Positives = 108/126 (85%), Gaps = 3/126 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
           MKDVEGTCSGRHGF VA+TG E+IGKG+IR+GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct: 31  MKDVEGTCSGRHGFVVAVTGIENIGKGIIRDGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
           MVNKMGF AEAG VQIF    LIPDDME QTGD+P+YTTSDGSVKIQKD E+ LKIIGT+
Sbjct: 91  MVNKMGFFAEAGPVQIFVSNHLIPDDMEFQTGDMPNYTTSDGSVKIQKDSEVRLKIIGTR 150

Query: 118 VDVTEI 123
           VD TEI
Sbjct: 151 VDATEI 156

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722267|ref|NP_001236982.1| DNA-directed RNA polymerase II subunit RPB7 [Glycine max] gi|356512183|ref|XP_003524800.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Glycine max] gi|1173137|sp|P46279.1|RPB7_SOYBN RecName: Full=DNA-directed RNA polymerase II subunit RPB7; Short=RNA polymerase II subunit B7 gi|170052|gb|AAA34005.1| RNA polymerase II [Glycine max] gi|255626843|gb|ACU13766.1| unknown [Glycine max]

 Score =  197 bits (500), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 98/126 (77%), Positives = 108/126 (85%), Gaps = 3/126 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
           MKDVEGTCSGRHGF VA+TG E+IGKGLIR+GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct: 31  MKDVEGTCSGRHGFVVAVTGIENIGKGLIRDGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
           MVNKMGF AEAG VQIF    LIPDDME Q+GD+P+YTTSDGSVKIQKD E+ LKIIGT+
Sbjct: 91  MVNKMGFFAEAGPVQIFVSNHLIPDDMEFQSGDMPNYTTSDGSVKIQKDSEVRLKIIGTR 150

Query: 118 VDVTEI 123
           VD TEI
Sbjct: 151 VDATEI 156

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388502464|gb|AFK39298.1| unknown [Lotus japonicus]

 Score =  196 bits (498), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 97/126 (76%), Positives = 108/126 (85%), Gaps = 3/126 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
           MKDVEGTCSGRHGF VA+TG E++GKGLIR+GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct: 31  MKDVEGTCSGRHGFVVAVTGIENVGKGLIRDGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
           MVNKMGF AEAG VQIF    LIPDDME Q+GD+P+YTTSDGSVKIQKD E+ LKIIGT+
Sbjct: 91  MVNKMGFFAEAGPVQIFVSNHLIPDDMEFQSGDMPNYTTSDGSVKIQKDSEVRLKIIGTR 150

Query: 118 VDVTEI 123
           VD TEI
Sbjct: 151 VDATEI 156

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225434800|ref|XP_002282298.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7 [Vitis vinifera] gi|147841138|emb|CAN75204.1| hypothetical protein VITISV_042914 [Vitis vinifera] gi|297745997|emb|CBI16053.3| unnamed protein product [Vitis vinifera]

 Score =  195 bits (495), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 97/126 (76%), Positives = 108/126 (85%), Gaps = 3/126 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
           +KDVEGTCSGRHGF VAITG E++GKGLIR+GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct: 31  VKDVEGTCSGRHGFVVAITGIENVGKGLIRDGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
           MVNKMGF AEAG VQIF    LIPDDME Q+GD+P+YTTSDGSVKIQKD E+ LKIIGT+
Sbjct: 91  MVNKMGFFAEAGPVQIFVSNHLIPDDMEFQSGDMPNYTTSDGSVKIQKDSEVRLKIIGTR 150

Query: 118 VDVTEI 123
           VD TEI
Sbjct: 151 VDATEI 156

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357133761|ref|XP_003568492.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB7-like [Brachypodium distachyon]

 Score =  194 bits (493), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 98/126 (77%), Positives = 106/126 (84%), Gaps = 3/126 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
           MKDVEGTCSGRHGF VAITG E IGKGLIR GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct: 31  MKDVEGTCSGRHGFVVAITGVEDIGKGLIREGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
           MVNKMGF AEAG VQIF    LIPDDME Q+GD+P+YTTSDGSVKIQK+ E+ LKIIGT+
Sbjct: 91  MVNKMGFFAEAGPVQIFVSNHLIPDDMEFQSGDVPNYTTSDGSVKIQKESEVRLKIIGTR 150

Query: 118 VDVTEI 123
           VD TEI
Sbjct: 151 VDATEI 156

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326497319|dbj|BAK02244.1| predicted protein [Hordeum vulgare subsp. vulgare] gi|326505504|dbj|BAJ95423.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  194 bits (492), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 98/126 (77%), Positives = 106/126 (84%), Gaps = 3/126 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
           MKDVEGTCSGRHGF VAITG E IGKGLIR GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct: 31  MKDVEGTCSGRHGFVVAITGVEDIGKGLIREGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
           MVNKMGF AEAG VQIF    LIPDDME Q+GD+P+YTTSDGSVKIQK+ E+ LKIIGT+
Sbjct: 91  MVNKMGFFAEAGPVQIFVSNHLIPDDMEFQSGDVPNYTTSDGSVKIQKESEVRLKIIGTR 150

Query: 118 VDVTEI 123
           VD TEI
Sbjct: 151 VDATEI 156

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	143
TAIR|locus:2168514	176	NRPB7 [Arabidopsis thaliana (t	0.860	0.698	0.761	4.8e-46
DICTYBASE|DDB_G0284891	172	rpb7 "DNA-directed RNA polymer	0.839	0.697	0.476	1.6e-24
UNIPROTKB|Q5E9B8	172	POLR2G "DNA-directed RNA polym	0.846	0.703	0.448	1.1e-23
UNIPROTKB|P62487	172	POLR2G "DNA-directed RNA polym	0.846	0.703	0.448	1.1e-23
UNIPROTKB|I3LJZ9	172	POLR2G "Uncharacterized protei	0.846	0.703	0.448	1.1e-23
MGI|MGI:1914960	172	Polr2g "polymerase (RNA) II (D	0.846	0.703	0.448	1.1e-23
RGD|621284	172	Polr2g "polymerase (RNA) II (D	0.846	0.703	0.448	1.1e-23
ZFIN|ZDB-GENE-030131-2808	172	polr2gl "polymerase (RNA) II (	0.846	0.703	0.456	1.1e-23
WB|WBGene00021845	197	rpb-7 [Caenorhabditis elegans	0.846	0.614	0.432	7.8e-23
FB|FBgn0051155	173	Rpb7 "Rpb7" [Drosophila melano	0.846	0.699	0.44	1.3e-22

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

 Score = 483 (175.1 bits), Expect = 4.8e-46, P = 4.8e-46
 Identities = 96/126 (76%), Positives = 107/126 (84%)

Query:     1 MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
             MKDVEGTCSGRHGF VAITG ++IGKGLIR+GT  VTF V+ QC+VFRPFKGEIL A VT
Sbjct:    31 MKDVEGTCSGRHGFVVAITGIDTIGKGLIRDGTGFVTFPVKYQCVVFRPFKGEILEAVVT 90

Query:    61 MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
             +VNKMGF AEAG VQIF    LIPDDME Q GD+P+YTTSDGSVKIQK+CE+ LKIIGT+
Sbjct:    91 LVNKMGFFAEAGPVQIFVSKHLIPDDMEFQAGDMPNYTTSDGSVKIQKECEVRLKIIGTR 150

Query:   118 VDVTEI 123
             VD T I
Sbjct:   151 VDATAI 156

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

DICTYBASE|DDB_G0284891 rpb7 "DNA-directed RNA polymerase II subunit 7" [Dictyostelium discoideum (taxid:44689)]

 Score = 280 (103.6 bits), Expect = 1.6e-24, P = 1.6e-24
 Identities = 60/126 (47%), Positives = 83/126 (65%)

Query:     3 DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
             +VEGTC+GR+GF + IT  + + KG +   +  V F V+ + I+F+PFKGE+L A VT V
Sbjct:    33 EVEGTCTGRYGFIITITSVDFLSKGKVLESSGYVVFNVKYKAIIFKPFKGEVLDAIVTKV 92

Query:    63 NKMGFLAEAGAVQIFC---LIPDDM--ELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
               +GF AEAG + IF    LIP DM  + Q+  +P + + DGS KI KD E+ L+I GT+
Sbjct:    93 TNLGFFAEAGPLSIFVSTQLIPSDMIFDAQSA-VPCFVSEDGSSKISKDDEVRLQIKGTR 151

Query:   118 VDVTEI 123
             VD TEI
Sbjct:   152 VDATEI 157

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=ISS

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

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

GO:0003697 "single-stranded DNA binding" evidence=ISS

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|Q5E9B8 POLR2G "DNA-directed RNA polymerase II subunit RPB7" [Bos taurus (taxid:9913)]

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 56/125 (44%), Positives = 81/125 (64%)

Query:     3 DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
             +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT V
Sbjct:    33 EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92

Query:    63 NKMGFLAEAGAVQIFCL---IPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
             NK+G   E G +  F     IP +ME     + P Y T D  + IQ+D E+ LKI+GT+V
Sbjct:    93 NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV 152

Query:   119 DVTEI 123
             D  +I
Sbjct:   153 DKNDI 157

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

GO:0005634 "nucleus" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

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

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

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P62487 POLR2G "DNA-directed RNA polymerase II subunit RPB7" [Homo sapiens (taxid:9606)]

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 56/125 (44%), Positives = 81/125 (64%)

Query:     3 DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
             +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT V
Sbjct:    33 EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92

Query:    63 NKMGFLAEAGAVQIFCL---IPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
             NK+G   E G +  F     IP +ME     + P Y T D  + IQ+D E+ LKI+GT+V
Sbjct:    93 NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV 152

Query:   119 DVTEI 123
             D  +I
Sbjct:   153 DKNDI 157

GO:0003723 "RNA binding" evidence=IEA

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

GO:0006915 "apoptotic process" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IDA;TAS

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

GO:0000398 "mRNA splicing, via spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0006370 "7-methylguanosine mRNA capping" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0050434 "positive regulation of viral transcription" evidence=TAS

GO:0006468 "protein phosphorylation" evidence=IDA

UNIPROTKB|I3LJZ9 POLR2G "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 56/125 (44%), Positives = 81/125 (64%)

Query:     3 DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
             +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT V
Sbjct:    33 EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92

Query:    63 NKMGFLAEAGAVQIFCL---IPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
             NK+G   E G +  F     IP +ME     + P Y T D  + IQ+D E+ LKI+GT+V
Sbjct:    93 NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV 152

Query:   119 DVTEI 123
             D  +I
Sbjct:   153 DKNDI 157

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

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

GO:0004672 "protein kinase activity" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

MGI|MGI:1914960 Polr2g "polymerase (RNA) II (DNA directed) polypeptide G" [Mus musculus (taxid:10090)]

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 56/125 (44%), Positives = 81/125 (64%)

Query:     3 DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
             +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT V
Sbjct:    33 EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92

Query:    63 NKMGFLAEAGAVQIFCL---IPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
             NK+G   E G +  F     IP +ME     + P Y T D  + IQ+D E+ LKI+GT+V
Sbjct:    93 NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV 152

Query:   119 DVTEI 123
             D  +I
Sbjct:   153 DKNDI 157

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISO

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0016740 "transferase activity" evidence=IEA

GO:0016779 "nucleotidyltransferase activity" evidence=IEA

RGD|621284 Polr2g "polymerase (RNA) II (DNA directed) polypeptide G" [Rattus norvegicus (taxid:10116)]

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 56/125 (44%), Positives = 81/125 (64%)

Query:     3 DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
             +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT V
Sbjct:    33 EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92

Query:    63 NKMGFLAEAGAVQIFCL---IPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
             NK+G   E G +  F     IP +ME     + P Y T D  + IQ+D E+ LKI+GT+V
Sbjct:    93 NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV 152

Query:   119 DVTEI 123
             D  +I
Sbjct:   153 DKNDI 157

GO:0003674 "molecular_function" evidence=ND

GO:0003723 "RNA binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=ISO;ISS

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=ISO;ISS

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISO;ISS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISO;ISS

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0006915 "apoptotic process" evidence=IEP

ZFIN|ZDB-GENE-030131-2808 polr2gl "polymerase (RNA) II (DNA directed) polypeptide G-like" [Danio rerio (taxid:7955)]

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 57/125 (45%), Positives = 81/125 (64%)

Query:     3 DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
             +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT V
Sbjct:    33 EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92

Query:    63 NKMGFLAEAGAVQIFCL---IPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
             NK+G   E G +  F     IP +ME     + P Y T D  V IQ+D E+ LKI+GT+V
Sbjct:    93 NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTVDEDVVIQQDDEIRLKIVGTRV 152

Query:   119 DVTEI 123
             D  +I
Sbjct:   153 DKNDI 157

GO:0003723 "RNA binding" evidence=IEA

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

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

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

GO:0004672 "protein kinase activity" evidence=ISS

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

GO:0005634 "nucleus" evidence=IEA

WB|WBGene00021845 rpb-7 [Caenorhabditis elegans (taxid:6239)]

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 54/125 (43%), Positives = 80/125 (64%)

Query:     3 DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
             +VEGTC+G++GF +A+T  ++IG GLI+ G   V + VR + IVFRPFKG+++   VT V
Sbjct:    56 EVEGTCTGKYGFVIAVTTIDTIGHGLIQPGRGFVIYPVRYKAIVFRPFKGQVVDGVVTQV 115

Query:    63 NKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
             NK+G   + G +  F     IP DME     + P Y T+D +  I+ D E+ +K+IGT+V
Sbjct:   116 NKVGIFCDIGPLSCFISRHCIPPDMEFDPNSEKPCYKTNDEANVIRNDDEIRVKLIGTRV 175

Query:   119 DVTEI 123
             D  +I
Sbjct:   176 DANDI 180

GO:0003723 "RNA binding" evidence=IEA

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

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

GO:0004601 "peroxidase activity" evidence=IEA

GO:0055114 "oxidation-reduction process" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0001703 "gastrulation with mouth forming first" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0043652 "engulfment of apoptotic cell" evidence=IMP

FB|FBgn0051155 Rpb7 "Rpb7" [Drosophila melanogaster (taxid:7227)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 55/125 (44%), Positives = 79/125 (63%)

Query:     3 DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
             +VEGTC+G++GF +A+T  + IG G+I+ G   V + V+ + IVFRPFKGE+L A V  +
Sbjct:    33 EVEGTCTGKYGFVIAVTTIDQIGSGVIQPGQGFVVYPVKYKAIVFRPFKGEVLDAVVKQI 92

Query:    63 NKMGFLAEAGAVQIFCL---IPDDMEL-QTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
             NK+G  AE G +  F     IP DM+    G+ P Y + D  V I  + ++ LKI+GT+V
Sbjct:    93 NKVGMFAEIGPLSCFISHHSIPADMQFCPNGNPPCYKSKDEDVVISGEDKIRLKIVGTRV 152

Query:   119 DVTEI 123
             D T I
Sbjct:   153 DATGI 157

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0003723 "RNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P38421	RPB7_ARATH	No assigned EC number	0.7619	0.8601	0.6988	yes	no
P46279	RPB7_SOYBN	No assigned EC number	0.7777	0.8601	0.6988	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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:
	estExt_Genewise1_v1.C_LG_I4990	hypothetical protein (176 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	grail3.0014029901	hypothetical protein (52 aa)				•	•	•	•		0.940
	estExt_Genewise1_v1.C_LG_IX3069	SubName- Full=Putative uncharacterized protein; (117 aa)				•	•	•	•		0.911
	fgenesh4_pg.C_LG_XII000913	hypothetical protein (152 aa)						•	•		0.908
	eugene3.00400106	RecName- Full=Nucleoside diphosphate kinase; EC=2.7.4.6; (149 aa)						•	•		0.908
	gw1.II.1445.1	SubName- Full=Putative uncharacterized protein; (164 aa)						•	•		0.906
	eugene3.00031452	hypothetical protein (211 aa)	•					•			0.905
	estExt_fgenesh4_pg.C_LG_I0458	hypothetical protein (204 aa)	•					•			0.905
	estExt_fgenesh4_pg.C_1570036	hypothetical protein (206 aa)				•	•	•	•		0.902
	grail3.0008036902	nucleoside-diphosphate kinase (EC-2.7.4.6) (237 aa)						•	•		0.900
	gw1.IX.2304.1	hypothetical protein (321 aa)				•	•	•	•		0.900

---

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	143
PTZ00162	176	PTZ00162, PTZ00162, DNA-directed RNA polymerase II	4e-32
cd04462	88	cd04462, S1_RNAPII_Rpb7, S1_RNAPII_Rpb7: Eukaryoti	2e-19
cd04329	80	cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-t	1e-17
COG1095	183	COG1095, RPB7, DNA-directed RNA polymerase, subuni	9e-12
pfam03876	70	pfam03876, SHS2_Rpb7-N, SHS2 domain found in N ter	3e-07
cd00655	80	cd00655, RNAP_Rpb7_N_like, RNAP_Rpb7_N_like: This	0.002

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

 Score =  111 bits (280), Expect = 4e-32
 Identities = 43/124 (34%), Positives = 73/124 (58%), Gaps = 4/124 (3%)

Query: 4   VEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVN 63
           VEG C+ ++G+ + +        G +++GT ++   V+ Q IVF+PFK E+L A VT VN
Sbjct: 34  VEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVN 93

Query: 64  KMGFLAEAGAVQIFC---LIPDDMELQTG-DLPSYTTSDGSVKIQKDCELWLKIIGTQVD 119
           K+GF A+AG ++ F     IP D    +    P Y +SDG ++I+ + E+ L++ G + D
Sbjct: 94  KLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYD 153

Query: 120 VTEI 123
            + +
Sbjct: 154 ASNL 157

Length = 176

>gnl|CDD|239909 cd04462, S1_RNAPII_Rpb7, S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain

 Score = 76.9 bits (190), Expect = 2e-19
 Identities = 38/77 (49%), Positives = 50/77 (64%), Gaps = 5/77 (6%)

Query: 51  KGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKD 106
           KGE++ A VT VNK GF AE G + IF    LIP DME       P +T+++  + I+KD
Sbjct: 1   KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNE-DIVIKKD 59

Query: 107 CELWLKIIGTQVDVTEI 123
            E+ LKIIGT+VD T+I
Sbjct: 60  TEVRLKIIGTRVDATDI 76

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. Length = 88

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

 Score = 71.4 bits (176), Expect = 1e-17
 Identities = 24/51 (47%), Positives = 37/51 (72%)

Query: 1  MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFK 51
          +++VEGTC+G +G+ +A+T  + IG+G I  GT  V F V+ + IVF+PFK
Sbjct: 30 LEEVEGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPFK 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

>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription]

 Score = 59.2 bits (144), Expect = 9e-12
 Identities = 26/130 (20%), Positives = 51/130 (39%), Gaps = 3/130 (2%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
            +  EG   G  G  V +   + IG+G+I  G       V+ + +VF+PF+GE++   V 
Sbjct: 31  KEKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVV 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ 117
            V + G     G +        I DD              +    ++   ++  +I+G  
Sbjct: 91  EVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVS 150

Query: 118 VDVTEIEKAR 127
           +      +++
Sbjct: 151 LKSRRPRESK 160

Length = 183

>gnl|CDD|202794 pfam03876, SHS2_Rpb7-N, SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397

 Score = 44.8 bits (107), Expect = 3e-07
 Identities = 14/47 (29%), Positives = 22/47 (46%)

Query: 1  MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVF 47
          ++  EG      G  +A+T  + IG+G I  G     F V  + +VF
Sbjct: 24 LEKYEGKYDPDLGVVIAVTDIKLIGEGKILPGDGAAYFKVTFRALVF 70

Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction. Length = 70

>gnl|CDD|238354 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

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 15/51 (29%), Positives = 23/51 (45%)

Query: 1  MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFK 51
           +  EG  +   G  +AI   + I +G IR G       V  + +VF+PF 
Sbjct: 30 QEKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFKPFS 80

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. Length = 80

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	143
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	100.0
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	100.0
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	100.0
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	100.0
KOG3297	202	consensus DNA-directed RNA polymerase subunit E' [	100.0
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	100.0
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	99.9
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	99.83
cd04330	80	RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-termin	99.78
cd04329	80	RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ri	99.77
cd00655	80	RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved	99.77
cd04331	80	RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprot	99.73
PF03876	70	SHS2_Rpb7-N: SHS2 domain found in N terminus of Rp	99.42
cd04328	89	RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal r	98.86
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.85
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.64
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	98.62
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	98.29
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.19
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	98.17
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.15
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.12
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.09
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	98.04
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.02
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.02
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.0
PRK11642	813	exoribonuclease R; Provisional	97.98
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	97.98
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	97.97
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	97.93
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	97.92
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	97.92
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	97.91
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	97.84
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	97.8
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	97.78
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	97.74
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	97.72
PRK08582	139	hypothetical protein; Provisional	97.69
KOG4134	253	consensus DNA-dependent RNA polymerase I [Transcri	97.68
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	97.67
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	97.66
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	97.65
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	97.65
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	97.64
PRK07252	120	hypothetical protein; Provisional	97.58
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	97.57
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	97.55
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	97.51
PRK08059	123	general stress protein 13; Validated	97.47
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	97.42
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.36
PRK05807	136	hypothetical protein; Provisional	97.33
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	97.28
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	97.21
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	97.2
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	97.18
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	97.09
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	96.98
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	96.95
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	96.87
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	96.87
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	96.81
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	96.8
PRK07400	318	30S ribosomal protein S1; Reviewed	96.8
PHA02945	88	interferon resistance protein; Provisional	96.78
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	96.75
COG0557	706	VacB Exoribonuclease R [Transcription]	96.74
PRK03987	262	translation initiation factor IF-2 subunit alpha;	96.74
PRK05054	644	exoribonuclease II; Provisional	96.72
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	96.6
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	96.59
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	96.58
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	96.45
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	96.43
PRK07400	318	30S ribosomal protein S1; Reviewed	96.39
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	96.37
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	96.29
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.28
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	96.26
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	96.14
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	95.95
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	95.93
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	95.87
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	95.8
COG1098	129	VacB Predicted RNA binding protein (contains ribos	95.71
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	95.69
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	95.49
COG2183	780	Tex Transcriptional accessory protein [Transcripti	95.46
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	95.38
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.27
PRK09202	470	nusA transcription elongation factor NusA; Validat	95.23
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	95.19
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	94.69
TIGR01953	341	NusA transcription termination factor NusA. This m	94.15
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	93.57
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	93.13
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	91.51
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	88.01
PRK12328	374	nusA transcription elongation factor NusA; Provisi	86.46
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	86.23
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	83.7
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	82.67

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

Probab=100.00  E-value=4.8e-44  Score=276.23  Aligned_cols=133  Identities=32%  Similarity=0.592  Sum_probs=127.5

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC---   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---   78 (143)
                      +++||||++++||||+++|+.++++|+|.||||+++|+|+|||++||||+|||++|+|++++++|+|+++||+++||   
T Consensus        32 ~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~  111 (176)
T PTZ00162         32 SQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRS  111 (176)
T ss_pred             HHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecCCCCEEEEEEEEEecceEEEEeeCeEEEEcHH
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999   


Q ss_pred             EcCCCceecCCC-CceEEcCCceEEEcCCCeEEEEEEEEEEccCCeEEEEEcccccc
Q 032315           79 LIPDDMELQTGD-LPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARREVGKQR  134 (143)
Q Consensus        79 ~lp~~~~fd~~~-~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ai~~~~~~~~  134 (143)
                      +||+++.||+++ .|+|.+++++.++++|+.|||||++++|+++++.|+|+|-+++-
T Consensus       112 ~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~i~T~~~~~L  168 (176)
T PTZ00162        112 AIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAIATINSDYL  168 (176)
T ss_pred             HCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEEEEEecCCCc
Confidence            999999999875 59999778899999999999999999999999999999988864

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

Probab=100.00  E-value=2.8e-39  Score=244.50  Aligned_cols=132  Identities=45%  Similarity=0.757  Sum_probs=125.5

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC---   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---   78 (143)
                      +++||+|.+++||+||++++.+|++|+|.+++|.+.|.|.|+|++||||+|||++|+|++++++|+|+++||+++|+   
T Consensus        32 ~~veg~ctg~~Gyvi~vt~ld~Ig~g~I~~~~G~v~FpVky~av~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~ssh  111 (170)
T KOG3298|consen   32 AEVEGKCTGKYGYVIAVTTLDNIGEGRIRPGTGFVTFPVKYKAVTFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSH  111 (170)
T ss_pred             HHhhccccccccEEEEEEEhhhccCCccccCCceEEEEEEEEEEEEeecCCcEEEEEEEEEeeeeEEEeccceEeeeecc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999   


Q ss_pred             EcCCCceecCCCC-ceEEcCCceEEEcCCCeEEEEEEEEEEccCCeEEEEEcccccc
Q 032315           79 LIPDDMELQTGDL-PSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARREVGKQR  134 (143)
Q Consensus        79 ~lp~~~~fd~~~~-~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ai~~~~~~~~  134 (143)
                      ++|++++|+++++ ++|+.+|.. .|++|++||++|++++|+.++++|+|+|=|++-
T Consensus       112 l~ppd~~f~p~~n~P~f~~~d~s-~I~~~~~VR~kiigtr~~~~~i~algtl~~D~L  167 (170)
T KOG3298|consen  112 LKPPDYEFDPGENPPNFQTEDES-VIQKGVEVRLKIIGTRVDETEIFALGTLKGDYL  167 (170)
T ss_pred             cCCCCcccCCCCCCCcccccccc-eeeeCcEEEEEEEEEEEeeeeEEEEEEecCccc
Confidence            8899999999875 778877654 999999999999999999999999999998863

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

Probab=100.00  E-value=4.9e-39  Score=248.16  Aligned_cols=128  Identities=20%  Similarity=0.354  Sum_probs=118.6

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC---   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---   78 (143)
                      ++|||||++++|+||+++|+.++++|+|.||||++||+|+||||+|+||+|||++|+|++++++|+|+++||+|+|+   
T Consensus        32 ~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~~~G~fV~igp~dglvh~s  111 (183)
T COG1095          32 EKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVS  111 (183)
T ss_pred             HHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEeccccEEEEEEEEEeecceEEEeccccccccHh
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999   


Q ss_pred             EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC---eEEEEEcc
Q 032315           79 LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE---IEKARREV  130 (143)
Q Consensus        79 ~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~---~~ai~~~~  130 (143)
                      |++|+ +.||++ +|.|.++++++++++||.||+||+++++++.+   ..+.++|-
T Consensus       112 qi~dd~~~~d~~-~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~~I~lTmr  166 (183)
T COG1095         112 QIMDDYIDYDEK-NKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMR  166 (183)
T ss_pred             hccCcccccCcc-cceeeecccceEEecCCEEEEEEEEEecccCccccceEEEEec
Confidence            88887 445555 68999999999999999999999999998864   77777664

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

Probab=100.00  E-value=5.1e-34  Score=220.02  Aligned_cols=130  Identities=16%  Similarity=0.203  Sum_probs=113.7

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC---   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---   78 (143)
                      ++|||||++++||||+++||.++++|+|.||||+++|+|+|||++|||++||+++|+|++++++|+|+++||++.++   
T Consensus        32 ~~~~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~  111 (179)
T TIGR00448        32 EKFEGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPELGEIVEGEVIEIVEFGAFVSLGPFDGLFHVS  111 (179)
T ss_pred             HHhcCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEeccCCCEEEEEEEEEEeeEEEEEeCCceEEEEcH
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999988555   


Q ss_pred             -EcCCCceecCCC-CceEEcCCceEEEcCCCeEEEEEEEEEEccC---CeEEEEEccccc
Q 032315           79 -LIPDDMELQTGD-LPSYTTSDGSVKIQKDCELWLKIIGTQVDVT---EIEKARREVGKQ  133 (143)
Q Consensus        79 -~lp~~~~fd~~~-~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~---~~~ai~~~~~~~  133 (143)
                       .+|+++.||+++ .|.|  ++++.+++.|+.||+||.++++++.   .....++|-.++
T Consensus       112 ~l~~~~~~~d~~~~~~~~--~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~~I~lt~k~~~  169 (179)
T TIGR00448       112 QVTDDYCYYDPKESALIG--KETKKVLDEGDKVRARIVALSLKDRRPEGSKIGLTMRQPL  169 (179)
T ss_pred             HhCCCceEEccccceEEE--ccCCeEEcCCCEEEEEEEEEEccCCCCCcceEEEEeccCc
Confidence             567778899876 4555  5667999999999999999998543   233466665444

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

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

Probab=100.00  E-value=1.5e-34  Score=222.58  Aligned_cols=130  Identities=14%  Similarity=0.271  Sum_probs=115.3

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccc-cEEEE--
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC--   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI--   78 (143)
                      +++-+|+++|+|||||++||+++++|+|.||||+++.+|.||++|||||.|||+.|+|++|+++|+++++|| .||||  
T Consensus        32 ~k~anKvl~nvGLCI~vyDi~~v~e~~v~pGDGas~~~V~FR~vVFrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~  111 (202)
T KOG3297|consen   32 RKLANKVLPNVGLCICVYDILEVEEGIVLPGDGASYARVWFRVVVFRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPK  111 (202)
T ss_pred             HHHHhhhcccccEEEEEeEeeeecceEEecCCCceEEEEEEEEEEEecccceEEEEEeecCCccceEEEEEeeeceeech
Confidence            356789999999999999999999999999999999999999999999999999999999999999999998 66999  


Q ss_pred             -EcCCCceecCCC-CceEEcC-----CceEEEcCCCeEEEEEEEEEEcc-CCeEEEEEccc
Q 032315           79 -LIPDDMELQTGD-LPSYTTS-----DGSVKIQKDCELWLKIIGTQVDV-TEIEKARREVG  131 (143)
Q Consensus        79 -~lp~~~~fd~~~-~~~~~~~-----~~~~~i~~g~~VR~RV~~v~~~~-~~~~ai~~~~~  131 (143)
                       .||+++.|++++ .|.|.++     .+++|++.|++|||||.+++|.. +...+-..++|
T Consensus       112 ~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e~f~d~~p~~~~~~~t~  172 (202)
T KOG3297|consen  112 EMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDESFVDVSPEGNSTAITG  172 (202)
T ss_pred             hhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeeecccccCcccccccccc
Confidence             999999999887 5999986     57899999999999999999833 33333333444

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

Probab=100.00  E-value=7.8e-33  Score=214.13  Aligned_cols=131  Identities=18%  Similarity=0.215  Sum_probs=115.5

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC---   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---   78 (143)
                      ++|||||++++||||+++||.++++|+|.||||+++|+|+|||++|+|++||+++|+|++++++|+|+++||.+.|+   
T Consensus        32 ~~~~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~  111 (187)
T PRK08563         32 EKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEVVEVVEFGAFVRIGPVDGLLHIS  111 (187)
T ss_pred             HHhhCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEeccCCCEEEEEEEEEEccEEEEEEeCceEEEEcH
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999888   


Q ss_pred             EcC-CCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe--EEEE-Eccccc
Q 032315           79 LIP-DDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI--EKAR-REVGKQ  133 (143)
Q Consensus        79 ~lp-~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~--~ai~-~~~~~~  133 (143)
                      +++ +++.||+++. .|..++.+.+++.|+.||+||.+++++..+.  .+|+ +|-+++
T Consensus       112 ~l~~~~~~~d~~~~-~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~~I~ls~~~~~  169 (187)
T PRK08563        112 QIMDDYISYDPKNG-RLIGKESKRVLKVGDVVRARIVAVSLKERRPRGSKIGLTMRQPG  169 (187)
T ss_pred             HcCCCceEEccccc-eEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCCEEEEEecCCC
Confidence            555 4588998853 5666677899999999999999999987654  3444 665553

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

Probab=99.90  E-value=4.5e-23  Score=143.13  Aligned_cols=82  Identities=46%  Similarity=0.690  Sum_probs=76.4

Q ss_pred             CCCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCC-CCceEEcCCceEEEcCCCeEEEEEEEEEEccCCeEEE
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTG-DLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKA  126 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~-~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ai  126 (143)
                      +|||++|+|++++++|+|+++||+++|+   ++|+++.|+++ +.|+|.. +++++|++|+.|||||.+++|++++++|+
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~-~~~~~i~~g~~VR~rV~~v~~~~~~~~~i   79 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTS-NEDIVIKKDTEVRLKIIGTRVDATDIFAI   79 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeC-CCcEEECCCCEEEEEEEEEEEccCceEEE
Confidence            6999999999999999999999999999   99999999985 5789974 46899999999999999999999999999


Q ss_pred             EEccccc
Q 032315          127 RREVGKQ  133 (143)
Q Consensus       127 ~~~~~~~  133 (143)
                      |+|-+++
T Consensus        80 gt~~~~~   86 (88)
T cd04462          80 GTIKDDY   86 (88)
T ss_pred             EEccCCC
Confidence            9999886

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=99.83  E-value=8.3e-20  Score=133.85  Aligned_cols=71  Identities=17%  Similarity=0.303  Sum_probs=60.9

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCC-CceEEc-CCceEEEcCCCeEEEEEEEEEEc
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGD-LPSYTT-SDGSVKIQKDCELWLKIIGTQVD  119 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~-~~~~~~-~~~~~~i~~g~~VR~RV~~v~~~  119 (143)
                      ||+|||+.|+|++++++|+++++|| .||||   +||+++.||+++ .|.|.+ ++++++++.|++|||||.+++|.
T Consensus         1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f~   77 (122)
T PF08292_consen    1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIFP   77 (122)
T ss_dssp             --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE-
T ss_pred             CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEEe
Confidence            8999999999999999999999998 66999   999999999886 599999 88899999999999999999993

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

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

Probab=99.78  E-value=3.3e-19  Score=121.84  Aligned_cols=50  Identities=22%  Similarity=0.382  Sum_probs=48.7

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecC
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFK   51 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~   51 (143)
                      ++||||+++++|+||+++|+.++++|+|.||||+++|+|+|||++||||+
T Consensus        31 ~ky~gkv~~~~Gl~v~v~di~~i~eG~I~~gdG~~~~~V~Fr~lvFrPf~   80 (80)
T cd04330          31 KKYANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV   80 (80)
T ss_pred             HHhCCcEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEECCC
Confidence            58999999999999999999999999999999999999999999999985

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.

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

Probab=99.77  E-value=4e-19  Score=121.41  Aligned_cols=50  Identities=48%  Similarity=0.886  Sum_probs=48.7

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecC
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFK   51 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~   51 (143)
                      +++||||.+++|+|||++|+.++++|+|.||||+++|+|+|||++||||+
T Consensus        31 ~~~egk~~~~~G~iv~v~di~~i~~G~I~~gdG~~~~~V~F~aivfrPf~   80 (80)
T cd04329          31 EEVEGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPFK   80 (80)
T ss_pred             HHhCCcCcCceeEEEEEEEeeEecCcEEEcCCCCEEEEEEEEEEEEEccC
Confidence            58999999999999999999999999999999999999999999999996

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=99.77  E-value=6.8e-19  Score=120.20  Aligned_cols=50  Identities=30%  Similarity=0.457  Sum_probs=48.6

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecC
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFK   51 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~   51 (143)
                      +++||||++++|+||+++|+.++++|+|.||||+++|+|+|||++||||+
T Consensus        31 ~k~~gkv~~~~G~~v~v~di~~i~~G~I~~gdG~~~~~V~F~~ivFrPf~   80 (80)
T cd00655          31 EKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFKPFS   80 (80)
T ss_pred             HHhCCeEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEEcCC
Confidence            58999999999999999999999999999999999999999999999985

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

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

Probab=99.73  E-value=3.2e-18  Score=116.99  Aligned_cols=49  Identities=29%  Similarity=0.441  Sum_probs=47.8

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeec
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPF   50 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf   50 (143)
                      +++||||++++|+||+++||.++++|+|.||||+++|+|+|||++|||.
T Consensus        31 ~~~egk~~~~~G~iv~v~di~~i~eG~I~~gdG~~~~~V~F~~ivFrP~   79 (80)
T cd04331          31 EKYEGRLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVFKPE   79 (80)
T ss_pred             HHhcCcCcCCCCEEEEEEEEEEecCCEEEcCCCCEEEEEEEEEEEEecC
Confidence            6899999999999999999999999999999999999999999999996

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=99.42  E-value=2.2e-13  Score=89.82  Aligned_cols=46  Identities=30%  Similarity=0.461  Sum_probs=43.7

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEE
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVF   47 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvF   47 (143)
                      +++|||+.+++|+||+++||..+++|+|.+|||+++|+|+|+|++|
T Consensus        25 ~~~~~k~~~~~G~~i~v~~i~~~~~g~I~~~~g~~~~~V~f~~lvF   70 (70)
T PF03876_consen   25 DKYEGKYIPELGVVIAVTDIKEISEGKIIPGDGFVYFKVTFRALVF   70 (70)
T ss_dssp             HHHTTEEETTTEEEEEEEEEEEESCEEE-TTTSSEEEEEEEEEEEE
T ss_pred             HHHhCcCcCCceEEEEEeeeeEecCcEEECCCCCEEEEEEEEEEEC
Confidence            5789999999999999999999999999999999999999999998

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 ....

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

Probab=98.86  E-value=4.9e-09  Score=72.44  Aligned_cols=45  Identities=18%  Similarity=0.303  Sum_probs=41.9

Q ss_pred             EEeCCe-eEEEEEeecceecc--eeEEcCCccEEEEEEEEEEEEeecC
Q 032315            7 TCSGRH-GFAVAITGAESIGK--GLIRNGTVLVTFLVRCQCIVFRPFK   51 (143)
Q Consensus         7 ~~~~~~-GliI~i~dI~~i~e--G~I~~gdG~~~~~V~F~~lvFrPf~   51 (143)
                      |+.+++ |+|++.+|+..+++  |+|.+++|.++++|+||++||||+.
T Consensus        42 ky~~~l~Gv~l~~~di~~~~~~~~~i~~~~~~~~~~V~~~~lVFrP~~   89 (89)
T cd04328          42 KYSPKLKGVVLAYSNIKLLEGELAKIVDDSPFIFVWISADFLVFRPKI   89 (89)
T ss_pred             hhcccCCeEEEEecceEeccccceeeeCCCcEEEEEEEEEEEEEecCC
Confidence            677889 99999999988867  9999999999999999999999984

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

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

Probab=98.85  E-value=3.7e-08  Score=65.63  Aligned_cols=71  Identities=14%  Similarity=0.245  Sum_probs=57.5

Q ss_pred             CCCEEEEEEEEEecccEEEEccc--cEEEE---EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      .|++++|+|++++++|+|+.+++  .++++   .++++ +.||+.. +.+..+.....++.||.|++||.++......
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~-~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~   77 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEEN-HALVGERTGKVFRLGDKVKVRVVRVDLDRRK   77 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccc-eEEEeccCCCEEcCCCEEEEEEEEeccccCE
Confidence            38999999999999999999997  77888   67654 6777664 4566666678999999999999999864444

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.

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

Probab=98.64  E-value=3e-07  Score=64.18  Aligned_cols=79  Identities=13%  Similarity=0.122  Sum_probs=61.6

Q ss_pred             CEEEEEEEEEecccEEEEccccEEEE---EcCC-CceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC--eEEE
Q 032315           53 EILGAGVTMVNKMGFLAEAGAVQIFC---LIPD-DMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE--IEKA  126 (143)
Q Consensus        53 EVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~-~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~--~~ai  126 (143)
                      |++.|+|+++++.|+|+.+++.++++   .+++ .+.|++.. .+|.+++.+..|+.||.|+++|.++..+...  +..+
T Consensus         1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i   79 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKN-KRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI   79 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhh-eeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence            68999999999999999999888888   5554 46677664 4788877778999999999999999876543  4444


Q ss_pred             E-Ecccc
Q 032315          127 R-REVGK  132 (143)
Q Consensus       127 ~-~~~~~  132 (143)
                      + ++-++
T Consensus        80 ~ls~k~~   86 (99)
T cd04460          80 GLTMRQP   86 (99)
T ss_pred             EEEEecC
Confidence            4 44433

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.

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

Probab=98.62  E-value=1.5e-07  Score=61.65  Aligned_cols=65  Identities=23%  Similarity=0.346  Sum_probs=51.9

Q ss_pred             eecCCCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      +|..|+++.|+|+++++.|+|+.+| ..++||   +++++          + .++....++.|+.|++||.++..+.+.+
T Consensus         1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~----------~-~~~~~~~~~~G~~v~v~v~~vd~~~~~i   69 (74)
T PF00575_consen    1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDD----------R-IDDPSEVYKIGQTVRVKVIKVDKEKGRI   69 (74)
T ss_dssp             -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSS----------E-ESSSHGTCETTCEEEEEEEEEETTTTEE
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCc----------c-ccccccccCCCCEEEEEEEEEECCCCeE
Confidence            5789999999999999999999999 799999   44322          1 2233457899999999999998876654

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 ....

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

Probab=98.29  E-value=3.7e-06  Score=56.12  Aligned_cols=66  Identities=15%  Similarity=0.172  Sum_probs=48.9

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceE-Ec-CCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSY-TT-SDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~-~~-~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .|+++.|+|++++++|+|++++| .++||.+.+ +      .|.| .. ++-...+++|+.|++||+++.-+.+.+
T Consensus         3 ~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~-l------s~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i   71 (74)
T cd05705           3 EGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQN-V------TKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLV   71 (74)
T ss_pred             CCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHH-c------cCccccChhhHhcccCCCCEEEEEEEEEECCCCEE
Confidence            68999999999999999999998 889993210 0      1112 11 111367899999999999998765543

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

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

Probab=98.19  E-value=1.4e-05  Score=50.33  Aligned_cols=61  Identities=16%  Similarity=0.280  Sum_probs=47.6

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      .|+++.|+|.++++.|+++.+++ .++|+   .++++.           .++....++.|+.++++|..+..+...
T Consensus         2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~-----------~~~~~~~~~~G~~v~~~V~~~~~~~~~   66 (72)
T smart00316        2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEEKGR   66 (72)
T ss_pred             CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccc-----------cCCHHHeecCCCEEEEEEEEEeCCCCE
Confidence            58999999999999999999985 88888   443221           122335689999999999999875543

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

Probab=98.17  E-value=1.3e-05  Score=51.63  Aligned_cols=61  Identities=11%  Similarity=0.173  Sum_probs=46.5

Q ss_pred             CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |+++.|+|++++++|+|+.+.+ .+.++   .++          |.....+....++.|+.|++||.++..+...
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~----------~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~   65 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDIS----------WTQRVRHPSEIYKKGQEVEAVVLNIDVERER   65 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCC----------CccccCChhhEECCCCEEEEEEEEEECCcCE
Confidence            6899999999999999999976 78888   332          1111223346789999999999998866544

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

>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=98.15  E-value=1.2e-05  Score=52.10  Aligned_cols=61  Identities=7%  Similarity=0.211  Sum_probs=47.4

Q ss_pred             CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      |++++|+|+++++.|+++++++ .++||   .++++.         +  ++....++.|+.+.+||.++..+.+.+
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~---------~--~~~~~~~~~Gd~i~~~V~~id~~~~~i   65 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVR---------L--KHPEKKFKPGLKVKCRVLSVEPERKRL   65 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCcc---------c--cCHHHcCCCCCEEEEEEEEEECCCCEE
Confidence            6899999999999999999975 88988   443220         1  122357899999999999988766553

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.

>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=98.12  E-value=2.2e-05  Score=51.26  Aligned_cols=62  Identities=24%  Similarity=0.165  Sum_probs=47.5

Q ss_pred             cCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           50 FKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        50 f~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      .+|+++.|+|+++++.|+++++++ .++|+   .++++  |+.         +-...++.||.++++|.++..+...
T Consensus         2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~--~~~---------~~~~~~~~Gd~v~~~V~~~d~~~~~   67 (73)
T cd05706           2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDD--YSE---------ALPYKFKKNDIVRACVLSVDVPNKK   67 (73)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCc--ccc---------ccccccCCCCEEEEEEEEEeCCCCE
Confidence            379999999999999999999986 88988   44322  111         1135689999999999998775443

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

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

Probab=98.09  E-value=2.3e-05  Score=51.67  Aligned_cols=63  Identities=21%  Similarity=0.306  Sum_probs=46.0

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccc--cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGA--VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD  119 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~  119 (143)
                      |-.|++++|+|++++++|+|+.+..  .+.|+.+.+ +      .|. ..++.+..++.||.|++||.++..+
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~se-l------~~~-~~~~~~~~~~~Gd~v~vkv~~vd~~   65 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSH-M------SSC-RVDDPSEVVDVGEKVWVKVIGREMK   65 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchh-h------CCC-cccCHhhEECCCCEEEEEEEEECCC
Confidence            5689999999999999999999932  578882210 0      111 1123346789999999999888764

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.

>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=98.04  E-value=1.9e-05  Score=51.10  Aligned_cols=60  Identities=12%  Similarity=0.101  Sum_probs=45.9

Q ss_pred             CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |+++.|+|+++++.|+|+++++ .+.|+   +|+++..+           +-...+++|+.+++||.++..+...
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~-----------~~~~~~~~G~~i~v~v~~~d~~~~~   64 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIK-----------DPEEHFRVGQVVKVKVLSCDPEQQR   64 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcC-----------CHHHcccCCCEEEEEEEEEcCCCCE
Confidence            6899999999999999999975 88888   45432111           1125689999999999998765544

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.

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

Probab=98.02  E-value=2.7e-05  Score=50.32  Aligned_cols=60  Identities=17%  Similarity=0.178  Sum_probs=46.2

Q ss_pred             CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |+++.|+|+++.+.|+|+++++ .++|+   +++++.           .++....+++|+.+++||.++......
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~-----------~~~~~~~~~~Gd~v~~~v~~~d~~~~~   64 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSY-----------LKDWKKRFKVGQLVKGKIVSIDPDNGR   64 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchh-----------hcCHhhccCCCCEEEEEEEEEeCCCCE
Confidence            6899999999999999999976 88888   554321           112235689999999999988765443

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

>TIGR02063 RNase_R ribonuclease R

Probab=98.02  E-value=3.2e-05  Score=70.72  Aligned_cols=78  Identities=13%  Similarity=0.199  Sum_probs=62.9

Q ss_pred             EEEeecCCCEEEEEEEEEecccEEEEccc--cEEEE---EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           45 IVFRPFKGEILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        45 lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      .-.++..|++.+|+|++++++|+|+.+.+  .+++|   .|+++ +.||+... .+..+..+..++.||.|++||.++..
T Consensus       621 ~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~-~l~g~~~~~~~~lGd~V~Vkv~~vd~  699 (709)
T TIGR02063       621 EYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGL-ALVGERTGKVFRLGDRVKVRVVKADL  699 (709)
T ss_pred             HhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccce-EEEeccCCcEECCCCEEEEEEEEEec
Confidence            34567889999999999999999999975  78888   77655 55776643 46666667889999999999999987


Q ss_pred             ccCCe
Q 032315          119 DVTEI  123 (143)
Q Consensus       119 ~~~~~  123 (143)
                      ....+
T Consensus       700 ~~~~I  704 (709)
T TIGR02063       700 DTGKI  704 (709)
T ss_pred             ccCeE
Confidence            66554

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.

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

Probab=98.00  E-value=3.9e-05  Score=69.74  Aligned_cols=77  Identities=8%  Similarity=0.157  Sum_probs=63.5

Q ss_pred             EEeecCCCEEEEEEEEEecccEEEEcc-c-cEEEE---EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315           46 VFRPFKGEILGAGVTMVNKMGFLAEAG-A-VQIFC---LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD  119 (143)
Q Consensus        46 vFrPf~gEVv~G~V~~v~~~Gi~v~iG-p-~~ifI---~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~  119 (143)
                      .++...|++.+|+|+++++.|+|+.+. + .+++|   +|+++ +.||+... .+..++++..++.||.|++||.++...
T Consensus       567 yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~-~l~g~~~~~~~~lGD~V~Vki~~vd~~  645 (654)
T TIGR00358       567 YLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKM-ALIGKGTGKVYRIGDRVTVKLTEVNME  645 (654)
T ss_pred             hhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEecccc-EEEeccCCcEECCCCEEEEEEEEEecc
Confidence            355677999999999999999999996 5 88888   78765 67887753 566667778999999999999999877


Q ss_pred             cCCe
Q 032315          120 VTEI  123 (143)
Q Consensus       120 ~~~~  123 (143)
                      ...+
T Consensus       646 ~~~I  649 (654)
T TIGR00358       646 TRSI  649 (654)
T ss_pred             cCeE
Confidence            6654

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.

>PRK11642 exoribonuclease R; Provisional

Probab=97.98  E-value=4.1e-05  Score=71.30  Aligned_cols=77  Identities=8%  Similarity=0.139  Sum_probs=63.1

Q ss_pred             EEEeecCCCEEEEEEEEEecccEEEEccc--cEEEE---EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           45 IVFRPFKGEILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        45 lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      -..+...|++++|+|++++++|+||.+..  .+++|   .|+++ +.||+... .+..++++..++.||.|++||..+..
T Consensus       637 ~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~-~L~g~~~~~~~~lGD~V~VkV~~vD~  715 (813)
T PRK11642        637 DFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQ-RLIGESSGQTYRLGDRVEVRVEAVNM  715 (813)
T ss_pred             hhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchhe-EEecccCCcEECCCCEEEEEEEEeec
Confidence            34566789999999999999999999964  88888   77766 56776643 56677777899999999999999988


Q ss_pred             ccCC
Q 032315          119 DVTE  122 (143)
Q Consensus       119 ~~~~  122 (143)
                      ....
T Consensus       716 ~~rk  719 (813)
T PRK11642        716 DERK  719 (813)
T ss_pred             CCCe
Confidence            7765

>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=97.98  E-value=4.8e-05  Score=49.63  Aligned_cols=62  Identities=19%  Similarity=0.316  Sum_probs=47.5

Q ss_pred             CCCEEEEEEEEEecccEEEEcc--ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           51 KGEILGAGVTMVNKMGFLAEAG--AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iG--p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .|+++.|+|+++++.|+|+.+.  ..++++   .++++.           ..+....+++||.|++||..+..+...+
T Consensus         2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~-----------~~~~~~~~~~Gd~v~v~i~~vd~~~~~i   68 (77)
T cd05708           2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNR-----------VADASKLFRVGDKVRAKVLKIDAEKKRI   68 (77)
T ss_pred             CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCc-----------cCCHhHeecCCCEEEEEEEEEeCCCCEE
Confidence            5899999999999999999997  478888   443211           1123467899999999999988765543

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.

>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.97  E-value=3.4e-05  Score=51.19  Aligned_cols=62  Identities=18%  Similarity=0.084  Sum_probs=46.6

Q ss_pred             CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |.++.|+|+++++.|+|++++| .+.||   .++++...  .       ++-...+++|+.|.+||+++..+.+.
T Consensus         1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~--~-------~~~~~~~~vG~~v~~kV~~id~~~~~   66 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSV--L-------EHPEKKFPIGQALKAKVVGVDKEHKL   66 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCcccc--c-------cCHHHhCCCCCEEEEEEEEEeCCCCE
Confidence            6789999999999999999998 88998   44321000  1       11235689999999999988776554

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 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=97.93  E-value=0.0001  Score=47.90  Aligned_cols=63  Identities=16%  Similarity=0.110  Sum_probs=47.5

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .|+++.|+|++++++|+|+.+.+ .++|+   .++.    +..      ..+....++.|+.|+++|.++..+...+
T Consensus         3 ~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~----~~~------~~~~~~~~~~Gd~v~v~v~~id~~~~~i   69 (72)
T cd05689           3 EGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDW----TNK------NIHPSKVVSLGDEVEVMVLDIDEERRRI   69 (72)
T ss_pred             CCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccC----ccc------ccCcccEeCCCCEEEEEEEEeeCCcCEE
Confidence            68999999999999999999976 78888   4421    100      1133467999999999999988655443

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

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

Probab=97.92  E-value=4.1e-05  Score=51.48  Aligned_cols=64  Identities=16%  Similarity=0.206  Sum_probs=49.5

Q ss_pred             ecCCCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      +..|+++.|+|++++++|+|+.++ ..++|+   .++++          + ..+-...++.|+.|++||.++..+.+.+
T Consensus        12 ~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~----------~-~~~~~~~~~~Gd~v~vkV~~id~~~~~i   79 (83)
T cd04461          12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDE----------F-VTDPSFGFKKGQSVTAKVTSVDEEKQRF   79 (83)
T ss_pred             CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcc----------c-ccCHHHhcCCCCEEEEEEEEEcCCCCEE
Confidence            568999999999999999999996 488988   44321          1 1133467899999999999988765443

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

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

Probab=97.92  E-value=7.8e-05  Score=47.29  Aligned_cols=64  Identities=17%  Similarity=0.248  Sum_probs=46.2

Q ss_pred             CCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      .|+++.|+|+++++.|+++.++..++|+...+ .      .|.+ ..+....++.||.|+++|.++....+.
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~~~~g~l~~~e-~------~~~~-~~~~~~~~~~Gd~v~v~i~~vd~~~~~   64 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISD-M------SWGR-VKHPSEVVNVGDEVEVKVLKIDKERKR   64 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHH-C------CCcc-ccCHhHEECCCCEEEEEEEEEECCCCE
Confidence            48999999999999999999998888882211 0      0111 112235689999999999998765443

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.

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

Probab=97.91  E-value=6.6e-05  Score=48.56  Aligned_cols=60  Identities=23%  Similarity=0.267  Sum_probs=46.0

Q ss_pred             CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |+++.|+|+++++.|+++.+++ .+.|+   .+.++.           .++....+++|+.+++||..+......
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~-----------~~~~~~~~~~Gd~v~~~v~~~d~~~~~   64 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDR-----------VEDATERFKVGDEVEAKITNVDRKNRK   64 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCcc-----------ccCHHHccCCCCEEEEEEEEEeCCCCE
Confidence            6899999999999999999964 88888   333211           112235689999999999998876543

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.

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

Probab=97.84  E-value=8.8e-05  Score=46.85  Aligned_cols=60  Identities=20%  Similarity=0.178  Sum_probs=45.2

Q ss_pred             CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |+++.|+|++++++|+|+.+++ .++|+   .++++        + +  .+....++.|+.+++||..+..+...
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~--------~-~--~~~~~~~~~Gd~v~v~i~~vd~~~~~   64 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADR--------F-V--SHPSDVVSVGDIVEVKVISIDEERGR   64 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCc--------c-c--cCHHHhcCCCCEEEEEEEEEECCCCE
Confidence            6889999999999999999986 77887   33321        1 1  12235689999999999998865443

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

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

Probab=97.80  E-value=8.7e-05  Score=46.92  Aligned_cols=56  Identities=16%  Similarity=0.283  Sum_probs=43.1

Q ss_pred             CCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           52 GEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      |+++.|+|++++++|+|+.++ +.++|+   .++++.          . .+....++.|+.+++||..+..
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~----------~-~~~~~~~~~Gd~v~v~v~~~~~   60 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKR----------V-KDVKDVLKEGDKVKVKVLSIDA   60 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcc----------c-CCHHHccCCCCEEEEEEEEECC
Confidence            689999999999999999997 488888   443221          1 1122568999999999988765

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

>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.78  E-value=0.00019  Score=47.88  Aligned_cols=53  Identities=19%  Similarity=0.190  Sum_probs=42.8

Q ss_pred             CCCEEEEEEEEEecccEEEEccc--cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV  120 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~  120 (143)
                      +|+++.|.|+++.++|+|+++|.  ++.|+   .++            |.     ..+++|+.+.+||.++.-+.
T Consensus         4 ~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~------------~~-----~~~~~Gq~v~~~V~~vd~~~   61 (74)
T cd05694           4 EGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAG------------NF-----SKLKVGQLLLCVVEKVKDDG   61 (74)
T ss_pred             CCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCC------------cc-----cccCCCCEEEEEEEEEECCC
Confidence            68999999999999999999984  67887   221            11     56899999999999876443

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 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=97.74  E-value=0.00019  Score=46.87  Aligned_cols=63  Identities=13%  Similarity=0.101  Sum_probs=47.0

Q ss_pred             ecCCCEEEEEEEEEecccEEEEcc--c-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAG--A-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iG--p-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |-.|+++.|+|+++.++|+|+.+.  + .++++   ++.++          + ..+-...++.||.|++||.++....+.
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~----------~-~~~~~~~~~~Gd~v~vkv~~~d~~~~~   69 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRR----------R-IRSIRKLVKVGRKEVVKVIRVDKEKGY   69 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCc----------c-cCCHHHeeCCCCEEEEEEEEEECCCCE
Confidence            567999999999999999999995  2 67887   33211          1 112245689999999999988775443

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

>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide

Probab=97.72  E-value=0.00055  Score=45.44  Aligned_cols=56  Identities=16%  Similarity=0.217  Sum_probs=43.0

Q ss_pred             CCEEEEEEEEEecccEEEEcc----ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315           52 GEILGAGVTMVNKMGFLAEAG----AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iG----p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      |+++.|+|+++.++|+|+.++    +.+.|+   .++++          |..++....++.|+.|+++|.++.
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~----------~~~~~~~~~~~~Gd~v~v~v~~vd   63 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFE----------GRVANPSDVVKRGQKVKVKVISIQ   63 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCC----------CCcCChhheeCCCCEEEEEEEEEe
Confidence            689999999999999999998    367887   33211          111233467899999999999987

The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.

>PRK08582 hypothetical protein; Provisional

Probab=97.69  E-value=0.00023  Score=53.08  Aligned_cols=59  Identities=19%  Similarity=0.201  Sum_probs=45.7

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      .-.|++++|+|++++++|+||.+++ .+++|   .+.++          |. .+-...+++||.|+++|+++..
T Consensus         3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~----------~v-~~~~~~l~vGD~VkvkV~~id~   65 (139)
T PRK08582          3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADN----------YV-KDINDHLKVGDEVEVKVLNVED   65 (139)
T ss_pred             CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcc----------cc-cccccccCCCCEEEEEEEEECC
Confidence            3479999999999999999999987 77887   33321          11 1223578999999999999875

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

Probab=97.68  E-value=0.00016  Score=58.19  Aligned_cols=75  Identities=23%  Similarity=0.340  Sum_probs=58.8

Q ss_pred             eeEEEEEeeccee-cceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEc-cccEEEE---EcCCCcee
Q 032315           12 HGFAVAITGAESI-GKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEA-GAVQIFC---LIPDDMEL   86 (143)
Q Consensus        12 ~GliI~i~dI~~i-~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~i-Gp~~ifI---~lp~~~~f   86 (143)
                      .|++++.-+|.-. ..++|.+.++..+.+++-...||+|..|.+|+|.|-.++...|-+-+ |-+..-|   ++|.+++|
T Consensus        67 ~GivLgydnIKvLg~~aki~~D~pf~hlwi~adfyVf~Pk~Gd~LeG~Vn~vS~sHIglLIhg~FNASIpk~nip~dw~f  146 (253)
T KOG4134|consen   67 DGIVLGYDNIKVLGQTAKIRADDPFMHLWINADFYVFRPKAGDILEGVVNHVSRSHIGLLIHGVFNASIPKTNIPADWEF  146 (253)
T ss_pred             CceEEeecceEeeccccceecCCCceEEEEeeeEEEECCCCCCeeeeeeeecchhhhceeehhhhhccCCCCCCccceee
Confidence            3677787777655 46999999999999999999999999999999999999988776554 4444444   45555544

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

Probab=97.67  E-value=8.7e-05  Score=50.04  Aligned_cols=68  Identities=10%  Similarity=0.101  Sum_probs=47.7

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      |.|-+|+++.|+|+++++.|+++.+++ .++++.+.+ +..+.-+.  + .++-...+++||.+++||.+..-
T Consensus         2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se-~~~~~~~~--~-~~~~~~~l~vGd~i~~~V~~~~~   70 (86)
T cd05789           2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSE-VNLPRTDE--D-ELNMRSYLDEGDLIVAEVQSVDS   70 (86)
T ss_pred             CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHH-ccCCCCcc--c-hHHHHhhCCCCCEEEEEEEEECC
Confidence            578999999999999999999999985 888882210 00000001  1 12223568999999999998743

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".

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

Probab=97.66  E-value=0.00025  Score=46.20  Aligned_cols=57  Identities=16%  Similarity=0.177  Sum_probs=42.9

Q ss_pred             CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceE-EcCCceEEEcCCCeEEEEEEEEEE
Q 032315           52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSY-TTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~-~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      |+++.|+|+++++.|+++++++ .++++   .+.+          .| ..++-...+++|+.|++||+++.-
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~----------~~~~~~~~~~~~~~Gd~i~~kVl~~d~   62 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFD----------EWPDGKNPLSKFKIGQKIKARVIGGHD   62 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhcc----------ccccccChhHhCCCCCEEEEEEEEEeC
Confidence            6899999999999999999976 88888   3321          12 111223557999999999998754

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

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

Probab=97.65  E-value=0.00029  Score=45.50  Aligned_cols=57  Identities=18%  Similarity=0.254  Sum_probs=42.8

Q ss_pred             CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315           52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD  119 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~  119 (143)
                      |+++.|+|.++++.|++++++. .+.++   .+.++          +. ++-...+++||.++++|.++.-+
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~----------~~-~~~~~~~~~Gd~i~~~i~~~~~~   61 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDD----------PI-ENGEDEVKVGDEVEVYVLRVEDE   61 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCcc----------cc-CCHhHcCCCCCEEEEEEEEEECC
Confidence            7899999999999999999975 77887   23211          11 11234579999999999998743

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.

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

Probab=97.65  E-value=0.00029  Score=44.69  Aligned_cols=56  Identities=16%  Similarity=0.180  Sum_probs=42.8

Q ss_pred             CCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           52 GEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      |+++.|+|+++.++|+|+.++. .+.|+   .++++          +. ......++.||.|+++|.++..
T Consensus         1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~----------~~-~~~~~~~~~Gd~v~v~v~~~d~   60 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDE----------RV-EKVEDVLKVGDEVKVKVIEVDD   60 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCc----------cc-cCHHHccCCCCEEEEEEEEECC
Confidence            6889999999999999999976 77888   33211          11 1223578999999999998764

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

>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.64  E-value=0.0004  Score=45.65  Aligned_cols=59  Identities=20%  Similarity=0.201  Sum_probs=44.3

Q ss_pred             CCEEE-EEEEEE-ecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           52 GEILG-AGVTMV-NKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        52 gEVv~-G~V~~v-~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      ||+++ |+|+++ .+.|+|+++.+ .++|+   +++++    ...       .-...+++|+.+.+||.++.-..+
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~----~~~-------~~~~~~~vG~~v~~kV~~id~~~~   65 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDD----KVP-------SDTGPFKAGTTHKARIIGYSPMDG   65 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcc----hhc-------CcccccCCCCEEEEEEEEEeCCCC
Confidence            78999 999999 69999999987 88998   45421    001       112558999999999988765443

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 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK07252 hypothetical protein; Provisional

Probab=97.58  E-value=0.00042  Score=50.53  Aligned_cols=62  Identities=10%  Similarity=0.090  Sum_probs=47.4

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .|+++.|+|++++++|+|+.+.+ .++|+   .|+++.         +  ++-...++.||.|++||.++....+.+
T Consensus         3 vG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~---------~--~~~~~~~~vGD~V~VkI~~iD~~~~ri   68 (120)
T PRK07252          3 IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGF---------I--DNIHQLLKVGEEVLVQVVDFDEYTGKA   68 (120)
T ss_pred             CCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCcc---------c--cChhhccCCCCEEEEEEEEEeCCCCEE
Confidence            58999999999999999999964 88888   443210         1  112356899999999999988765554

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

Probab=97.57  E-value=0.0006  Score=44.23  Aligned_cols=58  Identities=10%  Similarity=0.072  Sum_probs=44.0

Q ss_pred             CCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           52 GEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |.+++|+|+++.+.|+++++- -.+.|+   ++++      ...      . ...+++|+.|.+||+.+..+.+.
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~------~~~------~-~~~~~~G~~i~~kVi~id~~~~~   62 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDP------EKS------S-KSTYKEGQKVRARILYVDPSTKV   62 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCC------ccC------c-ccCcCCCCEEEEEEEEEeCCCCE
Confidence            679999999999999999984 388888   3321      111      1 35689999999999987765544

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

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

Probab=97.55  E-value=0.00027  Score=46.57  Aligned_cols=56  Identities=16%  Similarity=0.112  Sum_probs=42.6

Q ss_pred             CCCEEEEEEEEEec-ccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315           51 KGEILGAGVTMVNK-MGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        51 ~gEVv~G~V~~v~~-~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      .|+++.|+|+++.+ .|+|++++| .+.++   ++.++          |.. +-...+++||.||+||.+..
T Consensus         3 ~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~----------~~~-~~~~~~~~Gd~v~~kV~~~~   63 (72)
T cd05704           3 EGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDS----------YTE-NPLEGFKPGKIVRCCILSKK   63 (72)
T ss_pred             CCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCc----------ccC-CHHHhCCCCCEEEEEEEEec
Confidence            69999999999986 899999988 78888   33321          211 11246799999999998874

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

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

Probab=97.51  E-value=0.00035  Score=46.78  Aligned_cols=62  Identities=18%  Similarity=0.052  Sum_probs=47.2

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD  119 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~  119 (143)
                      |.|.+|.++.|+|++++..++++.++ ..+.++   ++..+          + .++....+++||.+++||..+.-+
T Consensus         2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~----------~-~~~~~~~~~~GD~i~~~V~~~~~~   67 (82)
T cd04454           2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK----------D-KKEIRKSLQPGDLILAKVISLGDD   67 (82)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCc----------c-hHHHHhcCCCCCEEEEEEEEeCCC
Confidence            57999999999999999999999996 578877   22211          0 112234579999999999987553

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".

>PRK08059 general stress protein 13; Validated

Probab=97.47  E-value=0.00055  Score=49.80  Aligned_cols=63  Identities=14%  Similarity=0.132  Sum_probs=47.8

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      .-.|+++.|+|+++++.|+|+.+++ .++++   .++++          +. .+-...+++||.|++||.++......
T Consensus         5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~----------~~-~~~~~~~~vGD~I~vkI~~id~~~~~   71 (123)
T PRK08059          5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHG----------FV-KDIHDFLSVGDEVKVKVLSVDEEKGK   71 (123)
T ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcc----------cc-cCHHHcCCCCCEEEEEEEEEECCCCe
Confidence            4579999999999999999999986 78888   44322          11 12235789999999999998765444

>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain

Probab=97.42  E-value=0.0008  Score=41.40  Aligned_cols=55  Identities=18%  Similarity=0.245  Sum_probs=41.0

Q ss_pred             EEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315           55 LGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV  120 (143)
Q Consensus        55 v~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~  120 (143)
                      +.|+|+++++.|+++.+++ .++|+   .+++..         +  .+....+++|+.|++||.++..+.
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~---------~--~~~~~~~~~G~~v~~~v~~~d~~~   59 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKF---------V--KDPSEVFKVGDEVEVKVLEVDPEK   59 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCcc---------c--cCHhhEeCCCCEEEEEEEEEcCCc
Confidence            4799999999999999984 78888   332110         1  223467899999999999986543

Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.36  E-value=0.00014  Score=66.56  Aligned_cols=88  Identities=15%  Similarity=0.088  Sum_probs=65.0

Q ss_pred             ecceecceeEEcCCccEEEEE--EEEEEEEeecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCce
Q 032315           20 GAESIGKGLIRNGTVLVTFLV--RCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPS   93 (143)
Q Consensus        20 dI~~i~eG~I~~gdG~~~~~V--~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~   93 (143)
                      ||.+-+..+|...++..+.++  .++.++..|.+|+++.|+|+++.++|+|+.+.| .++|+   ++.+.          
T Consensus       585 ~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~----------  654 (684)
T TIGR03591       585 DIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANE----------  654 (684)
T ss_pred             EEecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCC----------
Confidence            344445666666666666555  566677889999999999999999999999977 88888   33211          


Q ss_pred             EEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           94 YTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        94 ~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      + .++-...++.||.|++||.++..
T Consensus       655 ~-v~~~~~~~kvGD~V~VkVi~id~  678 (684)
T TIGR03591       655 R-VEKVEDVLKEGDEVKVKVLEIDK  678 (684)
T ss_pred             c-ccChhhccCCCCEEEEEEEEECC
Confidence            1 12334578999999999998764

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).

>PRK05807 hypothetical protein; Provisional

Probab=97.33  E-value=0.0012  Score=49.11  Aligned_cols=61  Identities=18%  Similarity=0.240  Sum_probs=44.1

Q ss_pred             cCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           50 FKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        50 f~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      -.|+++.|+|+.++++|+||.+.-.+++|.+.+-       .+.|.. +-..++++|+.|+++|..+.-
T Consensus         4 ~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhisei-------s~~~v~-~~~~~~kvGd~V~VkV~~id~   64 (136)
T PRK05807          4 KAGSILEGTVVNITNFGAFVEVEGKTGLVHISEV-------ADTYVK-DIREHLKEQDKVKVKVISIDD   64 (136)
T ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhc-------cccccc-CccccCCCCCEEEEEEEEECC
Confidence            3699999999999999999999546787722110       011211 223568999999999999865

>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain

Probab=97.28  E-value=0.0013  Score=45.32  Aligned_cols=72  Identities=11%  Similarity=0.088  Sum_probs=50.1

Q ss_pred             eecCCCEEEEEEEEEecc--cEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCeE
Q 032315           48 RPFKGEILGAGVTMVNKM--GFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIE  124 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~--Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~  124 (143)
                      +|-.|+++.|+|+++.+.  |+|+++++ .+.|+.+.+- .+..-   .+. ..-...+++||.|.++|..+-++...-.
T Consensus         4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~sei-s~~~~---~~v-~~~~~~~~~Gd~v~VqV~~~~~~~K~~~   78 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDI-LPAYF---KKH-KKIAKLLKEGQEILVQVVKEPIGTKGPR   78 (88)
T ss_pred             cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHc-Cchhc---ccc-CCHHHcCCCCCEEEEEEEEecCCCCCce
Confidence            356899999999999996  99999998 7898833211 01000   000 1113578999999999999877665533

RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th

>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.21  E-value=0.0009  Score=47.15  Aligned_cols=68  Identities=10%  Similarity=0.070  Sum_probs=46.6

Q ss_pred             cCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCC--C-----Cce---EEcCCceEEEcCCCeEEEEEEE
Q 032315           50 FKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTG--D-----LPS---YTTSDGSVKIQKDCELWLKIIG  115 (143)
Q Consensus        50 f~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~--~-----~~~---~~~~~~~~~i~~g~~VR~RV~~  115 (143)
                      ..|.++.|+|+++++.|+++++.+ .++|+   .+.++  |...  +     +..   -...+-...+++|+.||++|++
T Consensus         2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~   79 (100)
T cd05693           2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDA--YTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVS   79 (100)
T ss_pred             CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHH--HHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEE
Confidence            368999999999999999999965 88998   44322  2100  0     000   0011123568999999999999


Q ss_pred             EEEc
Q 032315          116 TQVD  119 (143)
Q Consensus       116 v~~~  119 (143)
                      +.-+
T Consensus        80 ~d~~   83 (100)
T cd05693          80 LDKS   83 (100)
T ss_pred             ccCC
Confidence            8865

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 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease

Probab=97.20  E-value=0.0023  Score=42.56  Aligned_cols=59  Identities=12%  Similarity=0.055  Sum_probs=45.1

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      ..+-.|+.++|+|++++++|+|+.+.+ .++++...+-                ...++.|+.+++||.++ .+.+.
T Consensus        12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~----------------~~~~~iGd~v~v~I~~i-~e~~~   71 (77)
T cd04473          12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL----------------LRDYEVGDEVIVQVTDI-PENGN   71 (77)
T ss_pred             hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhc----------------cCcCCCCCEEEEEEEEE-CCCCc
Confidence            345579999999999999999999976 7777733210                13489999999999998 44333

The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=97.18  E-value=0.00086  Score=56.52  Aligned_cols=64  Identities=9%  Similarity=0.071  Sum_probs=48.9

Q ss_pred             ecCCCEEEEEEEEEecccEEEEcc--c-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAG--A-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV  120 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iG--p-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~  120 (143)
                      |..|+++.|+|+++.++|+||+++  + .++||.+.+       -.|.|. ++=+..+++|+.|.++|+.+.-+.
T Consensus        15 P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSE-------lS~~ri-~~i~d~vkvGd~v~vkVl~VD~ek   81 (319)
T PTZ00248         15 PEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSE-------LSKRRI-RSINKLIRVGRHEVVVVLRVDKEK   81 (319)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHH-------hccccc-CCHHHhcCCCCEEEEEEEEEeCCC
Confidence            667999999999999999999995  3 889884421       123343 233467899999999999986544

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=97.09  E-value=0.0011  Score=53.25  Aligned_cols=65  Identities=14%  Similarity=0.155  Sum_probs=48.9

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEcc-ccEEEEEcCCCceecCCCCceEE---cCCceEEEcCCCeEEEEEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFCLIPDDMELQTGDLPSYT---TSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI~lp~~~~fd~~~~~~~~---~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      +.|..|++|.|+|++++..|++++++ +.+.++.+.+   +    .|.+.   ..+-+..+++||.|++||+.+.-
T Consensus        59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~---i----~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~  127 (235)
T PRK04163         59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSE---V----LGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR  127 (235)
T ss_pred             ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHH---c----CCCccccchhhhHhhCCCCCEEEEEEEEECC
Confidence            89999999999999999999999998 5888882211   0    11121   12234568999999999998753

>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain

Probab=96.98  E-value=0.0052  Score=39.40  Aligned_cols=58  Identities=24%  Similarity=0.208  Sum_probs=41.6

Q ss_pred             CCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           52 GEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |+++.|+|+++++.|++++++=.++|+   +|+..          +..+-. .  .+|+.+.+||.++.-+.+.
T Consensus         1 G~iv~g~V~~v~~~G~~v~l~g~~gfip~s~~~~~----------~~~~~~-~--~vG~~i~~~i~~vd~~~~~   61 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLR----------PVEDLD-E--YVGKELKFKIIEIDRERNN   61 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCc----------ccCChH-H--hCCCEEEEEEEEEeCCCCE
Confidence            789999999999999999994478888   34211          100001 1  3899999999998865443

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 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=96.95  E-value=0.0023  Score=59.10  Aligned_cols=65  Identities=11%  Similarity=-0.033  Sum_probs=48.5

Q ss_pred             eecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEE-cCCceEEEcCCCeEEEEEEEEE
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYT-TSDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~-~~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      .|-.|+++.|+|+++.++|+|++++| .++||.+.+=+    +-.| |. .++-...+++||.|.+||+++.
T Consensus       644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeis----dls~-~~rv~~~~dv~kvGd~V~VKVl~ID  710 (719)
T TIGR02696       644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIR----KLAG-GKRVENVEDVLSVGQKIQVEIADID  710 (719)
T ss_pred             cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhcc----cccc-ccCcCCHHHcCCCCCEEEEEEEEEC
Confidence            58999999999999999999999988 88988332100    0012 11 1222457899999999999987

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.87  E-value=0.003  Score=56.18  Aligned_cols=63  Identities=13%  Similarity=0.151  Sum_probs=47.7

Q ss_pred             CCCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           51 KGEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .|+++.|+|++++++|+|++++ ..++|+   .++.          .+..++....++.|+.|++||..+..+.+.+
T Consensus       373 ~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~----------~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i  439 (565)
T PRK06299        373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISW----------DKKGEEAVELYKKGDEVEAVVLKVDVEKERI  439 (565)
T ss_pred             CCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCc----------cccccChHhhCCCCCEEEEEEEEEeCCCCEE
Confidence            5999999999999999999998 488988   3431          1111233456899999999999887655443

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

Probab=96.87  E-value=0.014  Score=37.77  Aligned_cols=57  Identities=14%  Similarity=0.128  Sum_probs=42.7

Q ss_pred             cCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315           50 FKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV  120 (143)
Q Consensus        50 f~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~  120 (143)
                      ..|+++.|+|.++++.|+++.+|..+.|+...   ++.        ..   ..+++|+.|++.|.++.-+.
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~---e~~--------~~---~~~~~Gd~v~v~v~~v~~~~   58 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKK---EQI--------PG---ESYRPGDRIKAYVLEVRKTS   58 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHH---HCC--------CC---CcCCCCCEEEEEEEEEecCC
Confidence            57999999999999999999998777766110   000        01   23599999999999987543

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

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=96.81  E-value=0.0028  Score=55.89  Aligned_cols=61  Identities=11%  Similarity=0.116  Sum_probs=47.2

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      +|+++.|+|++++++|+|+.+.| +++||   .+++    +..       ++....++.|+.|++||+.+..+...
T Consensus       379 vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~----~~~-------~~~~~~~~~Gd~v~~~V~~id~e~~r  443 (491)
T PRK13806        379 PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISR----AGK-------PATYEKLKPGDSVTLVVEEIDTAKRK  443 (491)
T ss_pred             CCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCc----ccc-------cchhhcCCCCCEEEEEEEEEeCCCCE
Confidence            69999999999999999999987 88988   3331    111       12235679999999999988876655

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=96.80  E-value=0.0058  Score=56.23  Aligned_cols=63  Identities=17%  Similarity=0.172  Sum_probs=48.8

Q ss_pred             EEeecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315           46 VFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD  119 (143)
Q Consensus        46 vFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~  119 (143)
                      +..|..|+++.|+|+++.++|+|+++.+ .++++   ++++.          + .++-...++.||.|++||.++...
T Consensus       616 ~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~----------~-v~~~~~v~kvGD~V~VkV~~iD~~  682 (693)
T PRK11824        616 TAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADE----------R-VEKVEDVLKEGDEVKVKVLEIDKR  682 (693)
T ss_pred             cccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCc----------c-ccCccceeCCCCEEEEEEEEECCC
Confidence            3468899999999999999999999987 78888   44311          1 112236789999999999998643

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=96.80  E-value=0.0054  Score=51.43  Aligned_cols=64  Identities=17%  Similarity=0.168  Sum_probs=48.8

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .-.|+++.|+|++++++|+|+.++..++++   .++++          +. .+....+++|+.|+++|.++..+...+
T Consensus       194 ~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~----------~~-~~~~~~~~vGd~VkvkVl~iD~e~~rI  260 (318)
T PRK07400        194 LEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHE----------HI-ETPHSVFNVNDEMKVMIIDLDAERGRI  260 (318)
T ss_pred             CCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccc----------cc-cChhhccCCCCEEEEEEEEEeCCCCEE
Confidence            456999999999999999999998888888   33211          11 122356899999999999988765554

>PHA02945 interferon resistance protein; Provisional

Probab=96.78  E-value=0.012  Score=41.00  Aligned_cols=65  Identities=12%  Similarity=0.015  Sum_probs=47.1

Q ss_pred             eecCCCEEEEEEEEEecccEEEEcc--c-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAG--A-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iG--p-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      -|-.||++.|+|++ ..+|+|+++-  | ++.||.+.+.   ...+.|  ...  +.++ .|++|-+||+.+....+
T Consensus         8 ~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~sev---eva~~w--vK~--rd~l-~GqkvV~KVirVd~~kg   75 (88)
T PHA02945          8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQ---MHMNRY--FKY--RDKL-VGKTVKVKVIRVDYTKG   75 (88)
T ss_pred             CCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehh---hhccce--Eee--eeEe-cCCEEEEEEEEECCCCC
Confidence            38999999999999 9999999995  3 7788833210   112344  332  4566 99999999998876543

>TIGR00717 rpsA ribosomal protein S1

Probab=96.75  E-value=0.0044  Score=54.37  Aligned_cols=66  Identities=11%  Similarity=0.159  Sum_probs=48.6

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .|+++.|+|+++++.|+|+.+++ .++|+.+.+ +      .|.+...+....+++|+.|.+||+.+....+.+
T Consensus       359 ~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~-l------s~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i  425 (516)
T TIGR00717       359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSD-I------SWDKDGREADHLYKKGDEIEAVVLAVDKEKKRI  425 (516)
T ss_pred             CCCEEEEEEEEEecceEEEECCCCCEEEEEHHH-C------cCcccCCCHhHccCCCCEEEEEEEEEeCcCCEE
Confidence            69999999999999999999996 889983321 0      111111222367899999999999988765554

This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=96.74  E-value=0.0059  Score=56.15  Aligned_cols=73  Identities=21%  Similarity=0.275  Sum_probs=59.2

Q ss_pred             cCCCEEEEEEEEEecccEEEEcc-c-cEEEE---EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           50 FKGEILGAGVTMVNKMGFLAEAG-A-VQIFC---LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        50 f~gEVv~G~V~~v~~~Gi~v~iG-p-~~ifI---~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      ..||..+|+|++++.+|+|+.+- + ++.+|   .|+++ +.|++.. .....+.+...+..|+.|++|+.++......+
T Consensus       621 ~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~-~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i  699 (706)
T COG0557         621 RVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERG-QALVGEKSGKVYRLGDEVKVKVTSVDLDERKI  699 (706)
T ss_pred             hcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeecccc-ceeeccccccccccCCEEEEEEEEEcccccce
Confidence            46899999999999999999994 4 78888   77754 6777764 24566777889999999999999998866553

>PRK03987 translation initiation factor IF-2 subunit alpha; Validated

Probab=96.74  E-value=0.0052  Score=50.40  Aligned_cols=64  Identities=14%  Similarity=0.175  Sum_probs=48.3

Q ss_pred             eecCCCEEEEEEEEEecccEEEEcc---ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAG---AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iG---p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      .|-+|+++.|+|+++.++|+|+++.   ..++|+   .+++        .  |.. +-...++.|+.|++||..+..+..
T Consensus         5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~--------~--~i~-~i~~~~kvGd~V~vkVi~VD~~k~   73 (262)
T PRK03987          5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVAS--------G--WVK-NIRDHVKEGQKVVCKVIRVDPRKG   73 (262)
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCc--------c--ccc-CHHHhCCCCCEEEEEEEEEecccC
Confidence            4889999999999999999999995   267887   3321        1  211 123578999999999999877654


Q ss_pred             C
Q 032315          122 E  122 (143)
Q Consensus       122 ~  122 (143)
                      .
T Consensus        74 ~   74 (262)
T PRK03987         74 H   74 (262)
T ss_pred             e
Confidence            4

>PRK05054 exoribonuclease II; Provisional

Probab=96.72  E-value=0.015  Score=53.14  Aligned_cols=76  Identities=8%  Similarity=0.080  Sum_probs=55.0

Q ss_pred             EeecCC--CEEEEEEEEEecccEEEEccc--cEEEE---EcCCC---ceecCCCC-ceEEcCCceEEEcCCCeEEEEEEE
Q 032315           47 FRPFKG--EILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDD---MELQTGDL-PSYTTSDGSVKIQKDCELWLKIIG  115 (143)
Q Consensus        47 FrPf~g--EVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~---~~fd~~~~-~~~~~~~~~~~i~~g~~VR~RV~~  115 (143)
                      .+...|  +..+|.|+.++++|+||.+..  .+++|   .|+++   +.|+.++. -.+   .++..++.||.|++||.+
T Consensus       555 ~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~---~~~~~~~lGd~V~V~v~~  631 (644)
T PRK05054        555 LKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQI---KGETVYKLGDVIDVTLAE  631 (644)
T ss_pred             HhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEE---eCCEEEcCCCEEEEEEEE
Confidence            344555  499999999999999999963  77888   66654   33444431 122   234789999999999999


Q ss_pred             EEEccCCeEE
Q 032315          116 TQVDVTEIEK  125 (143)
Q Consensus       116 v~~~~~~~~a  125 (143)
                      +......+-+
T Consensus       632 vd~~~~~i~~  641 (644)
T PRK05054        632 VRMETRSIIA  641 (644)
T ss_pred             EccccCeEEE
Confidence            9887766543

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

Probab=96.60  E-value=0.0058  Score=54.84  Aligned_cols=68  Identities=19%  Similarity=0.278  Sum_probs=49.6

Q ss_pred             eecCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .--.|++++|+|++++++|+|+.+|=.|.++.+. ++.|..-..+       ..++++||+|.+||+.+.-..+++
T Consensus       189 ~l~~G~vV~G~V~~It~~GafVdigGvdGLlHis-eiS~~rv~~P-------~~vvkvGd~VkvkVi~~D~e~~RV  256 (541)
T COG0539         189 KLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHIS-EISWKRVDHP-------SEVVKVGDEVKVKVISLDEERGRV  256 (541)
T ss_pred             cCCCCceEEEEEEEeecCcEEEEecCeeeEEehh-hccccccCCH-------HHhcccCCEEEEEEEEEccCCCeE
Confidence            3467999999999999999999997799888221 1111111111       367899999999999987766553

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=96.59  E-value=0.0066  Score=53.60  Aligned_cols=66  Identities=12%  Similarity=0.137  Sum_probs=47.8

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .|+++.|+|++++++|+|+.++| .++|+.+.+ +.+..      ...+-...+++|+.|.+||.++..+.+.+
T Consensus       292 ~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~se-ls~~~------~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri  358 (491)
T PRK13806        292 AGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSE-MSWTR------RVNKPEDVVAPGDAVAVKIKDIDPAKRRI  358 (491)
T ss_pred             CCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHH-cCccc------ccCCHHHcCCCCCEEEEEEEEEEccCCEE
Confidence            59999999999999999999987 889883321 11100      01122356899999999999887765543

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.58  E-value=0.0062  Score=53.99  Aligned_cols=65  Identities=14%  Similarity=0.246  Sum_probs=48.1

Q ss_pred             CCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .|+++.|+|++++++|+|+.+|..++||.+.+ +      .|.+. ++-...+++|+.|.+||+.+..+.+++
T Consensus       208 ~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Se-l------s~~~v-~~~~~~~kvGd~V~vkVl~iD~e~~rI  272 (486)
T PRK07899        208 KGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSE-L------SWKHI-DHPSEVVEVGQEVTVEVLDVDMDRERV  272 (486)
T ss_pred             CCCEEEEEEEEEECCeEEEEECCEEEEEEHHH-C------CCccc-CCHHHhcCCCCEEEEEEEEEECCCCEE
Confidence            69999999999999999999988888882210 0      12111 122356899999999999988765553

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=96.45  E-value=0.006  Score=47.35  Aligned_cols=65  Identities=15%  Similarity=0.031  Sum_probs=45.2

Q ss_pred             EEEeecCCCEEEEEEEEEecccEEEEccc-----------cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEE
Q 032315           45 IVFRPFKGEILGAGVTMVNKMGFLAEAGA-----------VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKI  113 (143)
Q Consensus        45 lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-----------~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV  113 (143)
                      ....|..|+++.|+|++++..|++++++.           .+.++...+-       .|.+. ++-...+++||.|++||
T Consensus        58 ~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i-------~~~~~-~~~~~~~~~GD~V~akV  129 (189)
T PRK09521         58 TPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQV-------SDGYV-ESLTDAFKIGDIVRAKV  129 (189)
T ss_pred             CCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHc-------Chhhh-hhHHhccCCCCEEEEEE
Confidence            35778899999999999999999999852           4455511100       01010 11235689999999999


Q ss_pred             EEEE
Q 032315          114 IGTQ  117 (143)
Q Consensus       114 ~~v~  117 (143)
                      ..+.
T Consensus       130 ~~i~  133 (189)
T PRK09521        130 ISYT  133 (189)
T ss_pred             EecC
Confidence            9886

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=96.43  E-value=0.013  Score=55.22  Aligned_cols=64  Identities=14%  Similarity=0.191  Sum_probs=48.6

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      .|.++.|+|++++++|+|+++++ .++|+   .++++...+..        +....|+.|+.|+++|+++..+...
T Consensus       752 vG~iV~GkV~~v~~~GvFVeL~~gVeGlI~~s~lsdd~~~~~~--------~~~~~f~vGD~V~v~Vl~iD~~~rk  819 (863)
T PRK12269        752 VGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPG--------EALRKYAVGDRVKAVIVDMNVKDRK  819 (863)
T ss_pred             CCCEEEEEEEEEecCeEEEEcCCCeEEEEEHHHcCCcccccch--------hhccccCCCCEEEEEEEEEEcCCCE
Confidence            69999999999999999999965 88888   56543211111        1135689999999999988776554

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=96.39  E-value=0.014  Score=48.95  Aligned_cols=61  Identities=16%  Similarity=0.142  Sum_probs=45.0

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV  120 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~  120 (143)
                      .-.|+++.|+|.++++.|+++.+|. .++|+   .+.+.          +. ++....+++|++|+++|+++.-+.
T Consensus        29 ~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~----------~~-~~~~~~~~~G~~v~~~Vi~~~~~~   93 (318)
T PRK07400         29 FKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSIN----------RV-EGPEEVLQPNETREFFILSDENED   93 (318)
T ss_pred             cCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccc----------cc-cCHHHccCCCCEEEEEEEEEeCCC
Confidence            5789999999999999999999997 78988   23211          11 111245788899999998865443

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=96.37  E-value=0.01  Score=55.96  Aligned_cols=66  Identities=15%  Similarity=0.148  Sum_probs=48.8

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .|+++.|+|++++++|+|++++| .++||.+.+ +      .|....+.....+++|+.|.++|+++..+.+.+
T Consensus       665 vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~se-l------s~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI  731 (863)
T PRK12269        665 VGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDD-L------SWVKRTRPADHELEVGKEIECMVIECDPQARRI  731 (863)
T ss_pred             CCCEEEEEEEEEecceEEEEeCCCcEEEEEhHH-h------hccccccchhhccCCCCEEEEEEEEEeccCCEE
Confidence            49999999999999999999998 889884321 1      121111112346899999999999998766554

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.29  E-value=0.022  Score=50.58  Aligned_cols=62  Identities=16%  Similarity=0.246  Sum_probs=47.7

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .|+++.|+|++++++|+|+.+.+ .++++   .|+++.         +  +..+..++.|+.|++||..+..+...+
T Consensus       293 vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~---------v--~~~~~~~kvGd~V~VkIi~ID~e~rrI  358 (486)
T PRK07899        293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERH---------V--EVPEQVVQVGDEVFVKVIDIDLERRRI  358 (486)
T ss_pred             CCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCccc---------c--cCccceeCCCCEEEEEEEEEECCCCEE
Confidence            59999999999999999999975 88888   443210         1  112367899999999999988765553

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.28  E-value=0.0071  Score=57.08  Aligned_cols=66  Identities=14%  Similarity=0.264  Sum_probs=48.8

Q ss_pred             EEEeecCCCEEE-EEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           45 IVFRPFKGEILG-AGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        45 lvFrPf~gEVv~-G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      ++..|..|++++ |+|+++.++|+|+.+.| .+++|.+.+ +      .|-|. +.-...++.||.|++||+++..
T Consensus       747 l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISe-L------s~~rv-~~~~dv~kvGD~V~VkVi~ID~  814 (891)
T PLN00207        747 LTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISE-L------SSNWL-AKPEDAFKVGDRIDVKLIEVND  814 (891)
T ss_pred             HhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhh-c------CCccc-cCHHHhcCCCCEEEEEEEEECC
Confidence            445799999996 69999999999999988 788883321 0      11111 1223578999999999999874

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.26  E-value=0.014  Score=49.61  Aligned_cols=64  Identities=14%  Similarity=0.239  Sum_probs=46.7

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .-.|+++.|+|+++++.|+|+.++-.++|+   .+++          .+. ++-...+++|+.|++||.++..+.+.+
T Consensus       190 ~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~----------~~~-~~~~~~~~vGd~i~~~Vl~vd~~~~~i  256 (390)
T PRK06676        190 LKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSH----------ERV-EKPSEVVSVGQEVEVKVLSIDWETERI  256 (390)
T ss_pred             CCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCc----------ccc-CCHHHhcCCCCEEEEEEEEEeCCCCEE
Confidence            346999999999999999999998788888   3331          111 122345788999999998876654443

>TIGR02062 RNase_B exoribonuclease II

Probab=96.14  E-value=0.042  Score=50.18  Aligned_cols=70  Identities=6%  Similarity=0.055  Sum_probs=53.2

Q ss_pred             CCEEEEEEEEEecccEEEEc-cc-cEEEE---EcCC---CceecCCCC-ceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           52 GEILGAGVTMVNKMGFLAEA-GA-VQIFC---LIPD---DMELQTGDL-PSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~i-Gp-~~ifI---~lp~---~~~fd~~~~-~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      ++..+|.|+.++++|+|+.+ .. .++||   .|++   .+.||.++. -.+.++   ..++.|+.|+++|.++......
T Consensus       558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~---~~~~lgd~v~V~v~~vd~~~~~  634 (639)
T TIGR02062       558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGE---TVYKIGDVIDVVLTEVRMETRS  634 (639)
T ss_pred             CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEecc---EEEecCCEEEEEEEEeccccCc
Confidence            45899999999999999999 33 88888   5654   355777642 223322   4899999999999999887766


Q ss_pred             eE
Q 032315          123 IE  124 (143)
Q Consensus       123 ~~  124 (143)
                      +-
T Consensus       635 i~  636 (639)
T TIGR02062       635 II  636 (639)
T ss_pred             Ee
Confidence            54

This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.

>TIGR00717 rpsA ribosomal protein S1

Probab=95.95  E-value=0.028  Score=49.31  Aligned_cols=61  Identities=16%  Similarity=0.234  Sum_probs=47.0

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      .|+++.|.|++++++|+|+.++. .++|+   .++++          + .++....++.|+.+++||..+..+...
T Consensus       446 ~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~----------~-~~~~~~~~~~Gd~v~~~V~~id~~~~~  510 (516)
T TIGR00717       446 VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSEN----------R-DEDKTDEIKVGDEVEAKVVDIDKKNRK  510 (516)
T ss_pred             cceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCcc----------c-cccccccCCCCCEEEEEEEEEeCCCCE
Confidence            69999999999999999999977 78888   44321          1 112346789999999999988765444

This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=95.93  E-value=0.044  Score=46.58  Aligned_cols=63  Identities=14%  Similarity=0.097  Sum_probs=43.8

Q ss_pred             eecCCCEEEEEEEEEecccEEEEc-cc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEA-GA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~i-Gp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      ....|+++.|+|+++++.|+++.+ |+ .++|+   .+.+.    ..       ++-...+++|+.|+++|..+.-+.+
T Consensus        14 ~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~----~~-------~~~~~~~~vGd~v~~~V~~v~~~~~   81 (390)
T PRK06676         14 EVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSND----HI-------EDINDVVKVGDELEVYVLKVEDGEG   81 (390)
T ss_pred             cccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccc----cc-------cCcccccCCCCEEEEEEEEEECCCC
Confidence            456899999999999999999999 75 77888   33211    00       1112346777777777777765444

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=95.87  E-value=0.024  Score=50.51  Aligned_cols=65  Identities=12%  Similarity=0.124  Sum_probs=44.0

Q ss_pred             cCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           50 FKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        50 f~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      ..|+++.|+|+++++.|+|+.+++ .++|+.+.+ +.      |.....+....+++|+.|++||.++..+.+
T Consensus       285 ~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~se-l~------~~~~~~~~~~~~~~G~~v~v~V~~id~~~~  350 (565)
T PRK06299        285 PVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSE-MS------WTKKNKHPSKVVSVGQEVEVMVLEIDEEKR  350 (565)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHH-cC------ccccccCHHHhcCCCCEEEEEEEEEcCCCC
Confidence            359999999999999999999987 788882210 00      100011112456888888888888765433

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

Probab=95.80  E-value=0.03  Score=51.03  Aligned_cols=62  Identities=16%  Similarity=0.118  Sum_probs=46.6

Q ss_pred             cCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           50 FKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        50 f~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      ..|+++.|+|++++++|+|+.+.+ .++|+   .++++      .     .++.+..++.|+.|++||.++..+...
T Consensus       561 ~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~------~-----~~~~~~~~kvGd~V~vkV~~id~e~~r  626 (647)
T PRK00087        561 PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWK------R-----IDKPEDVLSEGEEVKAKILEVDPEEKR  626 (647)
T ss_pred             cCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCcc------c-----cCCHhhcCCCCCEEEEEEEEEeCCCCE
Confidence            369999999999999999999976 78887   33211      0     112235689999999999988765544

>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]

Probab=95.71  E-value=0.012  Score=43.48  Aligned_cols=62  Identities=16%  Similarity=0.133  Sum_probs=43.4

Q ss_pred             ecCCCEEEEEEEEEecccEEEEcc-ccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAG-AVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      +-.|+++.|+|+.++++|+||.+- =...+|.+.+-.     .+  |. ++-.-.+.+|++|-++|+++.-
T Consensus         3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa-----~~--fV-kdI~d~L~vG~eV~vKVl~ide   65 (129)
T COG1098           3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIA-----DG--FV-KDIHDHLKVGQEVKVKVLDIDE   65 (129)
T ss_pred             ccccceEEEEEEeeEecceEEEecCCCcceEEehHhh-----hh--hH-HhHHHHhcCCCEEEEEEEeecc
Confidence            567999999999999999999884 355666332100     00  11 1223467999999999998765

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

Probab=95.69  E-value=0.045  Score=37.81  Aligned_cols=73  Identities=12%  Similarity=0.154  Sum_probs=54.1

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEcc-ccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc-CCeE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV-TEIE  124 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~-~~~~  124 (143)
                      |.|..|.+|.|+|++++....+++++ |...++  | .+.|...      .++.+-.+++||.|-+||..+.-+. -++-
T Consensus         2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L--~-~~~f~ga------tk~~rp~L~~GDlV~ArV~~~~~~~~~eLt   72 (86)
T cd05790           2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASL--S-YLAFEGA------TKRNRPNLNVGDLVYARVVKANRDMEPELS   72 (86)
T ss_pred             CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEe--c-hHHcccc------cccccccCCCCCEEEEEEEecCCCCCeEEE
Confidence            67999999999999999999999996 455544  2 1334322      2345678999999999998886542 3466


Q ss_pred             EEEE
Q 032315          125 KARR  128 (143)
Q Consensus       125 ai~~  128 (143)
                      |+..
T Consensus        73 c~~~   76 (86)
T cd05790          73 CVDS   76 (86)
T ss_pred             EeCC
Confidence            7663

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".

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

Probab=95.49  E-value=0.026  Score=39.05  Aligned_cols=63  Identities=16%  Similarity=-0.030  Sum_probs=40.8

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEcc---------ccEEEEEcCCCceecCCCCceEEcC--CceEEEcCCCeEEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAG---------AVQIFCLIPDDMELQTGDLPSYTTS--DGSVKIQKDCELWLKIIG  115 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iG---------p~~ifI~lp~~~~fd~~~~~~~~~~--~~~~~i~~g~~VR~RV~~  115 (143)
                      +-|..|.++.|.|++++..-+.+.+-         |...++...+-.   +     ...+  +-...|++||.||+||.+
T Consensus         2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~---~-----~~~d~~~~~~~f~~GDiV~AkVis   73 (92)
T cd05791           2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIR---A-----TEKDKVEMYKCFRPGDIVRAKVIS   73 (92)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHcc---c-----cccchHHHHhhcCCCCEEEEEEEE
Confidence            56899999999999999999999661         122222110000   0     0001  112568999999999998


Q ss_pred             EE
Q 032315          116 TQ  117 (143)
Q Consensus       116 v~  117 (143)
                      ..
T Consensus        74 ~~   75 (92)
T cd05791          74 LG   75 (92)
T ss_pred             cC
Confidence            64

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".

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=95.46  E-value=0.026  Score=52.54  Aligned_cols=63  Identities=16%  Similarity=0.157  Sum_probs=49.1

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      -..|.++.|+|+++.++|+||.+|- .|++|   .+.+.+.+++.           .++++|+.|.++|..+-.+..+
T Consensus       656 Lk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~-----------~vv~vGdiV~v~V~~vD~~r~r  722 (780)
T COG2183         656 LKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPN-----------EVVKVGDIVKVKVIEVDTARKR  722 (780)
T ss_pred             ccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChH-----------HhcccCCEEEEEEEEEecccCe
Confidence            4679999999999999999999998 67888   44433333332           4678999999999988776544

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

Probab=95.38  E-value=0.038  Score=49.67  Aligned_cols=70  Identities=14%  Similarity=0.134  Sum_probs=53.0

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCeE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIE  124 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~  124 (143)
                      -+--.|.++.|+|+..+++|+|+.++| .+.|+.+++ +      .|..... -+.+++.|++|-++|+++..+..++.
T Consensus       273 ~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSE-i------sw~~~~~-P~evv~~Gq~V~V~Vl~id~e~rRIs  343 (541)
T COG0539         273 KKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSE-I------SWTKKNV-PSEVVKVGQEVEVKVLDIDPERRRIS  343 (541)
T ss_pred             hhcCCCCEEEEEEEEeecCcEEEEecCCccceeechh-h------cccccCC-HHHhcccCCEEEEEEEeeCchhceEE
Confidence            344578999999999999999999999 999883321 0      1222112 24678999999999999998877754

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.27  E-value=0.093  Score=45.04  Aligned_cols=61  Identities=10%  Similarity=0.171  Sum_probs=46.8

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      |++..|+++.|+|.+.++.|+++.+|=.+.|+  |.      .+ +  ..   +..+++|+.+++-|..+..+.+
T Consensus       130 f~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~L--P~------~E-~--ip---~e~~~~Gd~Ika~V~~V~~~~k  190 (362)
T PRK12327        130 FSEREGDIVTGVVQRRDNRFVYVNLGKIEAVL--PP------AE-Q--IP---GETYKHGDRIKVYVVKVEKTTK  190 (362)
T ss_pred             HHHhcCCEEEEEEEEEeCCcEEEEeCCeEEEe--cH------HH-c--CC---CCCCCCCCEEEEEEEEEecCCC
Confidence            66789999999999999999999998777766  21      00 0  00   1347899999999999987653

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=95.23  E-value=0.081  Score=46.84  Aligned_cols=61  Identities=11%  Similarity=0.189  Sum_probs=46.0

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      |+...||++.|+|.++++.|+++.+|=.+.|+  |.       +..  .   -+..+++|+.||+.|..+.-+.+
T Consensus       130 yk~~~GeIV~G~V~ri~~~giiVDLggvea~L--P~-------sE~--i---p~E~~~~GdrIka~I~~Vd~~~k  190 (470)
T PRK09202        130 YKDRVGEIITGVVKRVERGNIIVDLGRAEAIL--PR-------KEQ--I---PRENFRPGDRVRAYVYEVRKEAR  190 (470)
T ss_pred             HHhhcCCEEEEEEEEEecCCEEEEECCeEEEe--cH-------HHc--C---CCccCCCCCEEEEEEEEEecCCC
Confidence            44457999999999999999999998777776  20       000  0   11346999999999999987654

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

Probab=95.19  E-value=0.049  Score=49.69  Aligned_cols=61  Identities=15%  Similarity=0.206  Sum_probs=45.3

Q ss_pred             CCCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      .|+++.|+|+++++.|+|+.++..++|+   .+++          .+. .+-...+++|+.|++||.++....+.
T Consensus       477 ~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~----------~~~-~~~~~~~~vGd~V~vkV~~id~~~~~  540 (647)
T PRK00087        477 EGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISW----------GRV-EKPSDVLKVGDEIKVYILDIDKENKK  540 (647)
T ss_pred             CCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCc----------ccc-CCHHHhcCCCCEEEEEEEEEECCCCE
Confidence            6999999999999999999997788888   3321          111 11234578999999999887655443

>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=94.69  E-value=0.027  Score=46.38  Aligned_cols=64  Identities=17%  Similarity=0.149  Sum_probs=49.3

Q ss_pred             ecCCCEEEEEEEEEecccEEEEcc--c-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAG--A-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV  120 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iG--p-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~  120 (143)
                      |-.||+|-|+|.++.++|+|+++-  | .+.||.+.+     -.+.|.   ++-+.+++.|..+-++|+.+.-..
T Consensus         9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSE-----vas~wV---knIrd~vkegqkvV~kVlrVd~~r   75 (269)
T COG1093           9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISE-----VASGWV---KNIRDYVKEGQKVVAKVLRVDPKR   75 (269)
T ss_pred             CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHH-----HHHHHH---HHHHHHhhcCCeEEEEEEEEcCCC
Confidence            889999999999999999999995  4 778885531     112342   223468899999999999886544

>TIGR01953 NusA transcription termination factor NusA

Probab=94.15  E-value=0.22  Score=42.35  Aligned_cols=60  Identities=20%  Similarity=0.268  Sum_probs=44.0

Q ss_pred             EeecCCCEEEEEEEEEeccc-EEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315           47 FRPFKGEILGAGVTMVNKMG-FLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV  120 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~G-i~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~  120 (143)
                      |+...||++.|+|.++++.| +++.+|=.+.|+  |.       +.+  ...   ..+++|+.+++-|..+.-++
T Consensus       127 y~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~L--P~-------~E~--ip~---E~~~~Gd~ik~~V~~V~~~~  187 (341)
T TIGR01953       127 FSSKEGEIISGTVKRVNRRGNLYVELGKTEGIL--PK-------KEQ--IPG---EKFRIGDRIKAYVYEVRKTA  187 (341)
T ss_pred             HHhhcCCEEEEEEEEEecCCcEEEEECCeEEEe--cH-------HHc--CCC---cCCCCCCEEEEEEEEEEcCC
Confidence            55569999999999999998 599998767766  20       000  001   12789999999999998654

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

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

Probab=93.57  E-value=1.1  Score=36.56  Aligned_cols=71  Identities=13%  Similarity=0.182  Sum_probs=53.1

Q ss_pred             EEeecCCCEEEEEEEEEecccEEEEcc-ccEEEEEcCCC--ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           46 VFRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFCLIPDD--MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        46 vFrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI~lp~~--~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      -|.|-.|.+|.|.|.++...+..++++ |...++.+.+-  -.++..      ..+-+.++++||.|-+||..+.-+..-
T Consensus        59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~------~~~~r~~l~vGD~v~AkV~~vd~~~~~  132 (239)
T COG1097          59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENA------EKDLRPFLNVGDLVYAKVVDVDRDGEV  132 (239)
T ss_pred             cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhccccccc------ccccccccccCCEEEEEEEEccCCCce
Confidence            588999999999999999999999996 78887733211  011111      234568899999999999987654433

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=93.13  E-value=0.22  Score=45.91  Aligned_cols=65  Identities=15%  Similarity=0.097  Sum_probs=47.9

Q ss_pred             EEEeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315           45 IVFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        45 lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      ++=.|.+||+..|+|+.+..+|+|+++-| -++++.++.-.   ..     .-++-..+++.||.|++|+..+.
T Consensus       613 i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~---~~-----rv~kv~dvlk~Gd~v~Vkv~~iD  678 (692)
T COG1185         613 ITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLA---KE-----RVEKVEDVLKEGDEVKVKVIEID  678 (692)
T ss_pred             HHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhh---hh-----hhhcccceeecCceEEEEEeeec
Confidence            45668899999999999999999999988 66777322110   00     11223368899999999998764

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

Probab=91.51  E-value=0.29  Score=33.52  Aligned_cols=23  Identities=39%  Similarity=0.309  Sum_probs=17.1

Q ss_pred             ecCCCEEEEEEEEEecccEEEEc
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEA   71 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~i   71 (143)
                      |..|-++.|.|+++++.-+.+.+
T Consensus         2 P~vGdiV~~rVtrv~~~~a~v~I   24 (82)
T PF10447_consen    2 PKVGDIVIARVTRVNPRQAKVEI   24 (82)
T ss_dssp             --TT-EEEEEEEEE-SSEEEEEE
T ss_pred             CCCCCEEEEEEEEEeccEEEEEE
Confidence            88999999999999999988843

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

>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=88.01  E-value=1.2  Score=29.80  Aligned_cols=54  Identities=15%  Similarity=0.172  Sum_probs=39.5

Q ss_pred             CCEEEEEEEEEecccEEEEccc--cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeE-EEEEE
Q 032315           52 GEILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCEL-WLKII  114 (143)
Q Consensus        52 gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~V-R~RV~  114 (143)
                      |.+++|+|.+=++.++.+.+++  +..++   +|+|  .+..+. ..|      ..+++|+++ +.=|.
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD--~~~k~~-~~~------~klrvG~~L~~~lvL   60 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD--HVSNCP-LLW------HCLQEGDTIPNLMCL   60 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC--chhhCH-HHH------hhhhcCCCccceEEE
Confidence            6789999999999999999998  66777   7765  333332 123      457788877 66665

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 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=86.46  E-value=4.2  Score=35.21  Aligned_cols=61  Identities=13%  Similarity=0.145  Sum_probs=43.7

Q ss_pred             EeecCCCEEEEEEEEEecc-cEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           47 FRPFKGEILGAGVTMVNKM-GFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~-Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      |++..||++.|+|..++.. ++++.+|=.+.++  |..      ++   ..   +..|++|+.+|+=|..+.-++.
T Consensus       134 y~~~~Geiv~g~V~r~~~~~~i~vdlg~~ea~L--P~~------eq---ip---~E~~~~Gdrik~~i~~V~~~~k  195 (374)
T PRK12328        134 YKKKVGKIVFGTVVRVDNEENTFIEIDEIRAVL--PMK------NR---IK---GEKFKVGDVVKAVLKRVKIDKN  195 (374)
T ss_pred             HHHhcCcEEEEEEEEEecCCCEEEEcCCeEEEe--CHH------Hc---CC---CCcCCCCCEEEEEEEEEecCCC
Confidence            7889999999999999975 5899998655544  411      10   00   1346888888888888887665

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

Probab=86.23  E-value=2.5  Score=33.11  Aligned_cols=75  Identities=16%  Similarity=0.025  Sum_probs=44.5

Q ss_pred             EEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE--EcCCCceecCCC--CceEEcCCc----eEEEcCCCeE
Q 032315           38 FLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC--LIPDDMELQTGD--LPSYTTSDG----SVKIQKDCEL  109 (143)
Q Consensus        38 ~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI--~lp~~~~fd~~~--~~~~~~~~~----~~~i~~g~~V  109 (143)
                      .+..|..+  -|+.|.|+.+.|+.++..=+.+     +|+.  .+|-...|..--  +-.-..+.+    -..|++||.|
T Consensus        57 ~~~~~~~~--LP~~G~IVtarV~~i~~rfAkv-----~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiV  129 (193)
T KOG3409|consen   57 EKQLFNEL--LPFVGAIVTARVSRINLRFAKV-----DILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIV  129 (193)
T ss_pred             cccchhhc--CCccCcEEEEEEEeeccceeeE-----EEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEE
Confidence            33444444  4999999999999999888877     4444  333222222100  000001111    1467899999


Q ss_pred             EEEEEEEEEc
Q 032315          110 WLKIIGTQVD  119 (143)
Q Consensus       110 R~RV~~v~~~  119 (143)
                      |+||++..-.
T Consensus       130 lAkVis~~~~  139 (193)
T KOG3409|consen  130 LAKVISLGDG  139 (193)
T ss_pred             EEEEeecCCC
Confidence            9999994433

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=83.70  E-value=6.1  Score=34.51  Aligned_cols=75  Identities=15%  Similarity=0.110  Sum_probs=47.9

Q ss_pred             eecCCCEEEEEEEEEecc--cEEEEccc-cEEEE---EcCCCceecCCCCceE-EcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315           48 RPFKGEILGAGVTMVNKM--GFLAEAGA-VQIFC---LIPDDMELQTGDLPSY-TTSDGSVKIQKDCELWLKIIGTQVDV  120 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~--Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~-~~~~~~~~i~~g~~VR~RV~~v~~~~  120 (143)
                      .+..|.+..|+|.++.+.  |+||.+|. -++|+   .+.++..+........ ...+-...+++|+.|.++|...-...
T Consensus        22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~  101 (414)
T TIGR00757        22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGN  101 (414)
T ss_pred             cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCC
Confidence            356899999999999999  99999999 56999   3322211111000000 00011235889999999999866654


Q ss_pred             CC
Q 032315          121 TE  122 (143)
Q Consensus       121 ~~  122 (143)
                      ..
T Consensus       102 Kg  103 (414)
T TIGR00757       102 KG  103 (414)
T ss_pred             CC
Confidence            44

The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=82.67  E-value=1.8  Score=27.47  Aligned_cols=28  Identities=21%  Similarity=0.408  Sum_probs=17.3

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEE
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC   78 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI   78 (143)
                      .|++...+|++.++.|+|+..|- .++++
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlL   29 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLL   29 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEE
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEe
Confidence            37888999999999999999987 77887

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	143
2c35_B	172	Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii L		2e-24
3h0g_G	172	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		2e-20
2b8k_G	215	12-Subunit Rna Polymerase Ii Length = 215		3e-11
1nt9_G	171	Complete 12-Subunit Rna Polymerase Ii Length = 171		5e-11

>pdb|2C35|B Chain B, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii Length = 172

Iteration: 1
 Score =  107 bits (268), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 56/125 (44%), Positives = 81/125 (64%), Gaps = 4/125 (3%)
Query: 3   DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
           +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT V
Sbjct: 33  EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92
Query: 63  NKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
           NK+G   E G +  F     IP +ME     + P Y T D  + IQ+D E+ LKI+GT+V
Sbjct: 93  NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV 152
Query: 119 DVTEI 123
           D  +I
Sbjct: 153 DKNDI 157

>pdb|3H0G|G Chain G, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 172

Iteration: 1
 Score = 94.4 bits (233), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 51/129 (39%), Positives = 79/129 (61%), Gaps = 8/129 (6%)
Query: 1   MKDVEGTCSGRHGFAVAITGAESIG--KGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAG 58
           + DVEGTCSG++G+ + +  + +I   KG +  G     F V+ + +++RPF+GE++ A 
Sbjct: 32  LADVEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLWRPFRGEVVDAI 91
Query: 59  VTMVNKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKII 114
           VT VNKMGF A  G + +F    L+P DM+   T + P+Y+  D    I+K   + LKI+
Sbjct: 92  VTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQV--IEKGSNVRLKIV 149
Query: 115 GTQVDVTEI 123
           GT+ D TEI
Sbjct: 150 GTRTDATEI 158

>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii Length = 215

Iteration: 1
 Score = 63.9 bits (154), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 39/133 (29%), Positives = 74/133 (55%), Gaps = 14/133 (10%)
Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVT-----FLVRCQCIVFRPFKGEIL 55
           +++VEG+C+G+ G+ + +   ++I    I+ G +L T     F V+ + +VF+PFKGE++
Sbjct: 31  LEEVEGSCTGKFGYILCVLDYDNID---IQRGRILPTDGSAEFNVKYRAVVFKPFKGEVV 87
Query: 56  GAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTG-DLPSYTTSDGSVKIQKDCELWL 111
              V   ++ GF  + G +++F    L+P D+    G + PSY +S+  + I+    + +
Sbjct: 88  DGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIK--SRIRV 145
Query: 112 KIIGTQVDVTEIE 124
           KI G    V+ I 
Sbjct: 146 KIEGCISQVSSIH 158

>pdb|1NT9|G Chain G, Complete 12-Subunit Rna Polymerase Ii Length = 171

Iteration: 1
 Score = 63.2 bits (152), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 39/133 (29%), Positives = 74/133 (55%), Gaps = 14/133 (10%)
Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVT-----FLVRCQCIVFRPFKGEIL 55
           +++VEG+C+G+ G+ + +   ++I    I+ G +L T     F V+ + +VF+PFKGE++
Sbjct: 31  LEEVEGSCTGKFGYILCVLDYDNID---IQRGRILPTDGSAEFNVKYRAVVFKPFKGEVV 87
Query: 56  GAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTG-DLPSYTTSDGSVKIQKDCELWL 111
              V   ++ GF  + G +++F    L+P D+    G + PSY +S+  + I+    + +
Sbjct: 88  DGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKS--RIRV 145
Query: 112 KIIGTQVDVTEIE 124
           KI G    V+ I 
Sbjct: 146 KIEGCISQVSSIH 158

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	143
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	2e-20
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	6e-20
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	1e-18
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	5e-18
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	7e-18
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	3e-17
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	4e-17
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	1e-16

>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 = 81.1 bits (200), Expect = 2e-20
 Identities = 56/127 (44%), Positives = 81/127 (63%), Gaps = 4/127 (3%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
             +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVFRPFKGE++ A VT
Sbjct: 31  FTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVT 90

Query: 61  MVNKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGT 116
            VNK+G   E G +  F     IP +ME     + P Y T D  + IQ+D E+ LKI+GT
Sbjct: 91  QVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGT 150

Query: 117 QVDVTEI 123
           +VD  +I
Sbjct: 151 RVDKNDI 157

>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 = 80.9 bits (199), Expect = 6e-20
 Identities = 18/124 (14%), Positives = 37/124 (29%), Gaps = 7/124 (5%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
                       G  + I    ++ +G ++ G       V  + +VF+PF GEI+   ++
Sbjct: 31  NNKFANKIIPNVGLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVVFKPFLGEIVTGWIS 90

Query: 61  MVNKMGFLAEAGAVQIFCLIP-----DDMELQTGDLPSYTTSDGSVK--IQKDCELWLKI 113
                G       +     IP     +       +       D   K     + ++  +I
Sbjct: 91  KCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRI 150

Query: 114 IGTQ 117
               
Sbjct: 151 EREV 154

>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 = 76.5 bits (188), Expect = 1e-18
 Identities = 21/126 (16%), Positives = 43/126 (34%), Gaps = 3/126 (2%)

Query: 2   KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTM 61
           +  EG      GF ++I   + IG+G + +G       V  + +V+ P   E++   V  
Sbjct: 32  EKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVD 91

Query: 62  VNKMGFLAEAGAVQIF---CLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
           V + G     G +        I DD         +    +    ++    +  +I+   +
Sbjct: 92  VVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISL 151

Query: 119 DVTEIE 124
                 
Sbjct: 152 KAERKR 157

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

 Score = 75.5 bits (185), Expect = 5e-18
 Identities = 18/84 (21%), Positives = 33/84 (39%)

Query: 1   MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
            K          G A+ +     IG+G+I+ G       V  + I+FRPF+GE++   + 
Sbjct: 31  HKKYANKVIQNIGLAICVYDFLKIGEGIIKYGDGSSYMNVVFRLIIFRPFRGEVMLGKIK 90

Query: 61  MVNKMGFLAEAGAVQIFCLIPDDM 84
             ++ G            +  D +
Sbjct: 91  SCSEEGIRVTISFFDDIFIPKDML 114

>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 = 75.5 bits (185), Expect = 7e-18
 Identities = 36/130 (27%), Positives = 64/130 (49%), Gaps = 6/130 (4%)

Query: 1   MKDVEGTCSGRHGFAVAITGAE--SIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAG 58
           +++VEG+C+G+ G+ + +   +   I +G I        F V+ + +VF+PFKGE++   
Sbjct: 31  LEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGT 90

Query: 59  VTMVNKMGFLAEAGAVQIF---CLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIG 115
           V   ++ GF  + G +++F    L+P D+    G  P    S   V I     + +KI G
Sbjct: 91  VVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDV-ITIKSRIRVKIEG 149

Query: 116 TQVDVTEIEK 125
               V+ I  
Sbjct: 150 CISQVSSIHA 159

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

 Score = 72.7 bits (178), Expect = 3e-17
 Identities = 49/128 (38%), Positives = 75/128 (58%), Gaps = 6/128 (4%)

Query: 1   MKDVEGTCSGRHGFAVAITGA--ESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAG 58
           + DVEGTCSG++G+ + +  +    I KG +  G     F V+ + +++RPF+GE++ A 
Sbjct: 32  LADVEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLWRPFRGEVVDAI 91

Query: 59  VTMVNKMGFLAEAGAVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIG 115
           VT VNKMGF A  G + +F    L+P DM+      P   + +  V I+K   + LKI+G
Sbjct: 92  VTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQV-IEKGSNVRLKIVG 150

Query: 116 TQVDVTEI 123
           T+ D TEI
Sbjct: 151 TRTDATEI 158

>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 = 72.6 bits (178), Expect = 4e-17
 Identities = 36/130 (27%), Positives = 64/130 (49%), Gaps = 6/130 (4%)

Query: 1   MKDVEGTCSGRHGFAVAITGAE--SIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAG 58
           +++VEG+C+G+ G+ + +   +   I +G I        F V+ + +VF+PFKGE++   
Sbjct: 31  LEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGT 90

Query: 59  VTMVNKMGFLAEAGAVQIF---CLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIG 115
           V   ++ GF  + G +++F    L+P D+    G  P    S   V I     + +KI G
Sbjct: 91  VVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDV-ITIKSRIRVKIEG 149

Query: 116 TQVDVTEIEK 125
               V+ I  
Sbjct: 150 CISQVSSIHA 159

>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 Length = 180

 Score = 71.5 bits (175), Expect = 1e-16
 Identities = 22/128 (17%), Positives = 39/128 (30%), Gaps = 3/128 (2%)

Query: 2   KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTM 61
           +  +       G  +AI   ++  +G++  G       V    I + P   E++   V  
Sbjct: 32  QQYQEKILKDLGLVLAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQEVVEGEVLQ 91

Query: 62  VNKMGFLAEAGAVQIF---CLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
           V+  G     G +        I DD                   IQK  ++  ++I    
Sbjct: 92  VDNYGVFVNLGPMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVAS 151

Query: 119 DVTEIEKA 126
            VT     
Sbjct: 152 TVTGRLPR 159

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	143
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	100.0
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	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	99.97
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	99.97
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	99.96
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	99.96
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.94
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	99.92
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	98.29
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	98.22
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	98.18
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	98.12
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	97.99
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	97.98
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	97.91
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	97.9
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	97.73
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	97.72
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.69
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	97.66
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	97.5
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	97.46
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	97.46
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	97.43
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	97.41
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.33
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	97.26
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.23
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	97.05
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	97.03
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	97.0
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	96.96
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	96.94
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	96.94
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	96.85
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	96.71
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	96.3
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	96.3
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	96.22
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	94.79
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	94.32
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	94.09
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	93.21
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	92.87
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	86.44

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

Probab=100.00  E-value=1.9e-34  Score=225.40  Aligned_cols=132  Identities=18%  Similarity=0.266  Sum_probs=120.0

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccE-EEE--
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQ-IFC--   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~-ifI--   78 (143)
                      ++|||||++++||||+++|+.++++|+|.||||+++|+|+|+|++||||+||+++|+|++++++|+|+++||.+ +++  
T Consensus        32 ~~~egkv~~~~Gl~I~v~di~~i~~g~I~~GdG~~~~~V~fk~~~f~p~~GEv~~G~Vs~vt~~GifV~lg~~eglv~~~  111 (203)
T 3ayh_B           32 KKYANKVIQNIGLAICVYDFLKIGEGIIKYGDGSSYMNVVFRLIIFRPFRGEVMLGKIKSCSEEGIRVTISFFDDIFIPK  111 (203)
T ss_dssp             HHHTTEEETTTEEEEEEEEEEEECCCEECTTTCCEEEEEEEEEEEECCCTTCEEEEEEEEEETTEEEEECSSCCCEEEEG
T ss_pred             hhhCCEEeCCccEEEEEEEeeEecccEEeCCCCCEEEEEEEEEEEEccCCCCEEEEEEEEEeccEEEEEEeCceEEEEcH
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999966 666  


Q ss_pred             -EcCCCceecCCC-CceEEc------CCceEEEcCCCeEEEEEEEEEEc---------------------cCCeEEEEEc
Q 032315           79 -LIPDDMELQTGD-LPSYTT------SDGSVKIQKDCELWLKIIGTQVD---------------------VTEIEKARRE  129 (143)
Q Consensus        79 -~lp~~~~fd~~~-~~~~~~------~~~~~~i~~g~~VR~RV~~v~~~---------------------~~~~~ai~~~  129 (143)
                       .+|+++.||+++ .|.|.+      ++++.+|+.|+.|||||.+++++                     ...+.++|+|
T Consensus       112 ~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~p~~~~~~~~~~~~~~~~~~~~~~i~gs~  191 (203)
T 3ayh_B          112 DMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQIESEDFVDISPKRNKNATAITGTEALESVSPYTLIASC  191 (203)
T ss_dssp             GGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEEEEEEECC--------------------CCSEEEEEEB
T ss_pred             HhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEEEEEEccccCCCCccccccccccccccCCCCeEEEEEe
Confidence             668889999886 577866      77889999999999999999993                     3468899999


Q ss_pred             cccc
Q 032315          130 VGKQ  133 (143)
Q Consensus       130 ~~~~  133 (143)
                      -+++
T Consensus       192 ~~~g  195 (203)
T 3ayh_B          192 SRDG  195 (203)
T ss_dssp             CSTT
T ss_pred             cCCC
Confidence            7664

>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=1.3e-34  Score=220.94  Aligned_cols=130  Identities=38%  Similarity=0.679  Sum_probs=121.9

Q ss_pred             cceeEEEeCCeeEEEEEe--ecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE-
Q 032315            2 KDVEGTCSGRHGFAVAIT--GAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC-   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~--dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI-   78 (143)
                      +++||+|+++.|+||+++  ||.++++|+|.+|||+++|+|+|+|++|+|++||+++|+|++++++|+|+++||.++|| 
T Consensus        33 ~~~~g~vi~~~G~~I~i~~idi~~i~~G~I~~gdg~~~~~v~f~~ivf~p~~Gev~~G~V~~v~~fG~FV~l~~~~glVh  112 (172)
T 3h0g_G           33 ADVEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLWRPFRGEVVDAIVTTVNKMGFFANIGPLNVFVS  112 (172)
T ss_dssp             HHHTTCEETTTEEEEEECTTTSEEECCCEECTTTCCEEEEEEEEEEEECCCTTCEEECCCCEEETTEEECCBTTBCCEEE
T ss_pred             HHhCCcCcCCccEEEEEEeeeeeEeeCCEEECCCCcEEEEEEEEEeeeccCCCCEEEEEEEEEEcceEEEEeCCeEEEEE
Confidence            478999999999999999  99999999999999999999999999999999999999999999999999999999999 


Q ss_pred             --EcCCCceecCC-CCceEEcCCceEEEcCCCeEEEEEEEEEEccCCeEEEEEccccc
Q 032315           79 --LIPDDMELQTG-DLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARREVGKQ  133 (143)
Q Consensus        79 --~lp~~~~fd~~-~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ai~~~~~~~  133 (143)
                        +||+++.||++ ++|+|  ++++..++.||.||+||.+++++.++++|||+|-+++
T Consensus       113 ~s~l~~~~~~d~~~~~~~~--~~~~~~~~~Gd~VrvkV~~vd~~~~~~~~Igtm~~~~  168 (172)
T 3h0g_G          113 SHLVPPDMKFDPTANPPNY--SGEDQVIEKGSNVRLKIVGTRTDATEIFAIATMKEDY  168 (172)
T ss_dssp             GGGSCTTCCCBSSSSSCBE--ESSSCEECSSCCEEEEEEEEEESSSCEEEEEECCSTT
T ss_pred             HHHCCCccccCcccccceE--ecCCcEECCCCEEEEEEEEEECCCCCceEEEEcCCCC
Confidence              88888999987 46888  4566899999999999999999999999999987765

>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=7.3e-33  Score=218.92  Aligned_cols=120  Identities=14%  Similarity=0.236  Sum_probs=109.3

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEc-cccE-EEE-
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEA-GAVQ-IFC-   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~i-Gp~~-ifI-   78 (143)
                      ++|||||++++|||||++||.++++|+|.||||+++|+|+|+|++||||+||+++|+|++++++|+|+++ ||.+ +++ 
T Consensus        32 ~kyegkv~~~~Gl~I~v~di~~i~eG~I~~GdG~~~~~V~fk~~~f~p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~  111 (218)
T 2ckz_B           32 NKFANKIIPNVGLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIP  111 (218)
T ss_dssp             HHHTTEEETTTEEEEEEEEEEEECCCEECSSSSCEEEEEEEEEEEECCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEE
T ss_pred             HHhcCcCcCCccEEEEEEEeeeccCcEEeCCCCCEEEEEEEEEEEecCCCCCEEEEEEEEEccCcEEEEccCccceEEEc
Confidence            5789999999999999999999999999999999999999999999999999999999999999999999 9966 666 


Q ss_pred             --EcCCCceecCCC-CceEEc-CCceEEEcCCCeEEEEEEEEEEccC
Q 032315           79 --LIPDDMELQTGD-LPSYTT-SDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        79 --~lp~~~~fd~~~-~~~~~~-~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                        ++|+++.||+++ .|+|.+ ++++.+|+.|+.|||||.+++++..
T Consensus       112 s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~~~~  158 (218)
T 2ckz_B          112 QNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVDV  158 (218)
T ss_dssp             TTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEECCC
T ss_pred             HHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEcccC
Confidence              567789999886 477766 6778999999999999999999764

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

Probab=99.97  E-value=1.1e-30  Score=199.59  Aligned_cols=119  Identities=18%  Similarity=0.230  Sum_probs=107.6

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC---   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---   78 (143)
                      +++||+|+++.|+||+++||.++++|+|.+|||+++++|+|++++|||++||+++|+|++++++|+|+++||.+.++   
T Consensus        32 ~k~~~kv~~~~G~~I~v~di~~~~~g~I~~gdg~~~~~v~~~~iv~~p~~Gev~~G~V~~v~~~G~fv~l~~~~glvh~s  111 (180)
T 4ayb_E           32 QQYQEKILKDLGLVLAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQEVVEGEVLQVDNYGVFVNLGPMDGLVHIS  111 (180)
T ss_dssp             HHTTTCBCSSSCEEEEEEEEEEEEEEEECSSCSSEEEEEEEEEEEECCCTTCEEEEEEEEEETTEEEEECSSSEEEEEGG
T ss_pred             HHhcCeEcCCCcEEEEeeeEeecCceeEccCchHHHHHHhhheeeeeccCCCEEEEEEeeeccceEEEEECCccceEEee
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999888   


Q ss_pred             EcCC-CceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           79 LIPD-DMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        79 ~lp~-~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      +|++ .+.||+++. .|..++++.+++.||.||+||.+++.+.+
T Consensus       112 ~l~~d~~~~d~~~~-~~~g~~~~~~~~~Gd~VrvkV~~v~~~~~  154 (180)
T 4ayb_E          112 QITDDTLKYDNVRG-IIFGEKSKKVIQKGDKVRARVISVASTVT  154 (180)
T ss_dssp             GSCSSCEEECSSSC-CEEETTTCCCCCTTCEEEEEEEEECC---
T ss_pred             ecCCCccccchhcc-eEEEeccCeEECCCCEEEEEEEEEeCCCC
Confidence            5554 478998864 47778888999999999999999987654

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

Probab=99.97  E-value=4.2e-30  Score=195.32  Aligned_cols=131  Identities=43%  Similarity=0.743  Sum_probs=123.0

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC---   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---   78 (143)
                      .+++|+|+++.|+||+++||.++++|+|.||||.++++++|++++|+|+.||+++|+|++++++|+|+++||.++||   
T Consensus        32 ~~~~~~vi~~~G~~I~~~di~~i~~g~i~~~d~~~~~~~~~~~~~~~~~~Gev~~G~V~~v~~fG~fV~l~~~~glvhis  111 (172)
T 2c35_B           32 TEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRH  111 (172)
T ss_dssp             HHHTTCEETTTEEEEEEEEEEEECCCBCCTTCSSEEEEEEEEEEEECCCTTCEEEEEEEEEETTEEEEEETTEEEEEEGG
T ss_pred             HHHcCcCcCCceEEEEEEEeeecCCeEEeCCCCCEEEEEEEEEEEeeCCCCCEEEEEEEEEeCCEEEEEECCEEEEEEHH
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999   


Q ss_pred             EcCCCceecCCCC-ceEEcCCceEEEcCCCeEEEEEEEEEEccCCeEEEEEcccc
Q 032315           79 LIPDDMELQTGDL-PSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARREVGK  132 (143)
Q Consensus        79 ~lp~~~~fd~~~~-~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ai~~~~~~  132 (143)
                      +|++++.||+.++ |+|.+++++.+++.||.||+||.++.++.+++.++|+|-++
T Consensus       112 ~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~~~~igsm~~~  166 (172)
T 2c35_B          112 SIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDD  166 (172)
T ss_dssp             GSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEEEEEEECCST
T ss_pred             HCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCCCCcEEEEEecCC
Confidence            8888889998764 99999888899999999999999999999889999998554

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

Probab=99.96  E-value=3e-29  Score=190.70  Aligned_cols=130  Identities=28%  Similarity=0.572  Sum_probs=106.0

Q ss_pred             cceeEEEeCCeeEEEEEeecc--eecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE-
Q 032315            2 KDVEGTCSGRHGFAVAITGAE--SIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC-   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~--~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI-   78 (143)
                      .+++|+|+++.|+||+++||.  ++++|+|.+|||.+++++.|++++|+|+.||+++|+|++++++|+|+++||.++|| 
T Consensus        32 ~~~i~~vig~~G~~I~~~di~~~di~~g~i~~~d~~~~~~~~~~~~~~~~~~Gev~~G~V~~v~~fG~FV~l~~~dglvh  111 (171)
T 1y14_B           32 EEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVT  111 (171)
T ss_dssp             HHHTTEEETTTEEEEEECCGGGCBCC------------CEEEEEEEEECCCTTCEEEEEEEEEETTEEEEEETTEEEEEE
T ss_pred             HHHcCcCcCCceEEEEEEEecccccCccEEeCCCCCEEEEEEEEEEEccCCCCCEEEEEEEEEecCEEEEEecCeEEEEE
Confidence            367899999999999999999  99999999999999999999999999999999999999999999999999988999 


Q ss_pred             --EcCCCceecCCC-CceEEcCCceEEEcCCCeEEEEEEEEEEccCCeEEEEEccccc
Q 032315           79 --LIPDDMELQTGD-LPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARREVGKQ  133 (143)
Q Consensus        79 --~lp~~~~fd~~~-~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ai~~~~~~~  133 (143)
                        +||+++.||+.+ .|+|.+++  ..++.||.||+||.++.++.+++.++|+|-+++
T Consensus       112 is~l~~~~~~d~~~~~~~~~~~~--~~~~~Gd~V~vkV~~vd~~~~~~~~igsm~~~~  167 (171)
T 1y14_B          112 KHLMPQDLTFNAGSNPPSYQSSE--DVITIKSRIRVKIEGCISQVSSIHAIGSIKEDY  167 (171)
T ss_dssp             GGGSCTTCEECC-----CEECSS--CEECTTCEEEEEEEEEEEETTEEEEEEECCSTT
T ss_pred             HHHCCCCceECcccCceEEeccc--eEECCCCEEEEEEEEEEcCCCCcEEEEEcCCCC
Confidence              888888999876 58898866  459999999999999999999999999986553

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

Probab=99.96  E-value=8.8e-29  Score=195.25  Aligned_cols=130  Identities=28%  Similarity=0.572  Sum_probs=121.2

Q ss_pred             cceeEEEeCCeeEEEEEeecc--eecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE-
Q 032315            2 KDVEGTCSGRHGFAVAITGAE--SIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC-   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~--~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI-   78 (143)
                      .+++|+|+++.|+||+++||.  ++++|+|.||||.+++++.|++++|+|++||+++|+|++++++|+|+++||.++|| 
T Consensus        32 ~~~ig~vIg~~G~vI~~~dI~~~di~dG~I~~gdg~~~~~v~~~~i~~~p~vGev~~G~V~~vt~fG~FVelg~~dGlVh  111 (215)
T 2b8k_G           32 EEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVT  111 (215)
T ss_dssp             HSSTTCEETTTEEEEEECCSTTCBCCCEEECSSSCCEEEEEECCEEEECCCTTEEEEEEEEEEETTEEEEECTTSEEEEE
T ss_pred             HHHCCeEcCCCCEEEEEEEeeecccccceEeCCCHHHHHHHHhhhheeccCCCCEEEEEEEEEecceEEEEecCcEEEEE
Confidence            478999999999999999999  99999999999999999999999999999999999999999999999999999999 


Q ss_pred             --EcCCCceecCCC-CceEEcCCceEEEcCCCeEEEEEEEEEEccCCeEEEEEccccc
Q 032315           79 --LIPDDMELQTGD-LPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARREVGKQ  133 (143)
Q Consensus        79 --~lp~~~~fd~~~-~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ai~~~~~~~  133 (143)
                        +|++++.||+.+ .|.|.+++  ..++.||.||+||.++.++..++.++|+|-.++
T Consensus       112 iS~l~d~~~~d~~~~~w~~~~~~--~~~~~Gd~VrVkV~~vd~~~~~i~~IgSmk~~~  167 (215)
T 2b8k_G          112 KHLMPQDLTFNAGSNPPSYQSSE--DVITIKSRIRVKIEGCISQVSSIHAIGSIKEDY  167 (215)
T ss_dssp             GGGSCSSCCCBSSCSSCEEECSS--CEEETTCEEEEEEEEEEEETTEEEEEEECCSTT
T ss_pred             HHHCCccceeccccccceeeccc--cEECCCCEEEEEEEEEEcCCCccEEEEEcCCCC
Confidence              888888999876 58998876  569999999999999999999999999986653

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

Probab=99.94  E-value=2.2e-26  Score=176.52  Aligned_cols=119  Identities=17%  Similarity=0.238  Sum_probs=107.1

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEEccccEEEE---
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC---   78 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---   78 (143)
                      +++||||.++.|+||+++||.+.++|+|.++||.+++++.|++++|+|+.||+++|+|++++++|+|+++||.+.++   
T Consensus        32 ~~~~gk~~~~~G~~i~~idi~~~g~~~I~~~d~~~~~~~~~~~i~~~~~~Gev~~G~V~~v~~~G~fV~l~~~eglvhis  111 (187)
T 1go3_E           32 EKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVS  111 (187)
T ss_dssp             HHHTTCEETTTEEEEEEEEEEEECCCBCCTTCCSEEEEEEEEEEEECCCTTCEEEEEEEEEETTEEEEECSSSEEEEEGG
T ss_pred             HHhCCeEcCCccEEEEEEEEeeccCCEEeCCCccEEEEEEEEEEEEccCCCCEEEEEEEEEeCcEEEEEEcCccEEEEhH
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999998   


Q ss_pred             Ec-CCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           79 LI-PDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        79 ~l-p~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      ++ ++.+.||+++. .|..++.+.+++.||.||+||.++..+.+
T Consensus       112 ~l~~~~~~~d~~~~-~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  154 (187)
T 1go3_E          112 QIMDDYVSYDPKRE-AIIGKETGKVLEIGDYVRARIVAISLKAE  154 (187)
T ss_dssp             GSCSSCEEECCC---CEEETTTCCEECTTCEEEEEEEEEECCC-
T ss_pred             HhCCCcceECCccc-eEEecCCCeEEcCCCEEEEEEEEEEcccC
Confidence            44 45688998864 46666777899999999999999998765

>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=99.92  E-value=9.8e-25  Score=171.76  Aligned_cols=121  Identities=15%  Similarity=0.153  Sum_probs=93.8

Q ss_pred             EEeCCe-eEEEEEeecceecc------------eeEEcCCccEEEEEEEEEEEEeecCCCEEEEEEEEEecccEEEE-cc
Q 032315            7 TCSGRH-GFAVAITGAESIGK------------GLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAE-AG   72 (143)
Q Consensus         7 ~~~~~~-GliI~i~dI~~i~e------------G~I~~gdG~~~~~V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~-iG   72 (143)
                      ++.+++ |+|++++|+..+++            |+|.+|+|.++++|+|+++|||||+||+|+|+|+++++.|+.+. +|
T Consensus        72 ky~~~~~Gv~la~~di~~~~~~~~~~d~~~~~~g~I~~~~g~~~~~V~~~~iVFrPf~GevL~G~V~~~s~~~Ig~~~~G  151 (214)
T 2rf4_A           72 KYNNKVGGVVLGYEGLKILDADPLSKEDTSEKLIKITPDTPFGFTWCHVNLYVWQPQVGDVLEGYIFIQSASHIGLLIHD  151 (214)
T ss_dssp             SEETTTTEEEEEEEEEETTSCCC-----------------CCCEEEEEEEEEEECCCTTCEEEEEECCCCSSCEEEEETT
T ss_pred             cccCCCCEEEEEEECeEeccCCCcCccccccceeEEeCCCceEEEEEEEEEEEEecCCCCEEEEEEEEECCCcEEEEEeC
Confidence            455666 89999999865554            79999999999999999999999999999999999999998884 69


Q ss_pred             ccEEEE---EcCCCceecCCC----CceEEcCCceEEEcCCCeEEEEEEEEEEccCCeEEEEEcc
Q 032315           73 AVQIFC---LIPDDMELQTGD----LPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARREV  130 (143)
Q Consensus        73 p~~ifI---~lp~~~~fd~~~----~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~ai~~~~  130 (143)
                      |+++||   .||+++.|++++    .++|..+++..   .|++|||||.+++.+..-+..-|+|+
T Consensus       152 ~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~---ig~~IRFrV~~~~~~~~~lsI~Gsll  213 (214)
T 2rf4_A          152 AFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEP---IDGKLRFTVRNVHTTGRVVSVDGTLI  213 (214)
T ss_dssp             TEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCB---CCSEEEEEEEEEECCSSSCEEEEECC
T ss_pred             CEEEEEcHHHCCCcccccccccccCCCceEcCCCCC---CCCEEEEEEEEEEecCCEEEEEEEec
Confidence            999999   999999998764    35666544332   59999999999998655455566653

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

Probab=98.29  E-value=1.4e-06  Score=57.57  Aligned_cols=64  Identities=19%  Similarity=0.180  Sum_probs=48.0

Q ss_pred             eecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .|..|+++.|+|++++++|+|+.+++ .++++.+.+ +      .|.+.     ..++.||.|++||.++..+.+++
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~se-l------~~~~~-----~~~~~Gd~V~v~V~~vd~~~~~i   66 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRD-M------ISLRL-----ENLNVGDEIIVQAIDVRPEKREI   66 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGG-C------SSCCG-----GGCCTTCEEEEEEEEEETTTTEE
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHH-C------Ccccc-----eeeCCCCEEEEEEEEEECCCCEE
Confidence            47789999999999999999999985 788882211 0      01010     35899999999999988765543

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

Probab=98.22  E-value=1e-06  Score=62.28  Aligned_cols=76  Identities=16%  Similarity=0.159  Sum_probs=55.6

Q ss_pred             EEEEEEEeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315           41 RCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD  119 (143)
Q Consensus        41 ~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~  119 (143)
                      .|..+..+|..|++++|+|++++++|+|+.+++ .++||.+.+ +.++.      ..++.+..+++||.|++||.++..+
T Consensus        20 p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhise-l~~~~------~~~~~~~~~~vGd~V~vkV~~vd~~   92 (115)
T 2khi_A           20 HWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSE-MDWTN------KNIHPSKVVNVGDVVEVMVLDIDEE   92 (115)
T ss_dssp             -CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTS-SSCSS------TTCSSTTTCCTTCEEEEEEEEEETT
T ss_pred             CHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHH-CCccc------cccCcccEECCCCEEEEEEEEEECC
Confidence            355566789999999999999999999999986 889983321 11110      0123345789999999999999875


Q ss_pred             cCCe
Q 032315          120 VTEI  123 (143)
Q Consensus       120 ~~~~  123 (143)
                      .+.+
T Consensus        93 ~~rI   96 (115)
T 2khi_A           93 RRRI   96 (115)
T ss_dssp             TTEE
T ss_pred             CCEE
Confidence            5543

>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=98.18  E-value=8.2e-07  Score=63.37  Aligned_cols=69  Identities=19%  Similarity=0.234  Sum_probs=54.5

Q ss_pred             EEEEEEEeecCCCEEEEEEEEEecccEEEEccc--cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEE
Q 032315           41 RCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGA--VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIG  115 (143)
Q Consensus        41 ~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~  115 (143)
                      .++.+.+.|..|+++.|+|++++++|+|+.++.  .+.||   .|+++.           .++....++.||.|++||+.
T Consensus        12 ~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~-----------~~~~~~~~~~Gd~V~VkV~~   80 (119)
T 2cqo_A           12 RPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCR-----------VDKPSEIVDVGDKVWVKLIG   80 (119)
T ss_dssp             CCCCSCCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSC-----------CSCHHHHCCTTCEEEEEEEE
T ss_pred             chhhhhcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCccc-----------ccChhhcCCCCCEEEEEEEE
Confidence            366778899999999999999999999999954  48988   454221           12334568999999999999


Q ss_pred             EEEcc
Q 032315          116 TQVDV  120 (143)
Q Consensus       116 v~~~~  120 (143)
                      +..+.
T Consensus        81 vd~~~   85 (119)
T 2cqo_A           81 REMKN   85 (119)
T ss_dssp             EEECS
T ss_pred             Eeccc
Confidence            98754

>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=98.12  E-value=4.5e-06  Score=57.85  Aligned_cols=63  Identities=13%  Similarity=0.124  Sum_probs=49.4

Q ss_pred             EEeecCCCEEEEEEEEEecccEEEEcc----ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           46 VFRPFKGEILGAGVTMVNKMGFLAEAG----AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        46 vFrPf~gEVv~G~V~~v~~~Gi~v~iG----p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      .+.|..|+++.|+|+++.++|+|+.++    ..+.||   .|+++.         + .++....++.||.|++||+.+..
T Consensus         7 ~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~---------~-~~~~~~~~~~Gd~V~VkV~~vd~   76 (103)
T 2eqs_A            7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREG---------R-VANVADVVSKGQRVKVKVLSFTG   76 (103)
T ss_dssp             CSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSS---------C-CCCHHHHCCTTCEEEEEEEEEET
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCc---------c-cCCcccEeCCCCEEEEEEEEEEC
Confidence            457889999999999999999999997    588998   443211         1 12334568999999999999864

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

Probab=97.99  E-value=7.5e-06  Score=57.08  Aligned_cols=64  Identities=22%  Similarity=0.188  Sum_probs=48.5

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      ..+..|+++.|+|++++++|+|+.+++ .++||   .++++          + .++-...+++||.|++||..+..+..
T Consensus        27 ~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~----------~-~~~~~~~~~vGd~V~v~V~~vd~~~~   94 (109)
T 2khj_A           27 ALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRD----------R-VEDATLVLSVGDEVEAKFTGVDRKNR   94 (109)
T ss_dssp             TTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSS----------S-SSSGGGSCCTTCEEEEEEEEEETTTT
T ss_pred             hcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcc----------c-ccChhhccCCCCEEEEEEEEEECCCC
Confidence            356789999999999999999999986 77777   22211          1 12233568999999999999876543

>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=97.98  E-value=1.7e-05  Score=60.62  Aligned_cols=66  Identities=11%  Similarity=0.109  Sum_probs=45.1

Q ss_pred             ecCCCEEEEEEEEEecccEEEEc---cccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEA---GAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~i---Gp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |..|+++.|+|++++++|+|+.+   +..+++|.+.+ +      .|.+ .++-+..+++|+.|++||+++.-+.+.
T Consensus        13 p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSe-l------s~~~-v~~~~~~~~vGd~V~VkVl~vD~~~~r   81 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSE-L------SRRR-IRSINKLIRIGRNECVVVIRVDKEKGY   81 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGG-C-------------------CTTCEEEEEEEEEETTTTE
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHH-C------CCcc-cCCHHHhcCCCCEEEEEEEEEECCCCE
Confidence            68999999999999999999999   45899883321 0      1111 123346799999999999998765444

>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=97.91  E-value=2.8e-05  Score=58.97  Aligned_cols=66  Identities=11%  Similarity=0.083  Sum_probs=47.8

Q ss_pred             ecCCCEEEEEEEEEecccEEEEc---cccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEA---GAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~i---Gp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |-.|+++.|+|++++++|+|+.+   +..+++|.+.+ +      .|.| .++-+..+++|+.|++||+++..+.+.
T Consensus        13 p~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSe-l------s~~~-v~~~~~~~~vGd~V~vkVl~vd~~~~~   81 (175)
T 2a19_A           13 PEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSE-L------SRRR-IRSIQKLIRVGKNDVAVVLRVDKEKGY   81 (175)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC----------------CCCCCCCTTSEEEEEEEEEETTTTE
T ss_pred             CCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHH-c------CCcc-cCCHHHcCCCCCEEEEEEEEEECCCCe
Confidence            55899999999999999999999   45889883321 0      1111 123346789999999999998765544

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

Probab=97.90  E-value=1.9e-05  Score=56.96  Aligned_cols=63  Identities=13%  Similarity=0.134  Sum_probs=48.5

Q ss_pred             eecCCCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      .+..|+++.|+|++++++|+||.++ ..++||   .|.++.           ..+-...+++||.|++||+.+..+..
T Consensus         4 ~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~-----------~~~~~~~~~vGd~V~vkV~~vd~~~~   70 (130)
T 2k4k_A            4 KFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGF-----------VKDINEHLSVGDEVQVKVLAVDEEKG   70 (130)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSC-----------CSCGGGTCCTTCEEEEEEEEEETTTT
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCccc-----------ccCccccCCCCCEEEEEEEEEeCCCC
Confidence            4678999999999999999999995 488988   443221           11223568999999999999986443

>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=97.73  E-value=1.2e-05  Score=56.90  Aligned_cols=66  Identities=15%  Similarity=0.171  Sum_probs=46.9

Q ss_pred             eecCCCEEEEEEEEEecccEEEEccc--cEEEE--EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAGA--VQIFC--LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI--~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      .+..|++++|+|++++++|+|+.+++  ...++  .+.++        | +..++-+..++.||.|++||.++..+.+.
T Consensus        18 ~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~--------~-~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~   87 (119)
T 1wi5_A           18 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQE--------Y-IRQKNKGAKLKVGQYLNCIVEKVKGNGGV   87 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHH--------H-HHHHSSSCCCCTTCEEEEEEEECCTTSCE
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccc--------c-ccccCccCEeCCCCEEEEEEEEEeCCCCE
Confidence            36789999999999999999999993  55555  22111        1 11112235789999999999997655443

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

Probab=97.72  E-value=1.4e-05  Score=54.16  Aligned_cols=67  Identities=12%  Similarity=0.017  Sum_probs=46.9

Q ss_pred             eecCCCEEEEEEEEEecccEEEEcc---ccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAG---AVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iG---p~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      .|..|++++|+|+ ++++|+|+.+.   ..+++|.+...+      .|-|.... +..+ .|+.|++||+++..+.+++
T Consensus         8 ~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el------~~~~~~~~-~~~~-~Gd~V~VkV~~vd~~~~kI   77 (88)
T 1luz_A            8 LPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKM------HMDRYVEY-RDKL-VGKTVKVKVIRVDYTKGYI   77 (88)
T ss_dssp             CCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSC------CHHHHHHH-HHHH-TTCEEEEEEEEEETTTTEE
T ss_pred             CCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHh------CcccccCH-hHEe-CCCEEEEEEEEEECCCCEE
Confidence            4889999999999 99999999995   378988332011      11111111 2234 9999999999998765553

>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=97.69  E-value=8.1e-05  Score=56.53  Aligned_cols=64  Identities=3%  Similarity=0.020  Sum_probs=51.4

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccc--cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEc
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGA--VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVD  119 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~  119 (143)
                      |.|..|++|.|.|++++..++++++|+  .+.++.+.   .|+...      ++.+..+++||.|++||.++.-+
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---AFPNAS------KKNRPTLQVGDLVYARVCTAEKE   68 (175)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETT---SSTTCC------SSSCCCCCTTCEEEEEEEECCTT
T ss_pred             ccCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHH---HCCchh------hhhhccCCCCCEEEEEEEEecCC
Confidence            789999999999999999999999987  77877332   244221      34567899999999999987654

>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A

Probab=97.66  E-value=0.00012  Score=65.25  Aligned_cols=75  Identities=9%  Similarity=0.125  Sum_probs=59.5

Q ss_pred             EeecCCC--EEEEEEEEEecccEEEEcc-c-cEEEE---EcCC---CceecCCCCceEEcCCceEEEcCCCeEEEEEEEE
Q 032315           47 FRPFKGE--ILGAGVTMVNKMGFLAEAG-A-VQIFC---LIPD---DMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGT  116 (143)
Q Consensus        47 FrPf~gE--Vv~G~V~~v~~~Gi~v~iG-p-~~ifI---~lp~---~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v  116 (143)
                      +++..||  +.+|+|++++++|+||.+. + .+++|   .|++   .+.||+.....+.  +++..++.||.|++||.++
T Consensus       554 l~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d~~~~d~~~~~l~~--~~~~~~~lGD~V~VkV~~v  631 (644)
T 2id0_A          554 LKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQI--KGETVYKVTDVIDVTIAEV  631 (644)
T ss_dssp             HGGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEE--TTEEEEETTCEEEEEEEEE
T ss_pred             hhhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCceeEEcccccEEEe--cCCCEeCCCCEEEEEEEEE
Confidence            5677899  9999999999999999994 4 88999   6653   3677776543323  5668899999999999999


Q ss_pred             EEccCCe
Q 032315          117 QVDVTEI  123 (143)
Q Consensus       117 ~~~~~~~  123 (143)
                      ......+
T Consensus       632 d~~~~~I  638 (644)
T 2id0_A          632 RMETRSI  638 (644)
T ss_dssp             ETTTTEE
T ss_pred             eCCCCEE
Confidence            8876554

>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=97.50  E-value=0.00021  Score=56.20  Aligned_cols=65  Identities=12%  Similarity=0.178  Sum_probs=49.8

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEcc-ccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      |.|..|++|.|+|+++++.|++++++ |.+.+|.+.+   +... .+   .++-+..+++||.|++||+++.-
T Consensus        53 y~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~ise---v~~~-~~---~~~~~~~l~~GD~V~arVi~v~~  118 (229)
T 2ba0_A           53 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSE---NPEM-KP---NKKPNEVLDIGDAIIAKVLNIDP  118 (229)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGG---CTTC-CT---TSCGGGTCCTTCEEEEEEEEECT
T ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHH---cccc-cc---ccchhcccCCCCEEEEEEEEECC
Confidence            78999999999999999999999998 7898883321   1111 11   12344678999999999998853

>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=97.46  E-value=0.00012  Score=57.52  Aligned_cols=64  Identities=9%  Similarity=0.100  Sum_probs=48.9

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      |.|..|+++.|+|+++++.|+|+++| +.+.+|   ++.+    +....+   ..+-+..+++||.|++||+++.
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 YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLG----RPFNPA---VDDMQSLLKVGDYIKAKVVAFD  129 (235)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHT----SCCCTT---TTCCTTSSCTTCEEEEEEEEEC
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCC----Cccccc---hhhHhhcCCCCCEEEEEEEEEC
Confidence            78999999999999999999999998 699988   3332    111111   1122357899999999999986

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A

Probab=97.46  E-value=0.00024  Score=57.37  Aligned_cols=67  Identities=16%  Similarity=0.209  Sum_probs=49.3

Q ss_pred             eecCCCEEEEEEEEEecccEEEEcc---ccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAG---AVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iG---p~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      .|..|+++.|+|+++.++|+|+.++   ..++||.+.+-       .|.|. ++-...+++|+.|++||+++..+.+.
T Consensus         8 ~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSel-------s~~~v-~~~~~~~kvGd~V~vkVi~vD~~~~~   77 (275)
T 3aev_A            8 YPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEV-------ASTWV-RNIRDYLKEGQKVVAKVIRVDPRKGH   77 (275)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGS-------CSSCC-SCGGGTCCTTCEEEEEEEEEETTTTE
T ss_pred             CCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHc-------Ccccc-cCHHhccCCCCEEEEEEEEEECCCCE
Confidence            4668999999999999999999996   48899933210       01111 12235689999999999998865544

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1

Probab=97.43  E-value=0.00022  Score=58.49  Aligned_cols=66  Identities=11%  Similarity=0.085  Sum_probs=48.6

Q ss_pred             ecCCCEEEEEEEEEecccEEEEcc---ccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAG---AVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iG---p~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |..|+++.|+|++++++|+|+.++   ..++||.+.+ +      .|.| .++-...+++|+.|++||+.+..+.+.
T Consensus        11 ~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSe-l------s~~~-i~~~~~~~kvGd~V~VkVl~vD~~~~r   79 (308)
T 1q8k_A           11 PEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSE-L------SRRR-IRSINKLIRIGRNECVKVIRVDKEKGY   79 (308)
T ss_dssp             CSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGG-T------SCSS-CSCCTTTCSSSCEEEEEEEEEETTTTE
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHH-c------Cccc-ccCHHHhcCCCCEEEEEEEEEeCCCCE
Confidence            568999999999999999999996   4889983221 0      1111 122335689999999999998865444

>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=97.41  E-value=0.0002  Score=57.04  Aligned_cols=65  Identities=12%  Similarity=0.129  Sum_probs=49.4

Q ss_pred             EEeecCCCEEEEEEEEEecccEEEEcc-ccEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           46 VFRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        46 vFrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      .|.|..|++|.|+|+++++.|+|+++| |.+.+|   ++.+. .-+.+       .+-...+++||.|++||+++.-
T Consensus        69 ~y~p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei~~~-~~~~~-------~~~~~~l~vGD~V~arVi~v~~  137 (251)
T 2je6_I           69 FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGR-SINVG-------EDLRRYLDVGDYVIARIENFDR  137 (251)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTS-CCCTT-------CCCSSSCCTTCEEEEEEEEEET
T ss_pred             ccCCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCC-ccccc-------cchhhcCCCCCEEEEEEEEECC
Confidence            478999999999999999999999998 699988   33211 00110       2223578999999999999863

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

Probab=97.33  E-value=0.0002  Score=49.46  Aligned_cols=55  Identities=13%  Similarity=0.210  Sum_probs=49.4

Q ss_pred             ecceeEEcCCccEEEEEEEEEEE---E---eecCCCEEEEEEEEEecccEEEEccc-cEEEE
Q 032315           24 IGKGLIRNGTVLVTFLVRCQCIV---F---RPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC   78 (143)
Q Consensus        24 i~eG~I~~gdG~~~~~V~F~~lv---F---rPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI   78 (143)
                      -+-|.|.+.+|...+-|++++|.   |   +|..||+++++|++++++|+|+.+.+ .+.+|
T Consensus        28 kGfGFI~~~~gg~dvfvH~s~l~~~~~~~~~l~~Ge~V~g~V~~i~~fG~fv~l~~~~eGlv   89 (101)
T 2bh8_A           28 KGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITDFGIFIGLDGGIDGLV   89 (101)
T ss_dssp             GTEEEEEESSSSCEEEEECCCSCSSSCCCCCCCTTCEEEEEEEECCSEEEEECTTSCEEEEE
T ss_pred             CCCEEEEeCCCCcEEEEEEEEEecCCccccCCCCCCEEEEEEEEeCCcEEEEEcCCCceEEE
Confidence            46689999999999999999998   4   79999999999999999999999954 88887

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

Probab=97.26  E-value=4.1e-05  Score=69.20  Aligned_cols=88  Identities=17%  Similarity=0.089  Sum_probs=0.0

Q ss_pred             ecceecceeEEcCCccEEEEE--EEEEEEEeecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCce
Q 032315           20 GAESIGKGLIRNGTVLVTFLV--RCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPS   93 (143)
Q Consensus        20 dI~~i~eG~I~~gdG~~~~~V--~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~   93 (143)
                      ||.+-+.-.|...+.......  .++.++..|..|++++|+|+++.++|+|+.++| .++||   +|.++          
T Consensus       594 dI~~dg~v~I~~~~~~~~~~a~~~i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~~~----------  663 (723)
T 3cdi_A          594 EIEDDGTVKIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADK----------  663 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EecCCccEEEecCCHHHHHHHHHHHHHHhhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCc----------
Confidence            454444444544454443322  567788999999999999999999999999987 77887   34211          


Q ss_pred             EEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           94 YTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        94 ~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      + .++.+..++.||.|++||+++.-
T Consensus       664 ~-v~~~~~~~~vGd~V~VkVi~vd~  687 (723)
T 3cdi_A          664 R-VEKVTDYLQMGQEVPVKVLEVDR  687 (723)
T ss_dssp             -------------------------
T ss_pred             c-ccCcccccCCCCEEEEEEEEECC
Confidence            1 12334679999999999999875

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

Probab=97.23  E-value=1.1e-05  Score=72.96  Aligned_cols=88  Identities=13%  Similarity=0.034  Sum_probs=5.9

Q ss_pred             ecceecceeEEcCCccEEEE--EEEEEEEEeecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCce
Q 032315           20 GAESIGKGLIRNGTVLVTFL--VRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPS   93 (143)
Q Consensus        20 dI~~i~eG~I~~gdG~~~~~--V~F~~lvFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~   93 (143)
                      ||.+-+.-+|...|+.+...  -.++.++..|..|++++|+|+++.++|+||.+.| .+.+|   +|.++          
T Consensus       604 di~ddG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~~----------  673 (726)
T 4aid_A          604 DINDDGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNE----------  673 (726)
T ss_dssp             ----------CCSCHHHHHHHHHC--------------------------------------------------------
T ss_pred             eEECCceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCcc----------
Confidence            34444455555555544433  4588899999999999999999999999999977 78877   34311          


Q ss_pred             EEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           94 YTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        94 ~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      + .++-+..+++||.|++||+++.-
T Consensus       674 r-v~~~~d~~kvGD~V~VkVi~iD~  697 (726)
T 4aid_A          674 R-VAKPSDVLKEGQMVKVKLLGFDD  697 (726)
T ss_dssp             -------------------------
T ss_pred             c-ccCccccCCCCCEEEEEEEEECC
Confidence            1 12334679999999999999874

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A

Probab=97.05  E-value=0.00013  Score=66.58  Aligned_cols=61  Identities=15%  Similarity=0.177  Sum_probs=47.9

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV  120 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~  120 (143)
                      ...|+++.|+|++++++|+||.+|+ .+++|   .|.+...+           +....+++|+.|++||+++..+.
T Consensus       652 l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v~-----------d~~~~~~vGd~V~VkVi~VD~~~  716 (785)
T 3bzc_A          652 LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVK-----------DPYEVVKAGDIVKVKVMEVDIPR  716 (785)
T ss_dssp             CCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCCS-----------CHHHHCCTTCCCCCBEEEEETTT
T ss_pred             cCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCccccC-----------ChhheeCCCCEEEEEEEEEECCC
Confidence            5689999999999999999999997 78999   44322111           22356899999999999987644

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

Probab=97.03  E-value=0.00094  Score=50.41  Aligned_cols=61  Identities=15%  Similarity=0.018  Sum_probs=44.3

Q ss_pred             EEeecCCCEEEEEEEEEecccEEEEccc-----------cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEE
Q 032315           46 VFRPFKGEILGAGVTMVNKMGFLAEAGA-----------VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKII  114 (143)
Q Consensus        46 vFrPf~gEVv~G~V~~v~~~Gi~v~iGp-----------~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~  114 (143)
                      -+.|. |+++.|+|+++++.|+|+++++           .+.+|.+.+-   .    |.+. ++-...+++||.|++||+
T Consensus        53 ~y~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei---~----~~~~-~~~~~~~~~GD~V~akVi  123 (179)
T 3m7n_A           53 PEIVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNV---D----EGYV-KEISEAVGYLDILKARVI  123 (179)
T ss_dssp             CCCCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGT---T----SSCC-SSGGGTCCTTCEEEEEEE
T ss_pred             cccCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHc---C----cchh-hCHhhcCCCCCEEEEEEE
Confidence            36688 9999999999999999999964           5677733210   0    1111 223467899999999999


Q ss_pred             E
Q 032315          115 G  115 (143)
Q Consensus       115 ~  115 (143)
                      +
T Consensus       124 ~  124 (179)
T 3m7n_A          124 G  124 (179)
T ss_dssp             E
T ss_pred             C
Confidence            7

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}

Probab=97.00  E-value=0.0018  Score=61.50  Aligned_cols=62  Identities=13%  Similarity=0.037  Sum_probs=48.3

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCc-eecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDM-ELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~-~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      ...|+++.|+|++++++|+||.+++ .+++|   .|++.. ..++.           ..+++|+.|++||+++..+..
T Consensus       900 l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~p~-----------~v~kvGd~V~vkVl~VD~~~~  966 (1219)
T 3psi_A          900 FFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPAN-----------EIYEIGKTYPAKVIYIDYANI  966 (1219)
T ss_dssp             SCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTTSCSCST-----------TTSCTTCEEEEEEEEEEGGGT
T ss_pred             CCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCcccCCHH-----------HcCCCCCEEEEEEEEEECCCC
Confidence            4579999999999999999999987 88999   554332 22222           457999999999999876443

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=96.96  E-value=0.0012  Score=61.44  Aligned_cols=71  Identities=8%  Similarity=-0.051  Sum_probs=56.6

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccc--cEEEE---EcC--C-CceecCCCCceEEcCC----ceEEEcCCCeEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGA--VQIFC---LIP--D-DMELQTGDLPSYTTSD----GSVKIQKDCELWLKII  114 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp--~-~~~fd~~~~~~~~~~~----~~~~i~~g~~VR~RV~  114 (143)
                      +++. ||+.+|+|+.++++|+||.+.+  .+.+|   .|+  + .++||+... ....++    .+..++.||.|++||.
T Consensus       883 l~~~-ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~~d~y~fde~~~-~L~g~~~~g~~~~~~~lGD~V~VkV~  960 (977)
T 2wp8_J          883 MRNN-ESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEY-KLTFVPTNSDKPRDVYVFDKVEVQVR  960 (977)
T ss_dssp             HHHT-TCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSCGGGCEEETTTT-EEEECCTTCCSCEEEETTCEEEEEEC
T ss_pred             hccc-ceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCCCceeEEccccc-EEEeecCCCccCcEEccCCEEEEEEE
Confidence            4555 9999999999999999999975  78888   664  3 378998764 344554    3689999999999999


Q ss_pred             EEEEc
Q 032315          115 GTQVD  119 (143)
Q Consensus       115 ~v~~~  119 (143)
                      .+.-+
T Consensus       961 ~vd~~  965 (977)
T 2wp8_J          961 SVMDP  965 (977)
T ss_dssp             CCCCS
T ss_pred             EEcCc
Confidence            87653

>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=96.94  E-value=0.00053  Score=53.16  Aligned_cols=64  Identities=13%  Similarity=-0.032  Sum_probs=43.3

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEcc---------ccEEEEEcCCCceecCCCCceEEc-CCceEEEcCCCeEEEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAG---------AVQIFCLIPDDMELQTGDLPSYTT-SDGSVKIQKDCELWLKIIGT  116 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iG---------p~~ifI~lp~~~~fd~~~~~~~~~-~~~~~~i~~g~~VR~RV~~v  116 (143)
                      +.|..|++|.|+|+++++.|+|++++         +++.+|.+.+       -.|.... .+-...+++||.|++||+++
T Consensus        77 y~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhise-------i~~~~~~~~~~~~~l~~GD~V~akVisi  149 (209)
T 2nn6_I           77 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKED-------VRATEKDKVEIYKSFRPGDIVLAKVISL  149 (209)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEG-------GGTCSSCCCCGGGTCCSSSEEEEEEEEE
T ss_pred             CCCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHH-------cccccccccchhhhcCCCCEEEEEEEEE
Confidence            68999999999999999999999874         2333331100       0000000 02235689999999999998


Q ss_pred             E
Q 032315          117 Q  117 (143)
Q Consensus       117 ~  117 (143)
                      .
T Consensus       150 ~  150 (209)
T 2nn6_I          150 G  150 (209)
T ss_dssp             E
T ss_pred             e
Confidence            4

>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=96.94  E-value=0.00028  Score=57.89  Aligned_cols=69  Identities=16%  Similarity=0.164  Sum_probs=48.6

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEcc-ccEEEEEcCCCceecCCCCceEEc----CCceEEEcCCCeEEEEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFCLIPDDMELQTGDLPSYTT----SDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI~lp~~~~fd~~~~~~~~~----~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      |.|..|++|.|+|+++++.|++++++ |.+.++.++ .+.|+.... .-..    .+....+++||.||+||+++.
T Consensus        91 Y~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS-~v~f~gg~i-R~~~~~D~~~m~~~l~vGDlV~ArVisv~  164 (308)
T 2nn6_H           91 YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLS-SMNLPGGEL-RRRSAEDELAMRGFLQEGDLISAEVQAVF  164 (308)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESS-CCC--------------CHHHHHHSCSSCEECCEEEEEE
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEECCCcCCceech-hhcccccee-ecccchhhhhhhccCCCCCEEEEEEEEcC
Confidence            78999999999999999999999998 788777443 222221110 0000    112357999999999999987

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*

Probab=96.85  E-value=0.00032  Score=56.32  Aligned_cols=63  Identities=21%  Similarity=0.253  Sum_probs=46.3

Q ss_pred             eecCCCEEEEEEEEEecccEEEEcc--c-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAG--A-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iG--p-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      .|..|+++.|+|+++.++|+|+.++  + .++||.+.+ +      .|.| .++-...++.|+.|++||+.+.-
T Consensus         8 ~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSe-l------s~~~-v~~~~~~~~vGd~V~VkVi~vd~   73 (266)
T 3cw2_C            8 LPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSE-V------SSKW-VKNIRDVLKENRKVIVKVIRVDR   73 (266)
T ss_dssp             SCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGG-S------SCSS-CCCHHHHSCTTCEEEEEECCCCS
T ss_pred             cCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHH-c------Cccc-ccCHHHhCcCCCEEEEEEEEEeC
Confidence            4788999999999999999999995  4 778872211 0      0111 12334568999999999999854

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=96.71  E-value=0.0027  Score=57.54  Aligned_cols=70  Identities=9%  Similarity=-0.050  Sum_probs=51.1

Q ss_pred             eecCCCEEEEEEEEEecccEEEEccc--cEEEE---EcC--C-CceecCCCCceEEcCCc----eEEEcCCCeEEEEEEE
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAGA--VQIFC---LIP--D-DMELQTGDLPSYTTSDG----SVKIQKDCELWLKIIG  115 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iGp--~~ifI---~lp--~-~~~fd~~~~~~~~~~~~----~~~i~~g~~VR~RV~~  115 (143)
                      +... ++.+|+|++++++|+||.+..  .+++|   .|.  + .+.||+... ....+++    +..++.||.|++||..
T Consensus       667 ~~~~-~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d~~~fd~~~~-~l~g~~~~~~~~~~~~lGD~V~VkV~~  744 (760)
T 2vnu_D          667 RNNE-STETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEY-KLTFVPTNSDKPRDVYVFDKVEVQVRS  744 (760)
T ss_dssp             HTCC-SEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGGGCEEETTTT-EEEECCTTCSSCEEEETTCEEEEEEC-
T ss_pred             hcCc-eEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCceeEEccccc-EEEEecCCCccCcEEecCCEEEEEEEE
Confidence            3444 899999999999999999965  78888   563  3 378998764 3444443    6899999999999999


Q ss_pred             EEEc
Q 032315          116 TQVD  119 (143)
Q Consensus       116 v~~~  119 (143)
                      +..+
T Consensus       745 vd~~  748 (760)
T 2vnu_D          745 VMDP  748 (760)
T ss_dssp             ----
T ss_pred             EECc
Confidence            8765

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}

Probab=96.30  E-value=0.00064  Score=63.59  Aligned_cols=64  Identities=14%  Similarity=0.063  Sum_probs=0.0

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      ...|+++.|+|++++++|+||.+++ .+++|   .|.+.. |        . .+-...+++|+.|++||+++..+...
T Consensus       903 l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~-~--------v-~~~~~v~kvGd~V~vkVl~VD~~~~r  970 (1030)
T 3psf_A          903 FFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQ-L--------R-RPANEIYEIGKTYPAKVIYIDYANIT  970 (1030)
T ss_dssp             ------------------------------------------------------------------------------
T ss_pred             hcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCCc-c--------c-CCHHHcCCCCCEEEEEEEEEECCCCE
Confidence            4579999999999999999999986 78877   444321 0        1 11125689999999999998765433

>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=96.30  E-value=5.6e-05  Score=68.65  Aligned_cols=71  Identities=11%  Similarity=-0.016  Sum_probs=32.2

Q ss_pred             EEEEEE--EeecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEE
Q 032315           41 RCQCIV--FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKII  114 (143)
Q Consensus        41 ~F~~lv--FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~  114 (143)
                      ..+.++  ..|..|+++.|+|+++.++|+|+++.| .+++|   +|..      -..|-+ .++-...++.||.|++||+
T Consensus       655 ~i~~i~~p~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~------~~s~~r-v~~~~~~~~vGd~V~VkVi  727 (757)
T 1e3p_A          655 TINGIANPTSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRK------LAGGKR-VENVEDVLGVGQKVQVEIA  727 (757)
T ss_dssp             ------------------CBEEECC-CSCEECCC---CCCCC--------------------------CCSSCBCCCCCC
T ss_pred             HHHHhcchhhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhcc------ccCCCc-ccCcccccCCCCEEEEEEE
Confidence            356677  889999999999999999999999977 77766   3300      001111 1233467999999999999


Q ss_pred             EEEE
Q 032315          115 GTQV  118 (143)
Q Consensus       115 ~v~~  118 (143)
                      ++.-
T Consensus       728 ~vd~  731 (757)
T 1e3p_A          728 EIDS  731 (757)
T ss_dssp             CCCS
T ss_pred             EECC
Confidence            8865

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=96.22  E-value=0.013  Score=47.30  Aligned_cols=56  Identities=13%  Similarity=-0.016  Sum_probs=44.2

Q ss_pred             CCCEEEEEEEEEecccEEE-Eccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           51 KGEILGAGVTMVNKMGFLA-EAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v-~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      .|++++|+|.+++++|+|+ .+.+ .++||...+-+                ..++.|++|.+||+.++-+.++
T Consensus       152 ~G~~V~g~V~~i~~~G~fV~~i~~g~~Glih~SEl~----------------~~l~~Gd~v~~~V~~id~~d~k  209 (285)
T 3go5_A          152 QNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERY----------------AEPRLGQVLDARVIGFREVDRT  209 (285)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTTTEEEEECGGGCS----------------SCCCTTCEEEEEEEEEETTTTE
T ss_pred             CCCEEEEEEEEEeCCcEEEEEeCCCeEEEEEHHHcc----------------ccCCCCCEEEEEEEEEECCCCe
Confidence            6899999999999999999 9977 88888221100                1379999999999999864443

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=94.79  E-value=0.089  Score=43.66  Aligned_cols=59  Identities=17%  Similarity=0.026  Sum_probs=45.0

Q ss_pred             eecCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV  120 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~  120 (143)
                      +...|+++.|+|.++++.|+++.+|-.+.++...+-   .++           ..+++||.|++.|..+.-+.
T Consensus       131 ~~~~GeIV~G~V~ri~~~~v~VDlGk~EgiLp~sE~---ip~-----------E~~~vGD~Vkv~V~~V~~~~  189 (344)
T 1hh2_P          131 SELKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEW---IPG-----------EEIKAGDLVKVYIIDVVKTT  189 (344)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEEETTEEEEEEGGGS---CTT-----------CCCCTTCEEEEEEEEEEEET
T ss_pred             hhcCCCEEEEEEEEEecCcEEEEeCCeEEEEeHHHc---CCC-----------cCCCCCCEEEEEEEEEEcCC
Confidence            445699999999999999999999977887722100   011           25799999999999988654

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=94.32  E-value=0.095  Score=43.89  Aligned_cols=57  Identities=16%  Similarity=0.236  Sum_probs=46.2

Q ss_pred             EeecCCCEEEEEEEE----EecccEEEEccc----cEEEE----EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEE
Q 032315           47 FRPFKGEILGAGVTM----VNKMGFLAEAGA----VQIFC----LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKII  114 (143)
Q Consensus        47 FrPf~gEVv~G~V~~----v~~~Gi~v~iGp----~~ifI----~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~  114 (143)
                      |+...||++.|+|..    ++..++++.+|-    .+.++    ++|       .           ..|++||.||+-|.
T Consensus       126 f~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~EqiP-------~-----------E~~~~GDrVkvyV~  187 (366)
T 1k0r_A          126 FSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVP-------G-----------ESYEHGNRLRCYVV  187 (366)
T ss_dssp             -CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSCT-------T-----------CCCCTTCEEEEEEE
T ss_pred             HHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcCC-------C-----------ccCCCCCEEEEEEE
Confidence            567799999999999    999999999997    77766    222       1           25799999999999


Q ss_pred             EEEEccC
Q 032315          115 GTQVDVT  121 (143)
Q Consensus       115 ~v~~~~~  121 (143)
                      .+.-++.
T Consensus       188 ~V~~~~k  194 (366)
T 1k0r_A          188 GVTRGAR  194 (366)
T ss_dssp             EEECCSS
T ss_pred             EEecCCC
Confidence            9987653

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=94.09  E-value=0.1  Score=41.57  Aligned_cols=56  Identities=14%  Similarity=0.205  Sum_probs=45.3

Q ss_pred             EeecCCCEEEEEEEE----EecccEEEEccc----cEEEE----EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEE
Q 032315           47 FRPFKGEILGAGVTM----VNKMGFLAEAGA----VQIFC----LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKII  114 (143)
Q Consensus        47 FrPf~gEVv~G~V~~----v~~~Gi~v~iGp----~~ifI----~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~  114 (143)
                      |+...||++.|+|..    +++..+++.+|-    .+.++    ++|                  +..|+.||.||+-|.
T Consensus         3 ~~~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqip------------------~E~~~~GDrIkayV~   64 (251)
T 2asb_A            3 FSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVP------------------GESYEHGNRLRCYVV   64 (251)
T ss_dssp             -CCCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSCT------------------TCCCCTTCEEEEEEE
T ss_pred             hhhcCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcCC------------------CccCCCCCEEEEEEE
Confidence            778899999999999    888899999997    67766    222                  125799999999999


Q ss_pred             EEEEcc
Q 032315          115 GTQVDV  120 (143)
Q Consensus       115 ~v~~~~  120 (143)
                      .++-+.
T Consensus        65 ~V~~~~   70 (251)
T 2asb_A           65 GVTRGA   70 (251)
T ss_dssp             EEECCS
T ss_pred             EEEcCC
Confidence            998754

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=93.21  E-value=0.17  Score=40.69  Aligned_cols=66  Identities=9%  Similarity=-0.024  Sum_probs=46.0

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCCC--CceEEcCCc-------eEEEcCCCeEEEEEEEE
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTGD--LPSYTTSDG-------SVKIQKDCELWLKIIGT  116 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~~--~~~~~~~~~-------~~~i~~g~~VR~RV~~v  116 (143)
                      ...|+++.|+|+++++.|+|+.+|-.++|+   .+|+   .-.++  ...+..+++       .-.+++|+.+..+|.++
T Consensus         4 ~~~G~~v~g~V~~~~~~G~fv~~~g~egllp~se~~~---~vGdevev~v~~d~~~r~iat~~~p~~~~G~~~~g~V~~v   80 (285)
T 3go5_A            4 TNLASFIVGLIIDENDRFYFVQKDGQTYALAKEEGQH---TVGDTVKGFAYTDMKQKLRLTTLEVTATQDQFGWGRVTEV   80 (285)
T ss_dssp             TTTTEEEEEEEEEECSSEEEEEETTEEEEEEGGGCCC---CTTSEEEEEEEECTTSCEEEECSCCCSCSSSCEEEEEEEE
T ss_pred             ccCCCEEEEEEEEEECCEEEEEcCCeEEEEEHHHCcc---ccCCEEEEEEEECCCCCEEEecccccccCCCEEEEEEEEE
Confidence            357999999999999999999998778998   6664   11111  112221111       13468899999999987


Q ss_pred             E
Q 032315          117 Q  117 (143)
Q Consensus       117 ~  117 (143)
                      .
T Consensus        81 ~   81 (285)
T 3go5_A           81 R   81 (285)
T ss_dssp             E
T ss_pred             c
Confidence            5

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

Probab=92.87  E-value=0.11  Score=42.18  Aligned_cols=62  Identities=13%  Similarity=0.110  Sum_probs=46.7

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEcc-ccEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAG-AVQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iG-p~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      +.|..|.+|.|.|++++...+.++++ +.+.++.+.   .|....      ++.+..+++||.|++||....
T Consensus       123 YiP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~---~f~Gat------k~~r~~f~~GDlV~ArV~s~~  185 (289)
T 2nn6_G          123 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYL---SFEGAT------KRNRPNVQVGDLIYGQFVVAN  185 (289)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESC---SSSCCS------SCSSSSSCTTCEEEEEEEECC
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehh---hcCcch------hhhhhhcCCCCEEEEEEEEcC
Confidence            68999999999999999999999997 466666222   122111      233467899999999999754

>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A

Probab=86.44  E-value=1.3  Score=38.54  Aligned_cols=73  Identities=11%  Similarity=0.041  Sum_probs=47.4

Q ss_pred             EeecCCCEEEEEEEEEecc--cEEEEccc-cEEEEEcCCC--ceecCCCCceEEc-CCceEEEcCCCeEEEEEEEEEEcc
Q 032315           47 FRPFKGEILGAGVTMVNKM--GFLAEAGA-VQIFCLIPDD--MELQTGDLPSYTT-SDGSVKIQKDCELWLKIIGTQVDV  120 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~--Gi~v~iGp-~~ifI~lp~~--~~fd~~~~~~~~~-~~~~~~i~~g~~VR~RV~~v~~~~  120 (143)
                      =++.+|.+..|+|+++.+.  |+||.+|+ -+.|+.+.+-  -.+.....  ... .+-...++.|++|.++|...-...
T Consensus        41 ~~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~~~~~~~~~--~~~~~~i~d~lk~Gq~VlVQV~Ke~~g~  118 (517)
T 2bx2_L           41 HEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYS--AHGRPNIKDVLREGQEVIVQIDKEERGN  118 (517)
T ss_dssp             SCCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC---------CCCGGGTCCTTCEEEEEEEECCCTT
T ss_pred             CcCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcChhhhccccc--cccccchhhhccCCCEEEEEEEeecccc
Confidence            3467899999999999999  99999999 5699933211  01111000  000 011234789999999999866544


Q ss_pred             C
Q 032315          121 T  121 (143)
Q Consensus       121 ~  121 (143)
                      .
T Consensus       119 K  119 (517)
T 2bx2_L          119 K  119 (517)
T ss_dssp             C
T ss_pred             C
Confidence            3

---

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	143
d2c35b2	77	d.230.1.1 (B:1-77) N-terminal, heterodimerisation	2e-08
d1go3e2	78	d.230.1.1 (E:1-78) N-terminal, heterodimerisation	9e-08
d1y14b2	80	d.230.1.1 (B:1-80) N-terminal, heterodimerisation	1e-07
d2c35b1	94	b.40.4.5 (B:78-171) C-terminal domain of RNA polym	1e-06
d1y14b1	91	b.40.4.5 (B:81-171) C-terminal domain of RNA polym	2e-06

>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 = 46.2 bits (110), Expect = 2e-08
 Identities = 20/46 (43%), Positives = 33/46 (71%)

Query: 2  KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVF 47
           +VEGTC+G++GF +A+T  ++IG G+I+ G   V + V+ + IVF
Sbjct: 32 TEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVF 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 = 44.6 bits (106), Expect = 9e-08
 Identities = 12/47 (25%), Positives = 22/47 (46%)

Query: 1  MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVF 47
          M+  EG      GF ++I   + IG+G + +G       V  + +V+
Sbjct: 31 MEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVY 77

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

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]

 Score = 43.9 bits (104), Expect = 1e-07
 Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 1  MKDVEGTCSGRHGFAVAITGAE--SIGKGLIRNGTVLVTFLVRCQCIVFR 48
          +++VEG+C+G+ G+ + +   +   I +G I        F V+ + +VF+
Sbjct: 31 LEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK 80

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

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]

 Score = 41.8 bits (98), Expect = 1e-06
 Identities = 32/80 (40%), Positives = 44/80 (55%), Gaps = 4/80 (5%)

Query: 48  RPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLI----PDDMELQTGDLPSYTTSDGSVKI 103
           RPFKGE++ A VT VNK+G   E G +  F        +       + P Y T D  + I
Sbjct: 1   RPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVI 60

Query: 104 QKDCELWLKIIGTQVDVTEI 123
           Q+D E+ LKI+GT+VD  +I
Sbjct: 61  QQDDEIRLKIVGTRVDKNDI 80

>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]} Length = 91

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]

 Score = 41.0 bits (96), Expect = 2e-06
 Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 49  PFKGEILGAGVTMVNKMGFLAEAGAVQIFCLI---PDDMELQTGDLPSYTTSDGSVKIQK 105
           PFKGE++   V   ++ GF  + G +++F      P D+    G  P    S   V I  
Sbjct: 1   PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDV-ITI 59

Query: 106 DCELWLKIIGTQVDVTEI 123
              + +KI G    V+ I
Sbjct: 60  KSRIRVKIEGCISQVSSI 77

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	143
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	99.92
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	99.87
d1go3e2	78	N-terminal, heterodimerisation domain of RBP7 (Rpo	99.62
d2c35b2	77	N-terminal, heterodimerisation domain of RBP7 (Rpo	99.57
d1y14b2	80	N-terminal, heterodimerisation domain of RBP7 (Rpo	99.55
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.38
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.76
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	98.52
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	98.37
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	98.36
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.15
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.11
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	97.94
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	97.9
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	97.86
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	97.61
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	97.32
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	97.05
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	96.61
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	96.22
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	93.4
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	85.92

>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=99.92  E-value=7.6e-25  Score=150.28  Aligned_cols=87  Identities=41%  Similarity=0.644  Sum_probs=81.7

Q ss_pred             eecCCCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCCC-CceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTGD-LPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~~-~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      |||+||+++|+|++++++|+|+++||+++||   +||+++.|+.++ .|+|.+++++..|+.||.||+||.+++++++++
T Consensus         1 rPf~Gev~~g~V~~v~~~G~fv~lg~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~I   80 (94)
T d2c35b1           1 RPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDI   80 (94)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEE
T ss_pred             CCCCCCEEEEEEEEEEeeEEEEEecCceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCcc
Confidence            8999999999999999999999999999999   999998877664 699999999999999999999999999999999


Q ss_pred             EEEEEcccccc
Q 032315          124 EKARREVGKQR  134 (143)
Q Consensus       124 ~ai~~~~~~~~  134 (143)
                      +|+|+|-+++-
T Consensus        81 ~~igt~~~d~L   91 (94)
T d2c35b1          81 FAIGSLMDDYL   91 (94)
T ss_dssp             EEEEECCSTTC
T ss_pred             eEEEEccCCCc
Confidence            99999988863

>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=99.87  E-value=2e-22  Score=137.05  Aligned_cols=83  Identities=28%  Similarity=0.512  Sum_probs=73.8

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccccEEEE---EcCCCceecCCCC-ceEEcCCceEEEcCCCeEEEEEEEEEEccCCeE
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTGDL-PSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIE  124 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~~~fd~~~~-~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~  124 (143)
                      ||+||+++|+|++++++|+|+++||.++||   +||+++.||++.+ |.|.  +++..++.|+.||+||.+++++.++++
T Consensus         1 Pf~Gev~~g~I~~v~~~G~fv~lg~~eg~i~~~~l~~~~~~d~~~~~~~~~--~~~~~~~~Gd~VrvkV~~v~~~~~~i~   78 (91)
T d1y14b1           1 PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQ--SSEDVITIKSRIRVKIEGCISQVSSIH   78 (91)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTCEECC-----CEE--CSSCEECTTCEEEEEEEEEEEETTEEE
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEEcCeEEEEEhhhcCcceEEccccceeEec--ccCeEEeCCCEEEEEEEEEecccCccE
Confidence            999999999999999999999999999999   9999999998864 5554  455789999999999999999999999


Q ss_pred             EEEEccccc
Q 032315          125 KARREVGKQ  133 (143)
Q Consensus       125 ai~~~~~~~  133 (143)
                      |+|+|.+++
T Consensus        79 ~ig~~~~d~   87 (91)
T d1y14b1          79 AIGSIKEDY   87 (91)
T ss_dssp             EEEECCSTT
T ss_pred             EEEEccCCC
Confidence            999999886

>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=99.62  E-value=8.5e-17  Score=106.71  Aligned_cols=46  Identities=24%  Similarity=0.417  Sum_probs=45.0

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEE
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVF   47 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvF   47 (143)
                      +++||||.+++|+||+++|+.++++|+|.||||+++|+|+|||+||
T Consensus        32 ~~~egkv~~~~G~ii~v~di~~i~eG~I~~gdG~~~~~V~F~~lvF   77 (78)
T d1go3e2          32 EKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVY   77 (78)
T ss_dssp             HHHTTCEETTTEEEEEEEEEEEECCCBCCTTCCSEEEEEEEEEEEE
T ss_pred             HHhCCcCcCCcCEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEE
Confidence            5799999999999999999999999999999999999999999999

>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=99.57  E-value=5.9e-16  Score=102.04  Aligned_cols=46  Identities=43%  Similarity=0.874  Sum_probs=44.8

Q ss_pred             cceeEEEeCCeeEEEEEeecceecceeEEcCCccEEEEEEEEEEEE
Q 032315            2 KDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVF   47 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI~~i~eG~I~~gdG~~~~~V~F~~lvF   47 (143)
                      +++||||.++.|+|++++||.++++|+|.||||+++|+|+|+|+||
T Consensus        32 ~~~egk~~~~~G~~i~v~~i~~i~~G~I~~gdG~~~~~V~F~~lvF   77 (77)
T d2c35b2          32 TEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVF   77 (77)
T ss_dssp             HHHTTCEETTTEEEEEEEEEEEECCCBCCTTCSSEEEEEEEEEEEE
T ss_pred             HHhCCEEeCCCCEEEEEEEEEEecCCEEEcCCCCEEEEEEEEEEEC
Confidence            5799999999999999999999999999999999999999999998

>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=99.55  E-value=6.2e-16  Score=102.87  Aligned_cols=47  Identities=28%  Similarity=0.598  Sum_probs=32.0

Q ss_pred             cceeEEEeCCeeEEEEEeec--ceecceeEEcCCccEEEEEEEEEEEEe
Q 032315            2 KDVEGTCSGRHGFAVAITGA--ESIGKGLIRNGTVLVTFLVRCQCIVFR   48 (143)
Q Consensus         2 ~~~EG~~~~~~GliI~i~dI--~~i~eG~I~~gdG~~~~~V~F~~lvFr   48 (143)
                      +++||||.+++|++|||.++  .++++|+|.||||+++|+|+|||++||
T Consensus        32 ~~~egkv~~~~G~vi~V~~~~~~~i~~G~I~~gdG~~~~~V~F~alvFr   80 (80)
T d1y14b2          32 EEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFK   80 (80)
T ss_dssp             HHHTTEEETTTEEEEEECCGGGCBCC------------CEEEEEEEEEC
T ss_pred             HHhCCcCcCCcCEEEEEEEEeeeeccCCEEECCCCCEEEEEEEEEEEEC
Confidence            57999999999999999765  689999999999999999999999998

>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=99.38  E-value=1.4e-12  Score=90.24  Aligned_cols=74  Identities=14%  Similarity=0.152  Sum_probs=62.9

Q ss_pred             ecCCCEEEEEEEEEecccEEEEccccEEEE---EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAGAVQIFC---LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI---~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      |..||+++|+|++++++|+|+++++.++||   .|+++ +.||+... +|.+++.+..++.|+.|++||+++..+.+++
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~~ieGlv~~s~l~~~~~~~~~~~~-~~~~~~~~~~~~~Gd~v~vkV~~vd~~~~~~   78 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKRE-AIIGKETGKVLEIGDYVRARIVAISLKAERK   78 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC---CEEETTTCCEECTTCEEEEEEEEEECCC---
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEeeCeEEEEEeecccCceeeecccee-EEeecccccceeecceEEEEEEEEchhhccc
Confidence            789999999999999999999999999999   78866 56777653 5788888899999999999999999988663

>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=98.76  E-value=1.5e-08  Score=67.43  Aligned_cols=75  Identities=11%  Similarity=0.076  Sum_probs=60.3

Q ss_pred             CCCEEEEEEEEEecccEEEEcc--ccEEEE---EcCCC-ceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCeE
Q 032315           51 KGEILGAGVTMVNKMGFLAEAG--AVQIFC---LIPDD-MELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIE  124 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iG--p~~ifI---~lp~~-~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~  124 (143)
                      .++..+|+|+++++.|+||++-  ..+.||   .|+++ ++||.+..-.....+++..++.|+.|++||..+..+...+.
T Consensus         3 ~~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r~I~   82 (87)
T d2ix0a3           3 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSII   82 (87)
T ss_dssp             SCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTTEEE
T ss_pred             CCCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccCeEE
Confidence            4678899999999999999994  489999   78877 56775542223345667889999999999999999888775


Q ss_pred             E
Q 032315          125 K  125 (143)
Q Consensus       125 a  125 (143)
                      +
T Consensus        83 ~   83 (87)
T d2ix0a3          83 A   83 (87)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=98.52  E-value=7.7e-08  Score=62.64  Aligned_cols=64  Identities=11%  Similarity=0.158  Sum_probs=48.4

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      |.|-.|+++.|+|++++++|+|+++++ .+.|+.+.+ +      .|.+..++-...+++||+|++||.++.
T Consensus         1 Y~Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se-~------s~~~~~~~~~~~~~vGd~V~~kV~~vd   65 (83)
T d2ba0a1           1 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSE-N------PEMKPNKKPNEVLDIGDAIIAKVLNID   65 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGG-C------TTCCTTSCGGGTCCTTCEEEEEEEEEC
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEecCCCeeEEEeccc-c------cccccccChhhhcccccEEEEEEEEEC
Confidence            579999999999999999999999986 889883211 0      111111223356899999999999986

>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=98.37  E-value=2.3e-07  Score=60.99  Aligned_cols=68  Identities=10%  Similarity=0.140  Sum_probs=49.4

Q ss_pred             EEeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315           46 VFRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        46 vFrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      +|.|..|+++.|+|++++++|+|+.+++ .++|+.+.+ +..+..+.   ..++.+..+++||.|++||.++.
T Consensus         2 ~Y~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se-~~~~~~~~---~~~~~~~~~~vGd~V~~kV~~vd   70 (88)
T d2z0sa1           2 IYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQD-FLGRPFNP---AVDDMQSLLKVGDYIKAKVVAFD   70 (88)
T ss_dssp             CCCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHH-HHTSCCCT---TTTCCTTSSCTTCEEEEEEEEEC
T ss_pred             CcCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHH-hCcccccc---cccchhhhcccCcEEEEEEEEEC
Confidence            5889999999999999999999999986 889882210 00000000   01233467899999999999987

>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=98.36  E-value=3.2e-07  Score=60.21  Aligned_cols=63  Identities=13%  Similarity=0.048  Sum_probs=48.5

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      |.|..|+++.|+|++++++|+|+.++. .+.|+   .+++...-+        ..+-...+++||.|++||.++.
T Consensus         3 Y~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~~~--------~~~~~~~~~~Gd~v~~kV~~vd   69 (87)
T d2je6i1           3 YYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINV--------GEDLRRYLDVGDYVIARIENFD   69 (87)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCT--------TCCCSSSCCTTCEEEEEEEEEE
T ss_pred             ccCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceecc--------ccccchhhcccceEEEEEEEEC
Confidence            679999999999999999999999974 88988   343211100        1122356899999999999886

>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=98.15  E-value=3.3e-06  Score=55.04  Aligned_cols=67  Identities=12%  Similarity=0.104  Sum_probs=44.8

Q ss_pred             ecCCCEEEEEEEEEecccEEEEcc--c-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCe
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAG--A-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEI  123 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iG--p-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~  123 (143)
                      |-.|+++.|+|++++++|+|+++.  + .++||.+.+ +      .|.+. ++-...+++|+.|++||+++.-+.+.+
T Consensus        11 p~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~se-l------s~~~~-~~~~~~~~~Gd~v~~kV~~vd~~~~ki   80 (86)
T d1kl9a2          11 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSE-L------SRRRI-RSINKLIRIGRNECVVVIRVDKEKGYI   80 (86)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGG-C-------------------CTTCEEEEEEEEEETTTTEE
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeee-c------ccccc-ccceEEeecccEEEEEEEEEECCCCEE
Confidence            567999999999999999999995  4 789883221 0      11111 222356899999999999987655543

>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=98.11  E-value=9e-07  Score=57.49  Aligned_cols=66  Identities=20%  Similarity=0.236  Sum_probs=47.2

Q ss_pred             ecCCCEEEEEEEEEecccEEEEcc--c-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           49 PFKGEILGAGVTMVNKMGFLAEAG--A-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        49 Pf~gEVv~G~V~~v~~~Gi~v~iG--p-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |..|+++.|+|++++++|+|++++  + .++||.+.+ +      .|.|. ++-...+++|++|++||+.+.-+.+.
T Consensus         9 p~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~se-l------s~~~~-~~~~~~~~~G~~v~~kV~~vd~~~~~   77 (84)
T d2ahob2           9 PSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSE-V------SSKWV-KNIRDVLKENRKVIVKVIRVDRRKGT   77 (84)
T ss_dssp             CCTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGG-C------C------CHHHHTCSSCEEECEEEEEETTTTE
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccc-c------ccccc-cccceEeecccEEEEEEEEEECCCCE
Confidence            778999999999999999999996  3 688882210 0      11121 22235689999999999999765544

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

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

Probab=97.94  E-value=3.5e-06  Score=53.87  Aligned_cols=60  Identities=15%  Similarity=0.166  Sum_probs=44.1

Q ss_pred             cCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315           50 FKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        50 f~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      ..|+++.|+|++++++|+|+.+++ .++||.+. ++      .|.|. ++-+..+++|++|++||+++.
T Consensus         4 kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~s-el------s~~~~-~~~~~~~~~G~~v~v~Vi~id   64 (76)
T d1sroa_           4 EVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHIS-QI------ADKRV-EKVTDYLQMGQEVPVKVLEVD   64 (76)
T ss_dssp             CTTSEEEEEEEEEETTEEEEECSSSCCCBCCTT-SS------CSSCC-SCHHHHCCTTCEEEEEEEECC
T ss_pred             CCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhH-Hh------Ccccc-CCHHHccCCCCEEEEEEEEEC
Confidence            479999999999999999999987 77877221 11      11111 122356899999999999975

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

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

Probab=97.90  E-value=7.3e-06  Score=54.29  Aligned_cols=63  Identities=14%  Similarity=0.258  Sum_probs=48.9

Q ss_pred             CCCEEEEEEEEEecccEEEEccc-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCCeE
Q 032315           51 KGEILGAGVTMVNKMGFLAEAGA-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIE  124 (143)
Q Consensus        51 ~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~~~  124 (143)
                      .|+++.|+|+++++.|+|++++. +++||   .|.+.          | .++-...+++|+.|++||+.+.-+.+.+.
T Consensus        18 ~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~----------~-~~~~~~~~~vGq~v~~~V~~id~~~~~i~   84 (94)
T d3bzka4          18 PGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEK----------F-VKDPYEVVKAGDIVKVKVMEVDIPRNRVG   84 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSS----------C-CSCHHHHCCTTCEEEEEEEEEETTTTEEE
T ss_pred             CCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcc----------c-ccChhhhhccCcEEEEEEEEEECCCCEEE
Confidence            59999999999999999999986 88998   34311          1 12223568999999999999987666554

>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=97.86  E-value=8.9e-06  Score=54.11  Aligned_cols=71  Identities=10%  Similarity=-0.005  Sum_probs=48.0

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCC-ceecCCCC--ceEEcCCceEEEcCCCeEEEEEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDD-MELQTGDL--PSYTTSDGSVKIQKDCELWLKIIGTQV  118 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~-~~fd~~~~--~~~~~~~~~~~i~~g~~VR~RV~~v~~  118 (143)
                      |.|..|+++.|+|++++++|+|+++++ .+.++.+.+- +.......  -.+ ..+-...+++||.|.+||.++.-
T Consensus         4 Y~P~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~~~~rr~~~~~-~~~~~~~~~~Gd~V~~kV~~v~~   78 (95)
T d2nn6h1           4 YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAED-ELAMRGFLQEGDLISAEVQAVFS   78 (95)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC--------------CHHHHHHSCSSCEECCEEEEEET
T ss_pred             ccCCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchh-hhhhhhhcccccEEEEEEEEECC
Confidence            579999999999999999999999985 8898844321 00000000  000 00123468999999999999863

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {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 RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.61  E-value=1.2e-05  Score=55.39  Aligned_cols=63  Identities=14%  Similarity=0.161  Sum_probs=45.6

Q ss_pred             cCCCEEEEEEEEEecccEEEEcc-c-cEEEE---EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           50 FKGEILGAGVTMVNKMGFLAEAG-A-VQIFC---LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        50 f~gEVv~G~V~~v~~~Gi~v~iG-p-~~ifI---~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      ..|+++.|+|++++++|+|+++| + ++.||   .+.+.          +..++-...+++|+.|++||+.+.-+.+.
T Consensus        20 ~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~----------~~~~~~~~~~~vGq~v~~~V~~vd~~~~~   87 (119)
T d1wi5a_          20 KPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEY----------IRQKNKGAKLKVGQYLNCIVEKVKGNGGV   87 (119)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHH----------HHHHSSSCCCCTTCEEEEEEEECCTTSCE
T ss_pred             CCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhccc----------cccCCHHHhcccceEEEEEEEEEeCCCCE
Confidence            46999999999999999999998 4 78999   23211          11111123579999999999997644443

>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=97.32  E-value=8.6e-05  Score=48.78  Aligned_cols=62  Identities=15%  Similarity=0.147  Sum_probs=47.8

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      |.|-.|.++.|+|++++..++++.+++ .+.++.+   ++|+..      .++.+-+++.||.|.+||..+.
T Consensus         2 Y~P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~---~~f~g~------~k~~r~~l~~GD~V~arV~~v~   64 (88)
T d2nn6g1           2 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSY---LSFEGA------TKRNRPNVQVGDLIYGQFVVAN   64 (88)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEES---CSSSCC------SSCSSSSSCTTCEEEEEEEECC
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeH---HHcCcc------ccccCcccCCCCEEEEEEEEeC
Confidence            579999999999999999999999986 6676633   223211      2334456899999999998765

>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=97.05  E-value=0.00041  Score=45.55  Aligned_cols=78  Identities=10%  Similarity=0.126  Sum_probs=53.8

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEcc-CCeE
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDV-TEIE  124 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~-~~~~  124 (143)
                      |.|-.|.++.|+|++++..++++++|+ .+.++..  ...|+...      ++.+-.+++||.|-+||.++.-+. -++.
T Consensus         3 Y~P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~--~~~f~g~~------k~~r~~l~~GDlV~arV~~v~~~~~~~Ls   74 (90)
T d2ja9a1           3 YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLS--YMAFPNAS------KKNRPTLQVGDLVYARVCTAEKELEAEIE   74 (90)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEE--TTSSTTCC------SSSCCCCCTTCEEEEEEEECCTTSCCEEE
T ss_pred             ccCCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhh--hhccCccc------cccCCccCCCCEEEEEEEEECCCCCEEEE
Confidence            579999999999999999999999985 6665411  12233221      234566899999999999876443 2244


Q ss_pred             EEEEcccc
Q 032315          125 KARREVGK  132 (143)
Q Consensus       125 ai~~~~~~  132 (143)
                      |+....||
T Consensus        75 c~~~~~gK   82 (90)
T d2ja9a1          75 CFDSTTGR   82 (90)
T ss_dssp             SSCTTTCS
T ss_pred             EeccccCc
Confidence            44333444

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Streptomyces antibioticus [TaxId: 1890]

Probab=96.61  E-value=3.2e-05  Score=47.67  Aligned_cols=56  Identities=7%  Similarity=0.006  Sum_probs=30.9

Q ss_pred             EEEEEEecccEEEEccc-cEEEEEcCCCceecCCCCceEE-cCCceEEEcCCCeEEEEEEEEE
Q 032315           57 AGVTMVNKMGFLAEAGA-VQIFCLIPDDMELQTGDLPSYT-TSDGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        57 G~V~~v~~~Gi~v~iGp-~~ifI~lp~~~~fd~~~~~~~~-~~~~~~~i~~g~~VR~RV~~v~  117 (143)
                      |+|++++++|+|+++++ .+.||.+.   +.....  .|. .++-+..++.|++|++||+++.
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihis---eis~~~--~~~~v~~~~~~~~~G~~V~vkV~~iD   58 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHIS---QIRKLA--GGKRVENVEDVLGVGQKVQVEIAEID   58 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC------------------------CCSSCBCCCCCCCCC
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHH---Hccccc--ccccccCHHHhcCCCCEEEEEEEEEc
Confidence            78999999999999988 77777221   111111  121 1233467999999999998764

>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=96.22  E-value=0.014  Score=36.46  Aligned_cols=58  Identities=19%  Similarity=0.131  Sum_probs=46.5

Q ss_pred             EeecCCCEEEEEEEEEecccEEEEccccEEEE----EcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccCC
Q 032315           47 FRPFKGEILGAGVTMVNKMGFLAEAGAVQIFC----LIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTE  122 (143)
Q Consensus        47 FrPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI----~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~~  122 (143)
                      |+..+||++.|+|..++...+.+.+|-.+.++    ++|                  +-.+++||.||+=|..++-++..
T Consensus         4 f~~~~geiv~G~V~r~~~~~~~Vdlg~~eaiLp~~eqip------------------~E~~~~Gdrik~~i~~V~~~~kg   65 (72)
T d1hh2p1           4 YSELKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWIP------------------GEEIKAGDLVKVYIIDVVKTTKG   65 (72)
T ss_dssp             TTCCTTCEEEEEEEEECSSEEEEEETTEEEEEEGGGSCT------------------TCCCCTTCEEEEEEEEEEEETTE
T ss_pred             HhhccCcEEEEEEEEEcCCCEEEEECCcEEECCHHHcCC------------------CCCCCCCCEEEEEEEEEEEcCCC
Confidence            67789999999999999999999999877765    222                  13468999999999998865543

>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=93.40  E-value=0.035  Score=37.87  Aligned_cols=67  Identities=12%  Similarity=0.016  Sum_probs=39.8

Q ss_pred             eecCCCEEEEEEEEEecccEEEEccccEEEEEcCCCceecCC---CCce-EEcC--CceEEEcCCCeEEEEEEEEE
Q 032315           48 RPFKGEILGAGVTMVNKMGFLAEAGAVQIFCLIPDDMELQTG---DLPS-YTTS--DGSVKIQKDCELWLKIIGTQ  117 (143)
Q Consensus        48 rPf~gEVv~G~V~~v~~~Gi~v~iGp~~ifI~lp~~~~fd~~---~~~~-~~~~--~~~~~i~~g~~VR~RV~~v~  117 (143)
                      -|..|.++.|.|+++++..+++.+.-.+-- .++.+  |..-   +.-. ...+  +=...|++||.||+||++..
T Consensus         4 vP~vGDiVig~V~~v~~~~a~v~I~~v~~~-~l~~~--~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~   76 (125)
T d2nn6i1           4 LPDVGAIVTCKVSSINSRFAKVHILYVGSM-PLKNS--FRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLG   76 (125)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEEEEESSSS-CCCCS--SCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEE
T ss_pred             CCCCCCEEEEEEEEecCCEEEEEEeEecCc-ccccC--ccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEcc
Confidence            489999999999999999999966321100 11111  1100   0000 0001  11256799999999999864

>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]}

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: Mycobacterium tuberculosis [TaxId: 1773]

Probab=85.92  E-value=1  Score=27.69  Aligned_cols=59  Identities=14%  Similarity=0.220  Sum_probs=40.1

Q ss_pred             cCCCEEEEEEEEEeccc----EEEEccc----cEEEEEcCCCceecCCCCceEEcCCceEEEcCCCeEEEEEEEEEEccC
Q 032315           50 FKGEILGAGVTMVNKMG----FLAEAGA----VQIFCLIPDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVT  121 (143)
Q Consensus        50 f~gEVv~G~V~~v~~~G----i~v~iGp----~~ifI~lp~~~~fd~~~~~~~~~~~~~~~i~~g~~VR~RV~~v~~~~~  121 (143)
                      -.||++.|+|..+....    +++.+|-    .+.++  |.      +++   ..   .-.|+.||.||+=|..++-++.
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiL--p~------~eq---ip---~E~y~~Gdrik~~i~~V~~~~k   68 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVI--PA------AEQ---VP---GESYEHGNRLRCYVVGVTRGAR   68 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEE--CG------GGS---CT---TCCCCTTCEEEEEEEEEECCSS
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEEC--CH------HHc---CC---CcccCCCCEEEEEEEEEEecCC
Confidence            36999999999987543    7899984    55655  31      010   00   1246889999999999886554


Q ss_pred             C
Q 032315          122 E  122 (143)
Q Consensus       122 ~  122 (143)
                      .
T Consensus        69 G   69 (76)
T d2asba1          69 E   69 (76)
T ss_dssp             S
T ss_pred             C
Confidence            3