Citrus Sinensis ID: 024995

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------26
Protein Sequence
MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIVNN
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEEEEEEEEEccccEEEEEccHHHHHHHHcccccccEEEcEEEcEEEEEccccccccccEEEEEccccccccccHHHHcccccEEEEEEEEEEccccEEEEEcccccccccHHHHHHHccccccEEEEEEEEEcccccEEEEccccHHHHHHHHHccccccEEEcccccccccccccEEEEEEEccccccEEEEEEEccHHHHHHHHHHHHcccccccccccHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccEEEEccEEEEEEEEEcccccEEEEEEccccHHHHHHHcccccEEEccEEEEEEEccccccccccEEEEEEEcccccccccccHEEEcccEEEEEEEEEcccccEEEEEHHcccccHHHHHHHHHcccccEEEEEEEEEcccccEEEEEccccEEEEEEEEcccccccccccccccEEEEEEEEEEEEEEcccccHHHHHHHHHEEEEEEcccHHHHHHHHcHHHcccccHHHHHHcccccc
Coil and Loop (DISEMBL)
mspshsckepqKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWnkyssrvnvedifvgrdygafihlrfpdglyhlTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKqleedplletlekvipqdgsvisdsssmsssnsntieplpgLGAIFEELLqedgiddvriTRQGFEKRVVSQDLQLwlsnappsgkkFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIVNN
Flexible Loop (DISEMBL)
mspshsckepQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDilnegdevrvkvikidreksritlsikqleedplleTLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFhetaivnn
Low Complexity Region (SEG)
MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGsvisdsssmsssnsNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIVNN
Disordered region (IsUnstruct)
***************EIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL*************************************PGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIV**
Disordered Region (DISOPRED)
*SPS***KEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI*RQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV****************HCNEYWNVFHETAIV**
Disordered Region (DISEMBL)
***********KSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGS**************TIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIVNN
Disordered Region (DISPRO)
************SIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETA****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVFHETAIVNN
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	259	2.2.26 [Sep-21-2011]
P73530	328	30S ribosomal protein S1	N/A	no	0.447	0.353	0.338	2e-12
Q89AJ3	566	30S ribosomal protein S1	yes	no	0.416	0.190	0.333	4e-12
P29344	411	30S ribosomal protein S1,	N/A	no	0.559	0.352	0.279	2e-11
P37985	557	30S ribosomal protein S1	yes	no	0.243	0.113	0.463	3e-11
P14128	378	30S ribosomal protein S1	N/A	no	0.416	0.285	0.341	3e-11
P0AG70	557	30S ribosomal protein S1	yes	no	0.243	0.113	0.463	3e-11
P0AG67	557	30S ribosomal protein S1	N/A	no	0.243	0.113	0.463	3e-11
P0AG68	557	30S ribosomal protein S1	yes	no	0.243	0.113	0.463	3e-11
P0AG69	557	30S ribosomal protein S1	N/A	no	0.243	0.113	0.463	3e-11
Q83E09	551	30S ribosomal protein S1	yes	no	0.328	0.154	0.391	3e-11

>sp|P73530|RS1A_SYNY3 30S ribosomal protein S1 homolog A OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=rps1A PE=3 SV=1

 Score = 73.2 bits (178), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 43/127 (33%), Positives = 71/127 (55%), Gaps = 11/127 (8%)

Query: 13  SIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDY 67
           S  E  + L G  + +K ++ +EE  +LV S + A+  +  + + V  + VG     + Y
Sbjct: 150 SAREAKEDLVGEDLPLKFLEVDEERNRLVLSHRRALVERKMNGLEVAQVVVGSVRGIKPY 209

Query: 68  GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127
           GAFI +        ++GL+H+SE+S D I     + N  DE++V +I +D E+ RI+LS 
Sbjct: 210 GAFIDIG------GVSGLLHISEISHDHIDTPHSVFNVNDEIKVMIIDLDAERGRISLST 263

Query: 128 KQLEEDP 134
           KQLE +P
Sbjct: 264 KQLEPEP 270

Binds mRNA.
Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

>sp|Q89AJ3|RS1_BUCBP 30S ribosomal protein S1 OS=Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) GN=rpsA PE=3 SV=2

 Score = 72.0 bits (175), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 42/126 (33%), Positives = 73/126 (57%), Gaps = 18/126 (14%)

Query: 21  LTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNV------EDIFVG------RDYG 68
           L G  +  KVI+ +++   +V S +  + ++Y++  N+      E + V        DYG
Sbjct: 147 LEGKELEFKVIKLDQKRNNVVVSRRAVIESEYNAERNLLLETLQEGLIVSGIVKNLTDYG 206

Query: 69  AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
           AF+ L   DGL H+T      +++W  ++   +I+N GDEV++K++K DREK R++L +K
Sbjct: 207 AFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNIGDEVKIKILKFDREKIRVSLGLK 260

Query: 129 QLEEDP 134
           QL +DP
Sbjct: 261 QLSDDP 266

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.

Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) (taxid: 224915)

>sp|P29344|RR1_SPIOL 30S ribosomal protein S1, chloroplastic OS=Spinacia oleracea GN=RPS1 PE=1 SV=1

 Score = 69.3 bits (168), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 48/172 (27%), Positives = 87/172 (50%), Gaps = 27/172 (15%)

Query: 26  ISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLY 80
           I +K ++ +EE  +LV S + A+ +   +++ +  +  G     + YGAFI +       
Sbjct: 229 IPLKFVEVDEEQSRLVMSNRKAMADS-QAQLGIGSVVTGTVQSLKPYGAFIDIG------ 281

Query: 81  HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP------ 134
            + GL+HVS++S D + DI  +L  GD ++V ++  DRE+ R++LS K+LE  P      
Sbjct: 282 GINGLLHVSQISHDRVSDIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRN 341

Query: 135 ---LLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGI 183
              + E  E++       I+ + +M+ ++    +P  GL       L  DGI
Sbjct: 342 PKLVFEKAEEMAQTFRQRIAQAEAMARADMLRFQPESGL------TLSSDGI 387

Actively engaged in the initiation complex formation via a strong mRNA-binding activity. Possesses a poly(A)-binding activity which might play a role as a control element in chloroplast mRNA translation.

Spinacia oleracea (taxid: 3562)

>sp|P37985|RS1_DICD3 30S ribosomal protein S1 OS=Dickeya dadantii (strain 3937) GN=rpsA PE=3 SV=2

 Score = 69.3 bits (168), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 48/69 (69%), Gaps = 6/69 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L
Sbjct: 204 DYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSL 257

Query: 126 SIKQLEEDP 134
            +KQL EDP
Sbjct: 258 GLKQLGEDP 266

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.

Dickeya dadantii (strain 3937) (taxid: 198628)

>sp|P14128|RS1_PROSP 30S ribosomal protein S1 (Fragment) OS=Providencia sp. GN=rpsA PE=3 SV=1

 Score = 69.3 bits (168), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 43/126 (34%), Positives = 69/126 (54%), Gaps = 18/126 (14%)

Query: 21  LTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVNVEDIFVG-RDYG 68
           L G  +  KVI+ +++   +V S           E+D +       + V+ I     DYG
Sbjct: 42  LEGKELEFKVIKLDQKRNNVVVSRRAVIESESSAERDQLLENLQEGMEVKGIVKNLTDYG 101

Query: 69  AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
           AF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L +K
Sbjct: 102 AFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSLGLK 155

Query: 129 QLEEDP 134
           QL EDP
Sbjct: 156 QLGEDP 161

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.

Providencia sp (taxid: 589)

>sp|P0AG70|RS1_SHIFL 30S ribosomal protein S1 OS=Shigella flexneri GN=rpsA PE=3 SV=1

 Score = 69.3 bits (168), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 48/69 (69%), Gaps = 6/69 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L
Sbjct: 204 DYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSL 257

Query: 126 SIKQLEEDP 134
            +KQL EDP
Sbjct: 258 GLKQLGEDP 266

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.

Shigella flexneri (taxid: 623)

>sp|P0AG67|RS1_ECOLI 30S ribosomal protein S1 OS=Escherichia coli (strain K12) GN=rpsA PE=1 SV=1

 Score = 69.3 bits (168), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 48/69 (69%), Gaps = 6/69 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L
Sbjct: 204 DYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSL 257

Query: 126 SIKQLEEDP 134
            +KQL EDP
Sbjct: 258 GLKQLGEDP 266

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.

Escherichia coli (strain K12) (taxid: 83333)

>sp|P0AG68|RS1_ECOL6 30S ribosomal protein S1 OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=rpsA PE=3 SV=1

 Score = 69.3 bits (168), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 48/69 (69%), Gaps = 6/69 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L
Sbjct: 204 DYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSL 257

Query: 126 SIKQLEEDP 134
            +KQL EDP
Sbjct: 258 GLKQLGEDP 266

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.

Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (taxid: 199310)

>sp|P0AG69|RS1_ECO57 30S ribosomal protein S1 OS=Escherichia coli O157:H7 GN=rpsA PE=3 SV=1

 Score = 69.3 bits (168), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 48/69 (69%), Gaps = 6/69 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L
Sbjct: 204 DYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSL 257

Query: 126 SIKQLEEDP 134
            +KQL EDP
Sbjct: 258 GLKQLGEDP 266

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.

Escherichia coli O157:H7 (taxid: 83334)

>sp|Q83E09|RS1_COXBU 30S ribosomal protein S1 OS=Coxiella burnetii (strain RSA 493 / Nine Mile phase I) GN=rpsA PE=1 SV=1

 Score = 69.3 bits (168), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 58/92 (63%), Gaps = 7/92 (7%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYGAF+ L   DGL H+T      +++W  ++   D+LN GDEV VKV+K DR+K R++L
Sbjct: 200 DYGAFVDLGGVDGLLHIT------DMAWGRVKHPSDLLNVGDEVHVKVLKFDRDKKRVSL 253

Query: 126 SIKQLEEDPLLETLEKVIPQDGSVISDSSSMS 157
            +KQL +DP  + +E+  P +  V    ++++
Sbjct: 254 GMKQLADDPWAK-IERRYPVNSRVFGKVTNIT 284

Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence.

Coxiella burnetii (strain RSA 493 / Nine Mile phase I) (taxid: 227377)

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	259
225433644	390	PREDICTED: 30S ribosomal protein S1 homo	0.926	0.615	0.745	1e-99
224131510	299	predicted protein [Populus trichocarpa]	0.926	0.802	0.742	7e-99
356569689	378	PREDICTED: 40S ribosomal protein S1-like	0.926	0.634	0.725	6e-96
356538073	383	PREDICTED: 30S ribosomal protein S1 homo	0.926	0.626	0.717	3e-94
147802809	418	hypothetical protein VITISV_006784 [Viti	0.926	0.574	0.670	5e-94
449484641	379	PREDICTED: 30S ribosomal protein S1-like	0.926	0.633	0.696	2e-90
449468800	378	PREDICTED: 30S ribosomal protein S1-like	0.926	0.634	0.692	6e-90
18403854	392	ribosomal protein S1-like RNA-binding do	0.915	0.604	0.709	7e-89
297835412	392	S1 RNA-binding domain-containing protein	0.926	0.612	0.700	1e-87
357462911	399	Polyribonucleotide nucleotidyltransferas	0.926	0.601	0.669	2e-84

>gi|225433644|ref|XP_002264430.1| PREDICTED: 30S ribosomal protein S1 homolog [Vitis vinifera] gi|296089601|emb|CBI39420.3| unnamed protein product [Vitis vinifera]

 Score =  368 bits (945), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 187/251 (74%), Positives = 215/251 (85%), Gaps = 11/251 (4%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPSHSCKEP K+I EIAKGL GS+ISVKVI A+EE +KL+FSEK+A W K+S ++N+ D
Sbjct: 136 LSPSHSCKEPHKTIQEIAKGLIGSLISVKVILADEEKRKLIFSEKEAAWLKFSKQINIGD 195

Query: 61  IF---VG--RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           IF   VG   DYGAF+HLRFPDGLYHLTGLVHVSEVSWDL+QD+RD+LNEGDEVRVK++K
Sbjct: 196 IFEAMVGSVEDYGAFVHLRFPDGLYHLTGLVHVSEVSWDLVQDVRDVLNEGDEVRVKIVK 255

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           +DR KSRITLSIKQLEEDPLLETL+KVIPQDGS   D  S+ +S+S  IEPLPGL  IFE
Sbjct: 256 VDRVKSRITLSIKQLEEDPLLETLDKVIPQDGSTGPD--SLRTSDSYDIEPLPGLETIFE 313

Query: 176 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 235
           ELLQE+GI DVRI+RQGFEKRVVSQDLQLWLSNAP   K+FTLLARAGRQVQEIQL+ SL
Sbjct: 314 ELLQEEGISDVRISRQGFEKRVVSQDLQLWLSNAPAVDKQFTLLARAGRQVQEIQLTTSL 373

Query: 236 ----IRKASKR 242
               I+KA +R
Sbjct: 374 DQEGIKKALQR 384

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224131510|ref|XP_002321102.1| predicted protein [Populus trichocarpa] gi|222861875|gb|EEE99417.1| predicted protein [Populus trichocarpa]

 Score =  365 bits (938), Expect = 7e-99,   Method: Compositional matrix adjust.
 Identities = 187/252 (74%), Positives = 215/252 (85%), Gaps = 12/252 (4%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPSHSCK+PQK+IHEIAK LTG +ISVKVI A EE +KL+FSEK+AVW+K+S  +NV +
Sbjct: 44  LSPSHSCKDPQKTIHEIAKDLTGLLISVKVIHAEEENRKLIFSEKEAVWSKFSKGINVGE 103

Query: 61  IFVGR-----DYGAFIHLRFPDG-LYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVI 114
           IF GR     DYGAFIH+RFPDG LYHLTGLVHVSEVSWDL+QD+RDILN GDEV VK+I
Sbjct: 104 IFAGRVGSVEDYGAFIHMRFPDGSLYHLTGLVHVSEVSWDLVQDVRDILNVGDEVTVKII 163

Query: 115 KIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIF 174
            ID+ KSRITLSIKQLEEDPLLETL+KVIPQDGS+  D  SM   NS TIEPLPGL +IF
Sbjct: 164 DIDQGKSRITLSIKQLEEDPLLETLDKVIPQDGSIAPDPLSM--HNSITIEPLPGLESIF 221

Query: 175 EELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHS 234
           +EL +EDGIDD+RI+RQGFEKRVVSQDLQLWLSNAPP  +KFTLLARAGRQVQEIQL+ +
Sbjct: 222 QELTREDGIDDIRISRQGFEKRVVSQDLQLWLSNAPPINRKFTLLARAGRQVQEIQLTTT 281

Query: 235 L----IRKASKR 242
           L    I+KA +R
Sbjct: 282 LDQGGIKKALQR 293

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356569689|ref|XP_003553029.1| PREDICTED: 40S ribosomal protein S1-like [Glycine max]

 Score =  356 bits (913), Expect = 6e-96,   Method: Compositional matrix adjust.
 Identities = 182/251 (72%), Positives = 209/251 (83%), Gaps = 11/251 (4%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SP H+ KEP+KSI EIA+GL GSI+SVKVI A+E+ KKL+FSEK+A W+KYS +VNV D
Sbjct: 124 LSPVHASKEPEKSIQEIAQGLIGSIMSVKVILADEDNKKLIFSEKEAAWSKYSKQVNVGD 183

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           IF  R     DYGAF+HLRFPDGLYHLTGL+HVSEVSWDLIQD+RDIL  GDEVR KV+ 
Sbjct: 184 IFEVRVGYVEDYGAFVHLRFPDGLYHLTGLIHVSEVSWDLIQDVRDILKVGDEVRAKVVG 243

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           ID  KSRI LSI+QLEEDPLLETL+KVIPQDGS  +D  SMS  +S +IEPLPGL  I E
Sbjct: 244 IDWGKSRINLSIRQLEEDPLLETLDKVIPQDGS--ADPDSMSGGDSGSIEPLPGLETILE 301

Query: 176 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 235
           ELLQEDGI DVRI+RQGFEKRVVSQDLQLWLSNAPP+ ++FTLLARAGRQVQEI L+ SL
Sbjct: 302 ELLQEDGIYDVRISRQGFEKRVVSQDLQLWLSNAPPTNQRFTLLARAGRQVQEIHLTTSL 361

Query: 236 ----IRKASKR 242
               IR+A +R
Sbjct: 362 DQEGIRRALQR 372

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538073|ref|XP_003537529.1| PREDICTED: 30S ribosomal protein S1 homolog [Glycine max]

 Score =  350 bits (898), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 180/251 (71%), Positives = 208/251 (82%), Gaps = 11/251 (4%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SP H+ KEP+KSI EIA+GL GSI+SVKVI A+E+ KKL+FSEK+A W+K+S +VNV D
Sbjct: 129 LSPVHASKEPEKSIQEIAQGLIGSIMSVKVILADEDNKKLIFSEKEAAWSKFSKQVNVGD 188

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           IF  R     DYGAF+HLRFPDGLY LTGL+HVSEVSWDLIQD+RDIL  GDEVRVKV+ 
Sbjct: 189 IFEVRVGYVEDYGAFVHLRFPDGLYRLTGLIHVSEVSWDLIQDVRDILKVGDEVRVKVVG 248

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           ID  KSRI LSI+QLEEDPLLETL+KVIPQDGS  +D  SMS  +S +IEPLPGL  I E
Sbjct: 249 IDWGKSRINLSIRQLEEDPLLETLDKVIPQDGS--ADPDSMSGGDSGSIEPLPGLETILE 306

Query: 176 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 235
           ELLQEDGI DVRI+RQGFEKRVVSQDLQLWL NAPP+ ++FTLLARAGRQVQEI L+ SL
Sbjct: 307 ELLQEDGIYDVRISRQGFEKRVVSQDLQLWLCNAPPTNQRFTLLARAGRQVQEIHLTTSL 366

Query: 236 ----IRKASKR 242
               I+KA +R
Sbjct: 367 DQEGIKKALQR 377

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147802809|emb|CAN68483.1| hypothetical protein VITISV_006784 [Vitis vinifera]

 Score =  349 bits (896), Expect = 5e-94,   Method: Compositional matrix adjust.
 Identities = 187/279 (67%), Positives = 215/279 (77%), Gaps = 39/279 (13%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPSHSCKEP K+I EIAKGL GS+ISVKVI A+EE +KL+FSEK+A W K+S ++N+ D
Sbjct: 136 LSPSHSCKEPHKTIQEIAKGLIGSLISVKVILADEEKRKLIFSEKEAAWLKFSKQINIGD 195

Query: 61  IF---VG--RDYGAFIHLRFPDG----------LYHLTGLVHVSEVSWDLIQDIRDILNE 105
           IF   VG   DYGAF+HLRFPDG          LYHLTGLVHVSEVSWDL+QD+RD+LNE
Sbjct: 196 IFEAMVGSVEDYGAFVHLRFPDGTSFSVTYITGLYHLTGLVHVSEVSWDLVQDVRDVLNE 255

Query: 106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP------------------QDG 147
           GDEVRVK++K+DR KSRITLSIKQLEEDPLLETL+KVIP                  QDG
Sbjct: 256 GDEVRVKIVKVDRVKSRITLSIKQLEEDPLLETLDKVIPQIIFLLHRTKSSDVSHLLQDG 315

Query: 148 SVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLS 207
           S   D  S+ +S+S  IEPLPGL  IFEELLQE+GI DVRI+RQGFEKRVVSQDLQLWLS
Sbjct: 316 STGPD--SLRTSDSYDIEPLPGLETIFEELLQEEGISDVRISRQGFEKRVVSQDLQLWLS 373

Query: 208 NAPPSGKKFTLLARAGRQVQEIQLSHSL----IRKASKR 242
           NAP   K+FTLLARAGRQVQEIQL+ SL    I+KA +R
Sbjct: 374 NAPAVDKQFTLLARAGRQVQEIQLTTSLDQEGIKKALQR 412

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449484641|ref|XP_004156938.1| PREDICTED: 30S ribosomal protein S1-like [Cucumis sativus]

 Score =  338 bits (866), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 172/247 (69%), Positives = 201/247 (81%), Gaps = 7/247 (2%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPSHSCKEP KSI +IAK L GS+ISVKVIQA+E+ +KL+FSEK+A  +K+S +V V D
Sbjct: 125 LSPSHSCKEPYKSIQDIAKSLIGSLISVKVIQADEKNRKLIFSEKEAARSKFSGQVAVGD 184

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           ++ G+     DYGAF+HLR  DGLYHLTGLVHVSEVSWDL+QD+RDIL+EGDEV VKVI 
Sbjct: 185 VYEGKVGSVEDYGAFVHLRLSDGLYHLTGLVHVSEVSWDLVQDVRDILSEGDEVTVKVIN 244

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           +++ KSRITLSI+QLEEDPLLETL+KVIPQD S   D  S      + I PLPGL  I E
Sbjct: 245 VNKNKSRITLSIRQLEEDPLLETLDKVIPQDSSAEPD--SFGPKGDSEIIPLPGLETIIE 302

Query: 176 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 235
           ELLQE+GI DVR+ RQGFEKRVVSQDLQLWLSNAPP  KKFTLLARAGRQVQEIQL+ SL
Sbjct: 303 ELLQEEGIVDVRVNRQGFEKRVVSQDLQLWLSNAPPVEKKFTLLARAGRQVQEIQLTTSL 362

Query: 236 IRKASKR 242
            ++  KR
Sbjct: 363 DQEGIKR 369

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468800|ref|XP_004152109.1| PREDICTED: 30S ribosomal protein S1-like [Cucumis sativus]

 Score =  336 bits (861), Expect = 6e-90,   Method: Compositional matrix adjust.
 Identities = 171/247 (69%), Positives = 201/247 (81%), Gaps = 7/247 (2%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPSHSCKEP KSI +IAK L GS+ISVKVIQA+E+ +KL+FSEK+A  +K+S +V V D
Sbjct: 124 LSPSHSCKEPYKSIQDIAKSLIGSLISVKVIQADEKNRKLIFSEKEAARSKFSGQVAVGD 183

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           ++ G+     DYGAF+HLR  DGLYHLTGLVHVSEVSWDL+QD+RDIL+EGDEV VKVI 
Sbjct: 184 VYEGKVGSVEDYGAFVHLRLSDGLYHLTGLVHVSEVSWDLVQDVRDILSEGDEVTVKVIN 243

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           +++ KSRITLSI+QLEEDPLLETL+KVIPQ+ S   D  S      + I PLPGL  I E
Sbjct: 244 VNKNKSRITLSIRQLEEDPLLETLDKVIPQESSAEPD--SFGPKGDSEIIPLPGLETIIE 301

Query: 176 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 235
           ELLQE+GI DVR+ RQGFEKRVVSQDLQLWLSNAPP  KKFTLLARAGRQVQEIQL+ SL
Sbjct: 302 ELLQEEGIVDVRVNRQGFEKRVVSQDLQLWLSNAPPVEKKFTLLARAGRQVQEIQLTTSL 361

Query: 236 IRKASKR 242
            ++  KR
Sbjct: 362 DQEGIKR 368

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18403854|ref|NP_566737.1| ribosomal protein S1-like RNA-binding domain-containing protein [Arabidopsis thaliana] gi|9293944|dbj|BAB01847.1| unnamed protein product [Arabidopsis thaliana] gi|15146284|gb|AAK83625.1| AT3g23700/MYM9_3 [Arabidopsis thaliana] gi|22655022|gb|AAM98102.1| At3g23700/MYM9_3 [Arabidopsis thaliana] gi|332643282|gb|AEE76803.1| ribosomal protein S1-like RNA-binding domain-containing protein [Arabidopsis thaliana]

 Score =  332 bits (852), Expect = 7e-89,   Method: Compositional matrix adjust.
 Identities = 176/248 (70%), Positives = 201/248 (81%), Gaps = 11/248 (4%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPS SCKEPQKSIHEIAK L GS + VKV+QA+EE +KL+ SEK A+W KYS  VNV D
Sbjct: 138 LSPSRSCKEPQKSIHEIAKTLVGSKLPVKVVQADEENRKLILSEKLALWPKYSQNVNVGD 197

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           +F GR     DYGAFIHLRF DGLYHLTGLVHVSEVSWD +QD+RD+L +GDEVRV V  
Sbjct: 198 VFNGRVGSVEDYGAFIHLRFDDGLYHLTGLVHVSEVSWDYVQDVRDVLRDGDEVRVIVTN 257

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           ID+EKSRITLSIKQLE+DPLLETL+KVI +D    + S S+SS+N +TIEPLPGL  I E
Sbjct: 258 IDKEKSRITLSIKQLEDDPLLETLDKVILKD--SSTGSPSLSSNNGDTIEPLPGLETILE 315

Query: 176 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 235
           ELL+EDGI+ V+I RQGFEKRVVSQDLQLWLSN PPS  KF LLARAGRQVQEI L+ SL
Sbjct: 316 ELLKEDGIEAVKINRQGFEKRVVSQDLQLWLSNTPPSDGKFVLLARAGRQVQEIHLTTSL 375

Query: 236 ----IRKA 239
               I+KA
Sbjct: 376 EQGGIKKA 383

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297835412|ref|XP_002885588.1| S1 RNA-binding domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297331428|gb|EFH61847.1| S1 RNA-binding domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  328 bits (841), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 173/247 (70%), Positives = 199/247 (80%), Gaps = 7/247 (2%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SPS SCKEPQKSIHEIAK L GS + VKV+QA+EE +KL+ SEK A+W KYS  V+V D
Sbjct: 138 LSPSRSCKEPQKSIHEIAKTLVGSKLPVKVVQADEENRKLILSEKLALWPKYSQNVSVGD 197

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           +F GR     DYGAFIHLRF DGLYHLTGLVHVSEVSWD +QD+RD+L +GDEVRV V  
Sbjct: 198 VFTGRVGSVEDYGAFIHLRFDDGLYHLTGLVHVSEVSWDYVQDVRDVLRDGDEVRVIVTN 257

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           ID+EKSRITLSIKQLE+DPLLETL+KVI +D    S S S+SS+N +TIEPLPGL  I E
Sbjct: 258 IDKEKSRITLSIKQLEDDPLLETLDKVILKD--SSSGSPSLSSNNGDTIEPLPGLETILE 315

Query: 176 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 235
           ELL+EDGI+ V+I RQGFEKRVVSQDLQLWLSN PPS  KF LLARAGRQVQEI L+  L
Sbjct: 316 ELLKEDGIEAVKINRQGFEKRVVSQDLQLWLSNTPPSDGKFVLLARAGRQVQEIHLTTFL 375

Query: 236 IRKASKR 242
            +   K+
Sbjct: 376 EQGGIKK 382

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357462911|ref|XP_003601737.1| Polyribonucleotide nucleotidyltransferase [Medicago truncatula] gi|355490785|gb|AES71988.1| Polyribonucleotide nucleotidyltransferase [Medicago truncatula]

 Score =  318 bits (814), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 168/251 (66%), Positives = 203/251 (80%), Gaps = 11/251 (4%)

Query: 1   MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
           +SP HSC+EP ++I E A+ L G+I+SVKVI  +EE +KLV SEK+A W K+S  +N+ D
Sbjct: 145 LSPVHSCQEPDQTIKERARELIGAILSVKVIIVDEEKRKLVLSEKEASWFKHSKHINIGD 204

Query: 61  IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
           +F GR     DYGAF+HLRFPDGLYHLTGL+H+SEVSWDL+QD+RD L EG+EVRVKVI 
Sbjct: 205 LFEGRVGSVEDYGAFVHLRFPDGLYHLTGLIHISEVSWDLVQDVRDFLREGEEVRVKVIS 264

Query: 116 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFE 175
           ID  K R+TLSIKQLEEDPLLETL+KVI QDGS +   +S+SS+ S+ I+PLPGL  I E
Sbjct: 265 IDTVKMRLTLSIKQLEEDPLLETLDKVIRQDGSGV--PNSISSTTSSPIDPLPGLDTILE 322

Query: 176 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 235
           ELLQEDGI++ RI+RQGFEKRVVSQDLQLWLSNAPP  ++FTLLARAGRQVQEI L  SL
Sbjct: 323 ELLQEDGINEARISRQGFEKRVVSQDLQLWLSNAPPMDQRFTLLARAGRQVQEIHLKTSL 382

Query: 236 ----IRKASKR 242
               I+KA +R
Sbjct: 383 DQEGIKKAIQR 393

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	259
TAIR|locus:2095203	392	AT3G23700 [Arabidopsis thalian	0.926	0.612	0.684	4.5e-82
TAIR|locus:2010336	767	AT1G12800 [Arabidopsis thalian	0.861	0.290	0.295	8.3e-14
TIGR_CMR|SO_2402	555	SO_2402 "ribosomal protein S1"	0.374	0.174	0.390	5.8e-13
TAIR|locus:2145860	416	RPS1 "ribosomal protein S1" [A	0.451	0.281	0.333	4e-11
UNIPROTKB|P0AG67	557	rpsA "30S ribosomal subunit pr	0.455	0.211	0.328	7.1e-11
UNIPROTKB|Q71X59	117	LMOf2365_2340 "S1 RNA binding	0.277	0.615	0.428	8.8e-11
TIGR_CMR|NSE_0408	553	NSE_0408 "ribosomal protein S1	0.413	0.193	0.348	9.6e-11
TIGR_CMR|CBU_0528	551	CBU_0528 "ribosomal protein S1	0.277	0.130	0.443	1.9e-10
TIGR_CMR|CPS_2335	553	CPS_2335 "ribosomal protein S1	0.416	0.195	0.341	1.9e-10
TIGR_CMR|ECH_0402	567	ECH_0402 "putative ribosomal p	0.416	0.190	0.339	3.7e-10

TAIR|locus:2095203 AT3G23700 [Arabidopsis thaliana (taxid:3702)]

 Score = 823 (294.8 bits), Expect = 4.5e-82, P = 4.5e-82
 Identities = 169/247 (68%), Positives = 192/247 (77%)

Query:     1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVED 60
             +SPS SCKEPQKSIHEIAK L GS + VKV+QA+EE +KL+ SEK A+W KYS  VNV D
Sbjct:   138 LSPSRSCKEPQKSIHEIAKTLVGSKLPVKVVQADEENRKLILSEKLALWPKYSQNVNVGD 197

Query:    61 IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
             +F GR     DYGAFIHLRF DGLYHLTGLVHVSEVSWD +QD+RD+L +GDEVRV V  
Sbjct:   198 VFNGRVGSVEDYGAFIHLRFDDGLYHLTGLVHVSEVSWDYVQDVRDVLRDGDEVRVIVTN 257

Query:   116 IDREKSRITLSIKQLEEDPLLETLEKVIPQDGXXXXXXXXXXXXXXNTIEPLPGLGAIFE 175
             ID+EKSRITLSIKQLE+DPLLETL+KVI +D               +TIEPLPGL  I E
Sbjct:   258 IDKEKSRITLSIKQLEDDPLLETLDKVILKDSSTGSPSLSSNNG--DTIEPLPGLETILE 315

Query:   176 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSL 235
             ELL+EDGI+ V+I RQGFEKRVVSQDLQLWLSN PPS  KF LLARAGRQVQEI L+ SL
Sbjct:   316 ELLKEDGIEAVKINRQGFEKRVVSQDLQLWLSNTPPSDGKFVLLARAGRQVQEIHLTTSL 375

Query:   236 IRKASKR 242
              +   K+
Sbjct:   376 EQGGIKK 382

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0005634 "nucleus" evidence=IDA

GO:0009409 "response to cold" evidence=IEP;RCA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0006364 "rRNA processing" evidence=RCA

GO:0009773 "photosynthetic electron transport in photosystem I" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0042742 "defense response to bacterium" evidence=RCA

GO:0042793 "transcription from plastid promoter" evidence=RCA

TAIR|locus:2010336 AT1G12800 [Arabidopsis thaliana (taxid:3702)]

 Score = 190 (71.9 bits), Expect = 8.3e-14, P = 8.3e-14
 Identities = 71/240 (29%), Positives = 106/240 (44%)

Query:     8 KEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS--EKDAVWNKYSSRVNVEDIFVGR 65
             +E QK +        G  I V V+ AN   +KL+FS   ++        R  +  + VG 
Sbjct:   528 REKQKFL----SSFVGQKIKVNVVMANRNSRKLIFSMRPRENEEEVEKKRTLMAKLRVGD 583

Query:    66 DYGAFIHLRFPDGLY-HLTG---LVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS 121
                  I      G++  L G   LVH SEVSWD   D       G  V  KV ++D    
Sbjct:   584 VVKCCIKKITYFGIFCELEGVPALVHQSEVSWDATLDPASYFKIGQIVEAKVHQLDFALE 643

Query:   122 RITLSIKQLEEDPLLETLEKVIPQDGXXXXXXXXXXXXXXNTIEPLPGLGAIFEELLQED 181
             RI LS+K++  DPL E LE V+  D                     P + ++ +EL   +
Sbjct:   644 RIFLSLKEITPDPLTEALESVVGGDNDQLGGRLQAAELDAEW----PDVESLIKELEMVE 699

Query:   182 GIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASK 241
             GI  V  +R  F    ++   Q+++  AP    ++ LLARAG +VQE+ +  SL ++  K
Sbjct:   700 GIQSVSKSRF-FLSPGLAPTFQVYM--APMFENQYKLLARAGNRVQELIVEASLSKEEMK 756

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0006655 "phosphatidylglycerol biosynthetic process" evidence=RCA

GO:0009073 "aromatic amino acid family biosynthetic process" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0019344 "cysteine biosynthetic process" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0042793 "transcription from plastid promoter" evidence=RCA

TIGR_CMR|SO_2402 SO_2402 "ribosomal protein S1" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 180 (68.4 bits), Expect = 5.8e-13, P = 5.8e-13
 Identities = 41/105 (39%), Positives = 64/105 (60%)

Query:    43 SEKDAVWNKYSSRVNVEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRD 101
             +E+DA+         V+ I     DYGAF+ L   DGL H+T      +++W  ++   +
Sbjct:   180 AERDALLENLQEGQAVKGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSE 233

Query:   102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQD 146
             I+N GDE+ VKV+K DRE++R++L +KQL EDP LE + K  P++
Sbjct:   234 IVNVGDEINVKVLKYDRERTRVSLGLKQLGEDPWLE-ISKRYPEN 277

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

TAIR|locus:2145860 RPS1 "ribosomal protein S1" [Arabidopsis thaliana (taxid:3702)]

 Score = 171 (65.3 bits), Expect = 4.0e-11, P = 4.0e-11
 Identities = 43/129 (33%), Positives = 73/129 (56%)

Query:    11 QKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----R 65
             Q S    A+ L    I +K ++ +EE  KLV S + AV +   +++ +  + +G     +
Sbjct:   217 QISSKAAAEELLEKEIPLKFVEVDEEQTKLVLSNRKAVADS-QAQLGIGSVVLGVVQSLK 275

Query:    66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
              YGAFI +    G+    GL+HVS++S D + DI  +L  GD ++V ++  DR++ R++L
Sbjct:   276 PYGAFIDI---GGI---NGLLHVSQISHDRVSDIATVLQPGDTLKVMILSHDRDRGRVSL 329

Query:   126 SIKQLEEDP 134
             S K+LE  P
Sbjct:   330 STKKLEPTP 338

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0005739 "mitochondrion" evidence=ISM

GO:0009507 "chloroplast" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0006364 "rRNA processing" evidence=RCA

GO:0009773 "photosynthetic electron transport in photosystem I" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

UNIPROTKB|P0AG67 rpsA "30S ribosomal subunit protein S1" [Escherichia coli K-12 (taxid:83333)]

 Score = 171 (65.3 bits), Expect = 7.1e-11, P = 7.1e-11
 Identities = 45/137 (32%), Positives = 74/137 (54%)

Query:    21 LTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVNVEDIFVG-RDYG 68
             L G  +  KVI+ +++   +V S           E+D +       + V+ I     DYG
Sbjct:   147 LEGKELEFKVIKLDQKRNNVVVSRRAVIESENSAERDQLLENLQEGMEVKGIVKNLTDYG 206

Query:    69 AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
             AF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K DRE++R++L +K
Sbjct:   207 AFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSLGLK 260

Query:   129 QLEEDPLLETLEKVIPQ 145
             QL EDP +  + K  P+
Sbjct:   261 QLGEDPWV-AIAKRYPE 276

GO:2000766 "negative regulation of cytoplasmic translation" evidence=IEP;IDA

GO:0003729 "mRNA binding" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0006412 "translation" evidence=IMP

GO:0003735 "structural constituent of ribosome" evidence=IEA;IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|Q71X59 LMOf2365_2340 "S1 RNA binding domain protein" [Listeria monocytogenes serotype 4b str. F2365 (taxid:265669)]

 Score = 151 (58.2 bits), Expect = 8.8e-11, P = 8.8e-11
 Identities = 33/77 (42%), Positives = 49/77 (63%)

Query:    65 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT 124
             + YGAF+ L   D      GLVH+SE++   ++DI D L  G EV+VK++ ID EK++I+
Sbjct:    18 QSYGAFVAL---DN--STQGLVHISEITHGFVKDIHDFLEVGQEVKVKILDIDEEKNKIS 72

Query:   125 LSIKQLEEDPLLETLEK 141
             LSI+  EE P  +  +K
Sbjct:    73 LSIRATEEAPKEQPTKK 89

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|NSE_0408 NSE_0408 "ribosomal protein S1" [Neorickettsia sennetsu str. Miyayama (taxid:222891)]

 Score = 170 (64.9 bits), Expect = 9.6e-11, P = 9.6e-11
 Identities = 39/112 (34%), Positives = 63/112 (56%)

Query:    38 KKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 92
             +K + +  +A  ++Y S +   DI  GR      YG F+ +   D +  + GL++V+++S
Sbjct:   195 RKALGAVHEAARSEYISTIKEGDIIDGRVKSIASYGVFVQIHESDKVGVVDGLLYVNDIS 254

Query:    93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP 144
             W  +     I + G EVRVKVI +D EK RI+L +KQL E+P  +  +K  P
Sbjct:   255 WARVTHPSSIYSVGQEVRVKVIAVDPEKGRISLGVKQLTENPWKDVSKKYTP 306

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

TIGR_CMR|CBU_0528 CBU_0528 "ribosomal protein S1" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 168 (64.2 bits), Expect = 1.9e-10, P = 1.9e-10
 Identities = 35/79 (44%), Positives = 52/79 (65%)

Query:    66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
             DYGAF+ L   DGL H+T      +++W  ++   D+LN GDEV VKV+K DR+K R++L
Sbjct:   200 DYGAFVDLGGVDGLLHIT------DMAWGRVKHPSDLLNVGDEVHVKVLKFDRDKKRVSL 253

Query:   126 SIKQLEEDPLLETLEKVIP 144
              +KQL +DP  + +E+  P
Sbjct:   254 GMKQLADDPWAK-IERRYP 271

GO:0003735 "structural constituent of ribosome" evidence=ISS

TIGR_CMR|CPS_2335 CPS_2335 "ribosomal protein S1" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 168 (64.2 bits), Expect = 1.9e-10, P = 1.9e-10
 Identities = 43/126 (34%), Positives = 70/126 (55%)

Query:    21 LTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVNVEDIFVG-RDYG 68
             L G  +  KVI+ +++   +V S           E+D +    +    V+ I     DYG
Sbjct:   147 LEGKPLEFKVIKLDQKRNNVVVSRRAVIEAEGSAERDELLESLAEGQEVKGIVKNLTDYG 206

Query:    69 AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
             AF+ L   DGL H+T      +++W  ++   +I+N GDE++VKV+K DRE++R++L +K
Sbjct:   207 AFVDLGGIDGLLHIT------DMAWKRVKHPSEIVNVGDEIQVKVLKFDRERTRVSLGMK 260

Query:   129 QLEEDP 134
             QL EDP
Sbjct:   261 QLGEDP 266

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

TIGR_CMR|ECH_0402 ECH_0402 "putative ribosomal protein S1" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 166 (63.5 bits), Expect = 3.7e-10, P = 3.7e-10
 Identities = 39/115 (33%), Positives = 62/115 (53%)

Query:    38 KKLVFSEKDA-VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV 91
             +K +  E  A   + Y S++N  DI  G+      YG FI +     +  + GL+H++++
Sbjct:   209 RKAILEESLADAKSLYLSQLNEGDIIEGKVKSITKYGVFIEIHESPSVGVVDGLLHITDI 268

Query:    92 SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQD 146
             SW  +     + + G  V+ K+IKIDRE  +I+L +KQLEE P    +EK  P D
Sbjct:   269 SWSRVSHPSAVFSCGQTVKTKIIKIDRENKKISLGVKQLEESPW-SNIEKKYPVD 322

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	259
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	5e-20
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	1e-19
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	1e-18
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	2e-18
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	2e-18
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	4e-18
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	5e-18
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	2e-17
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	5e-17
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	2e-16
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	5e-16
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-15
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-15
PRK08059	123	PRK08059, PRK08059, general stress protein 13; Val	3e-15
COG1098	129	COG1098, VacB, Predicted RNA binding protein (cont	4e-15
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	4e-15
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	6e-15
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-14
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	2e-14
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	3e-14
pfam00575	74	pfam00575, S1, S1 RNA binding domain	9e-14
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	5e-13
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	6e-13
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	7e-13
PRK05807	136	PRK05807, PRK05807, hypothetical protein; Provisio	9e-13
PRK08582	139	PRK08582, PRK08582, hypothetical protein; Provisio	5e-12
cd05708	77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	8e-12
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	2e-11
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	2e-11
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	3e-11
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	1e-10
PRK03987	262	PRK03987, PRK03987, translation initiation factor	2e-10
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	5e-10
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	9e-10
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-09
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	1e-09
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	2e-09
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	3e-09
PRK07252	120	PRK07252, PRK07252, hypothetical protein; Provisio	4e-09
cd05691	73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	4e-09
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	5e-09
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	1e-08
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	6e-08
cd05684	79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	1e-07
cd04461	83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	2e-07
cd05690	69	cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: R	4e-07
COG2183	780	COG2183, Tex, Transcriptional accessory protein [T	3e-06
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	5e-06
cd05689	72	cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: R	7e-06
cd05686	73	cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-b	1e-05
cd05698	70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	1e-05
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	3e-05
cd05687	70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	6e-05
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	6e-04

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 88.7 bits (221), Expect = 5e-20
 Identities = 40/126 (31%), Positives = 67/126 (53%), Gaps = 18/126 (14%)

Query: 21  LTGSIISVKVIQANEEMKKLVFS-------EKDAVWNKYSSRVNVEDIFVGR-----DYG 68
           L G  +  KVI+ +++   +V S       E+     +    +    +  G      DYG
Sbjct: 157 LEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYG 216

Query: 69  AFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
           AF+       L  + GL+H++++SW  +    +++N GDEV+VKV+K D+EK R++L +K
Sbjct: 217 AFV------DLGGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLK 270

Query: 129 QLEEDP 134
           QL EDP
Sbjct: 271 QLGEDP 276

Length = 565

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 87.1 bits (217), Expect = 1e-19
 Identities = 46/135 (34%), Positives = 70/135 (51%), Gaps = 16/135 (11%)

Query: 26  ISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPD 77
           + VKV++ ++E K++    K      W     +  V     G+     DYGAF+ L   +
Sbjct: 251 VKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELE--E 308

Query: 78  GLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLL 136
           G+    GLVHVSE+SW    +    +++ G EV V V++ID EK RI+L +KQ +E+P  
Sbjct: 309 GI---EGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWE 365

Query: 137 ETLEKVIPQDGSVIS 151
           E  EK     G V+ 
Sbjct: 366 EFAEKYPV--GDVVE 378

Length = 565

>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 84.6 bits (210), Expect = 1e-18
 Identities = 38/125 (30%), Positives = 69/125 (55%), Gaps = 19/125 (15%)

Query: 23  GSIISVKVIQANEEMKK--------LVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGA 69
           G  + VK+I+ N + +K        ++  EK+    +  + +   D+  G      D+GA
Sbjct: 434 GQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGA 493

Query: 70  FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129
           F+ +    G+    GL+HVSE+SW  ++   D+L  GDE++V ++ ID+E  +++LS+K+
Sbjct: 494 FVDI---GGV---DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKK 547

Query: 130 LEEDP 134
           L  DP
Sbjct: 548 LLPDP 552

Length = 647

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 83.9 bits (208), Expect = 2e-18
 Identities = 41/135 (30%), Positives = 72/135 (53%), Gaps = 26/135 (19%)

Query: 23  GSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVNVEDIFVGR-----D 66
           G  +  K+++ +++   +V S           +++ + NK      V ++  G      D
Sbjct: 150 GKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKL----EVGEVVEGVVKNITD 205

Query: 67  YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126
           YGAF+ +        + GL+H+SE+SW  +    +++  GDEV+VKVI +D E+ R++LS
Sbjct: 206 YGAFVDI------GGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLS 259

Query: 127 IKQLEEDPLLETLEK 141
           +KQLEEDP     +K
Sbjct: 260 LKQLEEDPWEGIEKK 274

Length = 541

>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 83.0 bits (206), Expect = 2e-18
 Identities = 43/144 (29%), Positives = 74/144 (51%), Gaps = 28/144 (19%)

Query: 23  GSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVNVEDIFVG-----RD 66
           G  + VK+I+ + E  +++ S           +K+ +     S +   D+  G      D
Sbjct: 150 GKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELL----SSLKEGDVVEGTVARLTD 205

Query: 67  YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126
           +GAF+ +   DGL      VH+SE+S + ++   ++++ G EV VKV+ ID E  RI+LS
Sbjct: 206 FGAFVDIGGVDGL------VHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLS 259

Query: 127 IKQLEEDPLLETLEKVIPQDGSVI 150
           +K     P  E +E+ +P+ G VI
Sbjct: 260 LKDTLPGP-WEGVEEKLPE-GDVI 281

Length = 390

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 82.9 bits (206), Expect = 4e-18
 Identities = 47/139 (33%), Positives = 79/139 (56%), Gaps = 16/139 (11%)

Query: 22  TGSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHL 73
            G  + V V++ +EE +++    K      W +++ +  V D+  G+     D+GAF+  
Sbjct: 334 VGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFV-- 391

Query: 74  RFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE 132
               G+    GLVH+S++SWD   ++  ++  +GDEV   V+K+D EK RI+L IKQLEE
Sbjct: 392 GLEGGI---DGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEE 448

Query: 133 DPLLETLEKVIPQDGSVIS 151
           DP  E  +K   + GS+++
Sbjct: 449 DPFEEFAKKH--KKGSIVT 465

Length = 565

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 82.7 bits (205), Expect = 5e-18
 Identities = 45/120 (37%), Positives = 65/120 (54%), Gaps = 13/120 (10%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  + VKVI  +EE  ++  S K      W     +  V D   G+     DYGAF+ + 
Sbjct: 239 GDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIE 298

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
             +G+    GLVHVSE+SW       +++  G EV VKV+ ID E+ RI+L +KQL+E+P
Sbjct: 299 --EGV---EGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENP 353

Length = 541

>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 81.1 bits (201), Expect = 2e-17
 Identities = 44/120 (36%), Positives = 70/120 (58%), Gaps = 13/120 (10%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  I V ++  ++E KKL  S K  +   W     +  V  I +G+      +GAF+ L 
Sbjct: 524 GDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELE 583

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
              G+    GLVH+S++SW  I    D+L+EG+EV+ K++++D E+ RI LSIK++EE+P
Sbjct: 584 --PGV---DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP 638

Length = 647

>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 79.1 bits (196), Expect = 5e-17
 Identities = 44/143 (30%), Positives = 75/143 (52%), Gaps = 13/143 (9%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  + VKV+  + E +++  S KD +   W     ++   D+  G      D+GAF+ + 
Sbjct: 239 GQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEV- 297

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
              G+    GLVH+S++S   I    ++L EG EV+VKV++++ E+ RI+LSIK LEE P
Sbjct: 298 -LPGV---EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAP 353

Query: 135 LLETLEKVIPQDGSVISDSSSMS 157
             E   +   +   +  + +  S
Sbjct: 354 AEEEDRREEYRQYELPEEETGFS 376

Length = 390

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 78.1 bits (193), Expect = 2e-16
 Identities = 49/138 (35%), Positives = 76/138 (55%), Gaps = 15/138 (10%)

Query: 22  TGSIISVKVIQANEEMKKLVFSEKDAVWN---KYSSRVNVEDIFVGR-----DYGAFIHL 73
            G  + VKV+  + E +++    K    N   +++ +  V D+  G+     D+GAF+ L
Sbjct: 324 VGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAFVEL 383

Query: 74  RFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 133
               G+    GLVH+S++SWD   +  +   +GDEV  KV+ +D+EK RI+L IKQLEE 
Sbjct: 384 --EGGI---DGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLEES 438

Query: 134 PLLETLEKVIPQDGSVIS 151
           P  E  EK   + GSV+ 
Sbjct: 439 PWEEFSEK--YKKGSVVK 454

Length = 541

>gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed

 Score = 76.0 bits (187), Expect = 5e-16
 Identities = 42/127 (33%), Positives = 74/127 (58%), Gaps = 11/127 (8%)

Query: 13  SIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDY 67
           S  +  + L G  + +K ++ +EE  +LV S + A+  +  +R+ V ++ VG     + Y
Sbjct: 151 STRKPKEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPY 210

Query: 68  GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 127
           GAFI +        ++GL+H+SE+S + I+    + N  DE++V +I +D E+ RI+LS 
Sbjct: 211 GAFIDIG------GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLST 264

Query: 128 KQLEEDP 134
           KQLE +P
Sbjct: 265 KQLEPEP 271

Length = 318

>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 75.9 bits (187), Expect = 1e-15
 Identities = 42/128 (32%), Positives = 66/128 (51%), Gaps = 14/128 (10%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  + VKVI+ ++E  ++  S K      W     +  V D   GR     DYG F+ + 
Sbjct: 234 GQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIE 293

Query: 75  FPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 133
             +G+    GLVHVSE+SW         ++ +GDEV V ++ ID E+ R++L +KQ + +
Sbjct: 294 --EGI---EGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKAN 348

Query: 134 PLLETLEK 141
           P  +  EK
Sbjct: 349 PWEQFEEK 356

This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by PFAM model pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. 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 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 516

>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 74.8 bits (185), Expect = 2e-15
 Identities = 46/167 (27%), Positives = 78/167 (46%), Gaps = 31/167 (18%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  +   V++ + E +++    K      + +++ +     I  G      D GAF+ L 
Sbjct: 422 GDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVKDKGAFVEL- 480

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
             DG+    GL+  SE+S D ++D  ++L  GDEV  KVI IDR+  RI+LSIK L+E  
Sbjct: 481 -EDGV---EGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEA- 535

Query: 135 LLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQED 181
                     ++   I++ +S S S +        LG + +  L+  
Sbjct: 536 ----------EEKEAIAEYNSASDSKTT-------LGDLLKAALKGK 565

Length = 565

>gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated

 Score = 69.7 bits (171), Expect = 3e-15
 Identities = 33/70 (47%), Positives = 47/70 (67%), Gaps = 5/70 (7%)

Query: 65  RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           + YGAF+ L   D      GLVH+SE++   ++DI D L+ GDEV+VKV+ +D EK +I+
Sbjct: 19  QPYGAFVAL---DE--ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKIS 73

Query: 125 LSIKQLEEDP 134
           LSI+  EE P
Sbjct: 74  LSIRATEEAP 83

Length = 123

>gnl|CDD|224023 COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]

 Score = 69.6 bits (171), Expect = 4e-15
 Identities = 33/69 (47%), Positives = 46/69 (66%), Gaps = 6/69 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
            YGAF+      G    TGLVH+SE++   ++DI D L  G EV+VKV+ ID E  +I+L
Sbjct: 18  PYGAFV--ELEGGK---TGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDID-ENGKISL 71

Query: 126 SIKQLEEDP 134
           SI++LEE+P
Sbjct: 72  SIRKLEEEP 80

Length = 129

>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 74.3 bits (184), Expect = 4e-15
 Identities = 32/83 (38%), Positives = 52/83 (62%), Gaps = 15/83 (18%)

Query: 56  VNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 108
             V +I+ G+     D+GAF+ +  P  DGL      VH+SE++ + ++ + D+L EGDE
Sbjct: 619 PEVGEIYEGKVVRIVDFGAFVEI-LPGKDGL------VHISEIADERVEKVEDVLKEGDE 671

Query: 109 VRVKVIKIDREKSRITLSIKQLE 131
           V+VKV++ID ++ RI LS K + 
Sbjct: 672 VKVKVLEID-KRGRIRLSRKAVL 693

Length = 693

>gnl|CDD|240193 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

 Score = 67.3 bits (165), Expect = 6e-15
 Identities = 27/61 (44%), Positives = 42/61 (68%), Gaps = 6/61 (9%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           D+GAF+ L   DGL      +H+S++SW  ++   +++N GDEV VKV+KID+E+ RI+L
Sbjct: 14  DFGAFVDLGGVDGL------LHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67

Query: 126 S 126
            
Sbjct: 68  G 68

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. Length = 68

>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 72.5 bits (178), Expect = 1e-14
 Identities = 34/81 (41%), Positives = 50/81 (61%), Gaps = 6/81 (7%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           D+GAF+ L   DGL      +H++++SW  ++   + +  G EV+VKVIK D+EK RI+L
Sbjct: 200 DFGAFVDLGGVDGL------LHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISL 253

Query: 126 SIKQLEEDPLLETLEKVIPQD 146
           S+KQL EDP     +K    D
Sbjct: 254 SLKQLGEDPWEAIEKKFPVGD 274

This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by PFAM model pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. 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 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 516

>gnl|CDD|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional

 Score = 71.7 bits (176), Expect = 2e-14
 Identities = 41/135 (30%), Positives = 62/135 (45%), Gaps = 21/135 (15%)

Query: 16  EIAKGLTGSIISVKVIQANEEMKKLVFS-------EKDAVWNKYSSRVNVEDIFVGR--- 65
           E  +   G      + +  E  + +V S       E+      +   V   D+  G    
Sbjct: 153 EDPESYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTR 212

Query: 66  --DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS-- 121
              +GAF+ L  P     + G+VH+SE+SW  +Q   + ++ GD VRVKV+ I+R K   
Sbjct: 213 LAPFGAFVELA-PG----VEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGK 267

Query: 122 --RITLSIKQLEEDP 134
             RI+LSIKQ   DP
Sbjct: 268 GLRISLSIKQAGGDP 282

Length = 491

>gnl|CDD|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

 Score = 65.4 bits (160), Expect = 3e-14
 Identities = 28/63 (44%), Positives = 45/63 (71%), Gaps = 6/63 (9%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
            +GAF+ L    G+   +GLVH+S+++   ++D++D+L EGD+V+VKV+ ID    RI+L
Sbjct: 13  PFGAFVEL--GGGI---SGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARG-RISL 66

Query: 126 SIK 128
           SIK
Sbjct: 67  SIK 69

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. Length = 69

>gnl|CDD|216000 pfam00575, S1, S1 RNA binding domain

 Score = 64.2 bits (157), Expect = 9e-14
 Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 10/79 (12%)

Query: 55  RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEV 109
           +    D+  G        GAF+ L        + G + +SE+S D ++D  ++L  GDEV
Sbjct: 1   KPEEGDVVKGTVTRVTKGGAFVDL-----GNGVEGFIPISEISDDRVEDPDEVLKVGDEV 55

Query: 110 RVKVIKIDREKSRITLSIK 128
            VKV+K+D+E+ RI LSI+
Sbjct: 56  EVKVLKVDKERGRIILSIR 74

The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Length = 74

>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 67.8 bits (166), Expect = 5e-13
 Identities = 39/121 (32%), Positives = 64/121 (52%), Gaps = 14/121 (11%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  + V ++  + E ++L    K      W ++  +  V D   G+     D+GAF+ L 
Sbjct: 321 GDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELE 380

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNE-GDEVRVKVIKIDREKSRITLSIKQLEED 133
              G+    GL+H+S++SWD      D L + GDE+   V+ +D+EK RI+L +KQL E+
Sbjct: 381 --GGI---DGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTEN 435

Query: 134 P 134
           P
Sbjct: 436 P 436

This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by PFAM model pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. 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 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 516

>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

 Score = 67.6 bits (166), Expect = 6e-13
 Identities = 34/82 (41%), Positives = 53/82 (64%), Gaps = 11/82 (13%)

Query: 56  VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVR 110
           V V +++ G      D+GAF+ L  P       GLVH+S+++ + ++ + D+L EGDEV+
Sbjct: 617 VEVGEVYEGTVVRIVDFGAFVEL-LPGK----DGLVHISQLAKERVEKVEDVLKEGDEVK 671

Query: 111 VKVIKIDREKSRITLSIKQLEE 132
           VKVI+ID ++ RI LSIK + E
Sbjct: 672 VKVIEID-KQGRIRLSIKAVLE 692

Length = 692

>gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain

 Score = 61.9 bits (151), Expect = 7e-13
 Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 10/77 (12%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
            V D+  G        GAF+ L        + GL+ +SE+S   ++D  ++L  GDEV+V
Sbjct: 1   EVGDVVEGTVTEITPGGAFVDL-----GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKV 55

Query: 112 KVIKIDREKSRITLSIK 128
           KV+ +D EK RI LS+K
Sbjct: 56  KVLSVDEEKGRIILSLK 72

Length = 72

>gnl|CDD|235614 PRK05807, PRK05807, hypothetical protein; Provisional

 Score = 63.6 bits (155), Expect = 9e-13
 Identities = 31/68 (45%), Positives = 47/68 (69%), Gaps = 7/68 (10%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           ++GAF+ +   +G    TGLVH+SEV+   ++DIR+ L E D+V+VKVI ID +  +I+L
Sbjct: 18  NFGAFVEV---EGK---TGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISL 70

Query: 126 SIKQLEED 133
           SIKQ  + 
Sbjct: 71  SIKQAMKQ 78

Length = 136

>gnl|CDD|236305 PRK08582, PRK08582, hypothetical protein; Provisional

 Score = 61.6 bits (150), Expect = 5e-12
 Identities = 31/69 (44%), Positives = 48/69 (69%), Gaps = 6/69 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           ++GAF+ L  P+G    TGLVH+SEV+ + ++DI D L  GDEV VKV+ ++ +  +I L
Sbjct: 18  NFGAFVEL--PEGK---TGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDD-GKIGL 71

Query: 126 SIKQLEEDP 134
           SIK+ ++ P
Sbjct: 72  SIKKAKDRP 80

Length = 139

>gnl|CDD|240213 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

 Score = 59.3 bits (144), Expect = 8e-12
 Identities = 29/63 (46%), Positives = 41/63 (65%), Gaps = 4/63 (6%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYG FI +   DG  +++GL H SE+S + + D   +   GD+VR KV+KID EK RI+L
Sbjct: 15  DYGVFIDI---DGT-NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISL 70

Query: 126 SIK 128
            +K
Sbjct: 71  GLK 73

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. Length = 77

>gnl|CDD|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional

 Score = 63.2 bits (154), Expect = 2e-11
 Identities = 44/135 (32%), Positives = 67/135 (49%), Gaps = 18/135 (13%)

Query: 23  GSIISVKV--IQANEEMK--KLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAF 70
           G  + VKV  I+  ++ K  ++  S K A    W+    R+   D   G+      +GAF
Sbjct: 250 GDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAF 309

Query: 71  IHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129
           + +     L  + GLVHVSE+SW   +    D++  GD V VK+  ID  K RI+LS++ 
Sbjct: 310 VEI-----LPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRD 364

Query: 130 LEEDPLLETLEKVIP 144
            E DP  +  E+  P
Sbjct: 365 AEGDPWADVAERFAP 379

Length = 491

>gnl|CDD|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain

 Score = 57.8 bits (140), Expect = 2e-11
 Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 5/61 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
            +G F+ L        + GLVH+SE+S   ++D  ++   GDEV VKV+++D EK RI+L
Sbjct: 10  KFGVFVEL-----EDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64

Query: 126 S 126
           S
Sbjct: 65  S 65

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. Length = 65

>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 62.9 bits (154), Expect = 3e-11
 Identities = 30/79 (37%), Positives = 49/79 (62%), Gaps = 15/79 (18%)

Query: 54  SRVNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDLIQDIRDILNEG 106
           +   V  I+ G+     D+GAF+ +  P  DGL      VH+SE++ + ++ + D+L EG
Sbjct: 614 AEPEVGKIYEGKVVRIMDFGAFVEI-LPGKDGL------VHISEIANERVEKVEDVLKEG 666

Query: 107 DEVRVKVIKIDREKSRITL 125
           DEV+VKV++ID+ + RI L
Sbjct: 667 DEVKVKVLEIDK-QGRIKL 684

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) [Transcription, Degradation of RNA]. Length = 684

>gnl|CDD|239918 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

 Score = 56.0 bits (136), Expect = 1e-10
 Identities = 29/73 (39%), Positives = 47/73 (64%), Gaps = 11/73 (15%)

Query: 60  DIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVI 114
            I+ G+     D+GAF+ +  P       GLVH+SE+S + ++ + D+L  GDEV+VKVI
Sbjct: 2   KIYEGKVVKIKDFGAFVEI-LPGK----DGLVHISELSDERVEKVEDVLKVGDEVKVKVI 56

Query: 115 KIDREKSRITLSI 127
           ++D ++ RI+LS 
Sbjct: 57  EVD-DRGRISLSR 68

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. Length = 68

>gnl|CDD|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha; Validated

 Score = 59.1 bits (144), Expect = 2e-10
 Identities = 28/78 (35%), Positives = 47/78 (60%), Gaps = 8/78 (10%)

Query: 57  NVEDIFVGRDYGAFIHL-RFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
            V+++    D+GAF+ L  +P       G +H+SEV+   +++IRD + EG +V  KVI+
Sbjct: 15  TVKEVK---DFGAFVTLDEYPG----KEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIR 67

Query: 116 IDREKSRITLSIKQLEED 133
           +D  K  I LS+K++ E 
Sbjct: 68  VDPRKGHIDLSLKRVNEH 85

Length = 262

>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

 Score = 58.1 bits (141), Expect = 5e-10
 Identities = 26/86 (30%), Positives = 50/86 (58%), Gaps = 6/86 (6%)

Query: 56  VNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 115
             V+ +    DYGA++ L    G     G +H+SEV+   +++IRD + EG +V  KV++
Sbjct: 17  GTVKQVA---DYGAYVELDEYPGK---EGFIHISEVASGWVKNIRDYVKEGQKVVAKVLR 70

Query: 116 IDREKSRITLSIKQLEEDPLLETLEK 141
           +D ++  I LS+K++ E    + +++
Sbjct: 71  VDPKRGHIDLSLKRVTEHQRRKKIQE 96

Length = 269

>gnl|CDD|236126 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 58.1 bits (141), Expect = 9e-10
 Identities = 32/82 (39%), Positives = 47/82 (57%), Gaps = 15/82 (18%)

Query: 53  SSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVK 112
           SS VN         +GAF+ L   DGL      VHVSE+SW  I    +++  G EV V+
Sbjct: 217 SSIVN---------FGAFVDLGGVDGL------VHVSELSWKHIDHPSEVVEVGQEVTVE 261

Query: 113 VIKIDREKSRITLSIKQLEEDP 134
           V+ +D ++ R++LS+K  +EDP
Sbjct: 262 VLDVDMDRERVSLSLKATQEDP 283

Length = 486

>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 57.8 bits (140), Expect = 1e-09
 Identities = 34/114 (29%), Positives = 60/114 (52%), Gaps = 13/114 (11%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVG-----RDYGAFIHLR 74
           G  I   V+  ++E K++    K      W K++++  V  +  G     +D+GAF+   
Sbjct: 408 GDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFV--E 465

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
            P G+    GL+  SE+S +  +D  D +  GDEV  KV+ ID++  +++LS+K
Sbjct: 466 LPGGV---EGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516

This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by PFAM model pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. 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 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 516

>gnl|CDD|240190 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

 Score = 53.0 bits (128), Expect = 1e-09
 Identities = 24/61 (39%), Positives = 39/61 (63%), Gaps = 5/61 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           D+GAF+ +    G+    GL+H+S+++   +    D+++ GD V VKVI ID E+ RI+L
Sbjct: 13  DFGAFVDI----GV-KQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISL 67

Query: 126 S 126
           S
Sbjct: 68  S 68

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. Length = 68

>gnl|CDD|239899 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

 Score = 52.6 bits (127), Expect = 2e-09
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 8/75 (10%)

Query: 56  VNVEDIFVGRDYGAFIHL-RFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVI 114
           V V+ I    D GA++ L  + +    + G++ +SE+S   I+ IR ++  G +  VKVI
Sbjct: 9   VTVKSIA---DMGAYVSLLEYGN----IEGMILLSELSRRRIRSIRKLVKVGRKEVVKVI 61

Query: 115 KIDREKSRITLSIKQ 129
           ++D+EK  I LS K+
Sbjct: 62  RVDKEKGYIDLSKKR 76

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 complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein. Length = 76

>gnl|CDD|236126 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 56.6 bits (137), Expect = 3e-09
 Identities = 29/67 (43%), Positives = 43/67 (64%), Gaps = 5/67 (7%)

Query: 67  YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126
           +GAF+  R  +G+    GLVH+SE++   ++    ++  GDEV VKVI ID E+ RI+LS
Sbjct: 307 FGAFV--RVEEGI---EGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLS 361

Query: 127 IKQLEED 133
           +KQ  E 
Sbjct: 362 LKQANEG 368

Length = 486

>gnl|CDD|180908 PRK07252, PRK07252, hypothetical protein; Provisional

 Score = 53.2 bits (128), Expect = 4e-09
 Identities = 25/67 (37%), Positives = 39/67 (58%), Gaps = 5/67 (7%)

Query: 67  YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126
           YGAF+ L         TGL+H+SE+    I +I  +L  G+EV V+V+  D    + +LS
Sbjct: 17  YGAFVALENGT-----TGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLS 71

Query: 127 IKQLEED 133
           ++ LEE+
Sbjct: 72  LRTLEEE 78

Length = 120

>gnl|CDD|240196 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain

 Score = 51.5 bits (124), Expect = 4e-09
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 81  HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 131
            + G +  +E+S D ++D  +    GDEV  K+  +DR+  +I+LSIK  E
Sbjct: 23  GVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE 73

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. Length = 73

>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein S1; Provisional

 Score = 56.3 bits (135), Expect = 5e-09
 Identities = 62/238 (26%), Positives = 100/238 (42%), Gaps = 40/238 (16%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           G  I +KVI+ ++  K++  S K      W ++ ++  V D+  GR     D+GAFI L 
Sbjct: 540 GQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIEL- 598

Query: 75  FPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 133
             +G+    GL H+SE SW        D++  GDEV   ++  D +  R++L +KQ+  +
Sbjct: 599 -AEGI---EGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTAN 654

Query: 134 PLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGF 193
           P  E +E   P           + +  +  I  +   GA  E    E+GID       GF
Sbjct: 655 P-WEEIEARYP-----------VGARFTRRIVKVTNAGAFIE---MEEGID-------GF 692

Query: 194 EKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHSLIRKASKRHCNEYWNVF 251
               +  D   W+    P+  +  +       V E       IR   K+  +  W VF
Sbjct: 693 ----LHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVF 746

Length = 863

>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein S1; Provisional

 Score = 55.1 bits (132), Expect = 1e-08
 Identities = 31/92 (33%), Positives = 53/92 (57%), Gaps = 11/92 (11%)

Query: 51  KYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNE 105
           ++ + V++ED   G       +GAFI L   DGL      +HV+++SW  +   R+ + +
Sbjct: 486 EFFNSVHIEDSVSGVVKSFTSFGAFIDLGGFDGL------LHVNDMSWGHVARPREFVKK 539

Query: 106 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLE 137
           G  + +KVI++D+ + RI LS+K  + DP LE
Sbjct: 540 GQTIELKVIRLDQAEKRINLSLKHFQPDPWLE 571

Length = 863

>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 52.7 bits (127), Expect = 6e-08
 Identities = 41/138 (29%), Positives = 64/138 (46%), Gaps = 20/138 (14%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVG-----RDYGAFIHLR 74
           G  +  KV+  ++E +++    K      W ++S +     +  G     +D GAF+   
Sbjct: 411 GDEVEAKVLAVDKEKERISLGIKQLEESPWEEFSEKYKKGSVVKGKVKSVKDKGAFV--E 468

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
              G+    GL+ +SE+S       RD+L  GDEV   V+ ID++  +I LSIK LE   
Sbjct: 469 LGGGV---EGLIRLSELS-------RDVLKVGDEVEAVVVSIDKKNRKILLSIKALERKE 518

Query: 135 LLETLEKVIPQDGSVISD 152
             E LE     D S + D
Sbjct: 519 EKEALESYNKDDDSSLGD 536

Length = 541

>gnl|CDD|240189 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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 5/64 (7%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           D+G F+ L    G     GLVH+S++S++  + +  D++  G +V+VKVI I   K  I+
Sbjct: 13  DFGCFVQLEGLKG--RKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGK--IS 68

Query: 125 LSIK 128
           LS+K
Sbjct: 69  LSMK 72

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. Length = 79

>gnl|CDD|239908 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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 5/62 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
            YG F+   F      LTGL   S +S + + D      +G  V  KV  +D EK R  L
Sbjct: 27  PYGVFV--EFL---GGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLL 81

Query: 126 SI 127
           S+
Sbjct: 82  SL 83

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. Length = 83

>gnl|CDD|240195 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain

 Score = 45.9 bits (109), Expect = 4e-07
 Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 6/61 (9%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           D+G F+ L    G+    GLVH+S++SW   ++   +I  +G EV   V+ ID E+ RI+
Sbjct: 13  DFGIFVGL--DGGI---DGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERIS 67

Query: 125 L 125
           L
Sbjct: 68  L 68

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. Length = 69

>gnl|CDD|225094 COG2183, Tex, Transcriptional accessory protein [Transcription]

 Score = 48.0 bits (115), Expect = 3e-06
 Identities = 27/67 (40%), Positives = 45/67 (67%), Gaps = 5/67 (7%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           D+GAF+ +    G+ H  GLVH+S++S   ++D  +++  GD V+VKVI++D  + RI L
Sbjct: 671 DFGAFVDI----GV-HQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIAL 725

Query: 126 SIKQLEE 132
           S++  EE
Sbjct: 726 SMRLDEE 732

Length = 780

>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 46.9 bits (112), Expect = 5e-06
 Identities = 17/59 (28%), Positives = 36/59 (61%)

Query: 83  TGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK 141
            G++ + E++ D I  +++ +  GDE+ VKV+K++ E   + LS K+ + +   + LE+
Sbjct: 327 EGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEE 385

Length = 647

>gnl|CDD|240194 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain

 Score = 42.6 bits (100), Expect = 7e-06
 Identities = 27/62 (43%), Positives = 39/62 (62%), Gaps = 8/62 (12%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR--DILNEGDEVRVKVIKIDREKSRI 123
           DYG F+ L   +G+    GLVHVSE+ W   ++I    +++ GDEV V V+ ID E+ RI
Sbjct: 16  DYGCFVELE--EGV---EGLVHVSEMDWT-NKNIHPSKVVSLGDEVEVMVLDIDEERRRI 69

Query: 124 TL 125
           +L
Sbjct: 70  SL 71

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. Length = 72

>gnl|CDD|240191 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-binding domain

 Score = 42.1 bits (99), Expect = 1e-05
 Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 5/63 (7%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           +YGAF+ +    G     GLVH S +S   + D  ++++ G++V VKVI  +  K ++ L
Sbjct: 16  EYGAFVKI---PG-CRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGRE-MKDKMKL 70

Query: 126 SIK 128
           S+ 
Sbjct: 71  SLS 73

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. Length = 73

>gnl|CDD|240203 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

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 65  RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           +  G  +   F + +    G +  SE+S   I+D  +    G  V+VKV+  D E+ R+ 
Sbjct: 12  KPNGCIV--SFYNNV---KGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLL 66

Query: 125 LSIK 128
           LS K
Sbjct: 67  LSCK 70

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. Length = 70

>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 44.5 bits (106), Expect = 3e-05
 Identities = 21/58 (36%), Positives = 39/58 (67%)

Query: 84  GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK 141
           G++ +SE+S D I+DI D++  GDE+ V V+K++  +  + LS ++LE +   + LE+
Sbjct: 44  GVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEE 101

Length = 390

>gnl|CDD|240192 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain

 Score = 39.8 bits (94), Expect = 6e-05
 Identities = 16/45 (35%), Positives = 29/45 (64%)

Query: 84  GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 128
           G++ +SE S D I++  D +  GDEV V V++++ E+  + LS +
Sbjct: 26  GIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70

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. Length = 70

>gnl|CDD|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional

 Score = 40.5 bits (95), Expect = 6e-04
 Identities = 28/112 (25%), Positives = 51/112 (45%), Gaps = 13/112 (11%)

Query: 23  GSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-DYGAFIHLR 74
           G  ++VK+   +   +++  S +DA       V  +++    V      R  +G F++L 
Sbjct: 341 GDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLA 400

Query: 75  FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126
            P     +TGL+  S +S        + L  GD V + V +ID  K +I+L+
Sbjct: 401 -PG----VTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447

Length = 491

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	259
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.98
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.97
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.97
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.97
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.97
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.97
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.96
PRK07400	318	30S ribosomal protein S1; Reviewed	99.96
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.95
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.95
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.93
PRK07400	318	30S ribosomal protein S1; Reviewed	99.85
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.75
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.67
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.58
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.55
PRK08582	139	hypothetical protein; Provisional	99.52
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.47
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.47
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.47
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.47
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.46
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.45
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.43
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.43
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.42
PHA02945	88	interferon resistance protein; Provisional	99.42
PRK07252	120	hypothetical protein; Provisional	99.41
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.4
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.4
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.39
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.36
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.36
PRK08059	123	general stress protein 13; Validated	99.36
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.36
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.35
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.34
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.34
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.34
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	99.34
PRK05807	136	hypothetical protein; Provisional	99.33
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.33
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.3
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.29
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.28
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.24
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.21
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.21
PRK03987	262	translation initiation factor IF-2 subunit alpha;	99.19
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.19
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.18
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.16
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.16
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.15
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.14
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.12
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.12
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.1
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	99.06
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.03
COG2183	780	Tex Transcriptional accessory protein [Transcripti	99.02
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.97
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.95
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.91
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.89
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.87
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.86
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	98.85
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.83
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	98.8
PRK08582	139	hypothetical protein; Provisional	98.77
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	98.74
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.73
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.72
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	98.71
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.66
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	98.64
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	98.62
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.59
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.59
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.56
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.56
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.55
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	98.54
PRK07252	120	hypothetical protein; Provisional	98.51
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	98.5
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.45
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	98.43
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	98.43
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.42
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.41
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	98.4
PHA02945	88	interferon resistance protein; Provisional	98.4
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	98.38
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	98.36
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	98.36
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.34
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	98.33
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.32
PRK11642	813	exoribonuclease R; Provisional	98.31
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.31
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	98.29
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.28
PRK05807	136	hypothetical protein; Provisional	98.27
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	98.24
PRK08059	123	general stress protein 13; Validated	98.23
TIGR01953	341	NusA transcription termination factor NusA. This m	98.23
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	98.23
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.22
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.19
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.17
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.06
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	98.02
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.01
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	98.0
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	97.97
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	97.92
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	97.91
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.88
KOG2916	304	consensus Translation initiation factor 2, alpha s	97.87
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	97.78
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	97.73
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	97.72
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	97.7
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	97.62
COG2183	780	Tex Transcriptional accessory protein [Transcripti	97.62
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	97.55
PRK05054	644	exoribonuclease II; Provisional	97.53
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.53
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	97.46
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.44
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	97.41
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.4
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	97.33
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.32
PRK09202	470	nusA transcription elongation factor NusA; Validat	97.31
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.25
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.24
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	97.23
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.16
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	97.01
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	96.98
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	96.97
COG0557	706	VacB Exoribonuclease R [Transcription]	96.94
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	96.78
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	96.69
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	96.68
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	96.66
PRK11642	813	exoribonuclease R; Provisional	96.56
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	96.53
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	96.45
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.19
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	96.17
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	96.11
KOG2916	304	consensus Translation initiation factor 2, alpha s	96.05
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	96.04
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	96.02
TIGR01953	341	NusA transcription termination factor NusA. This m	95.91
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	95.65
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	95.25
PRK12327	362	nusA transcription elongation factor NusA; Provisi	94.86
PRK10811	1068	rne ribonuclease E; Reviewed	94.78
PRK11712	489	ribonuclease G; Provisional	94.56
PRK12329	449	nusA transcription elongation factor NusA; Provisi	93.87
PRK05054	644	exoribonuclease II; Provisional	90.89
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	89.8
PRK12328	374	nusA transcription elongation factor NusA; Provisi	87.46
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	87.37
COG0557	706	VacB Exoribonuclease R [Transcription]	85.7
COG4044	247	Uncharacterized protein conserved in archaea [Func	82.33
PF09876	103	DUF2103: Predicted metal-binding protein (DUF2103)	82.06
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	81.48
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	81.42
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	81.2
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	80.38

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

Probab=100.00  E-value=3.3e-43  Score=335.03  Aligned_cols=206  Identities=26%  Similarity=0.524  Sum_probs=187.1

Q ss_pred             hhcccCCCCEEEEEEEEEeCCCCEEEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEE
Q 024995           16 EIAKGLTGSIISVKVIQANEEMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLT   83 (259)
Q Consensus        16 ~~~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~~-------~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~   83 (259)
                      +++..++|+++.++|+++|.+++++++|+|...       ++.+++.+++|+++.|+     +|||||+|+      |++
T Consensus       143 ~d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdig------Gvd  216 (541)
T COG0539         143 RDLDPLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIG------GVD  216 (541)
T ss_pred             ccccccCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEec------Cee
Confidence            445678999999999999999999999999753       45678999999999999     999999998      899


Q ss_pred             EEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceee
Q 024995           84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNT  163 (259)
Q Consensus        84 glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~  163 (259)
                      ||||++||||.++.+|++.|++||+|+|+|+++|.+++||+||+|++.++||.... +.++.        |+.+.|+|++
T Consensus       217 GLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~-~~~~~--------g~~v~G~Vt~  287 (541)
T COG0539         217 GLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIE-KKYPV--------GDKVEGKVTN  287 (541)
T ss_pred             eEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHh-hhcCC--------CCEEEEEEEE
Confidence            99999999999999999999999999999999999999999999999999997654 44675        4559999999


Q ss_pred             eccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhh
Q 024995          164 IEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRK  238 (259)
Q Consensus       164 i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~l  238 (259)
                      ++|||    +|+++  .+||+||+ +|+++            |..... |..    +++.||.|    ++||++++||||
T Consensus       288 i~~~G----afVei--~~GvEGlvhvSEis------------w~~~~~-P~e----vv~~Gq~V~V~Vl~id~e~rRIsL  344 (541)
T COG0539         288 LTDYG----AFVEI--EEGVEGLVHVSEIS------------WTKKNV-PSE----VVKVGQEVEVKVLDIDPERRRISL  344 (541)
T ss_pred             eecCc----EEEEe--cCCccceeechhhc------------ccccCC-HHH----hcccCCEEEEEEEeeCchhceEEe
Confidence            99999    99999  99999999 89998            665554 554    77999999    899999999999


Q ss_pred             hhchhhhhhhHHhhhhcccCC
Q 024995          239 ASKRHCNEYWNVFHETAIVNN  259 (259)
Q Consensus       239 s~k~~~~~p~~~~~~~~~~~~  259 (259)
                      ||||+.++||+.++++|++|.
T Consensus       345 ~iKq~~~~pw~~~~~~~~~g~  365 (541)
T COG0539         345 GLKQLKENPWEEFADKHPVGD  365 (541)
T ss_pred             eehhhhcChhhhhhhhcCCCC
Confidence            999999999999999999984

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

Probab=100.00  E-value=4.8e-41  Score=320.25  Aligned_cols=214  Identities=31%  Similarity=0.505  Sum_probs=194.5

Q ss_pred             CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEE
Q 024995            1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIH   72 (259)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~---~~~~~~~~l~~G~iv~G~-----~~G~fV~   72 (259)
                      |||.|+ .||+..+.      +||+|.|+|+++|.+++|++||+|+.   +|+.+...+.+|+.+.|+     +|||||+
T Consensus       224 iS~~rv-~~P~~vvk------vGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVe  296 (541)
T COG0539         224 ISWKRV-DHPSEVVK------VGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVE  296 (541)
T ss_pred             cccccc-CCHHHhcc------cCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEE
Confidence            688886 89998877      99999999999999999999999986   699999999999999999     9999999


Q ss_pred             EccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccC
Q 024995           73 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISD  152 (259)
Q Consensus        73 l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~  152 (259)
                      +.     +|++||+|+|||||.+...|++++++||+|.|+|+++|++++||+||+|++..|||..+.+. ++.|      
T Consensus       297 i~-----~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~-~~~g------  364 (541)
T COG0539         297 IE-----EGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADK-HPVG------  364 (541)
T ss_pred             ec-----CCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhh-cCCC------
Confidence            99     69999999999999998889999999999999999999999999999999999999877665 6765      


Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                        ..++|.|.++++||    +|++|  ++|++||+| |.++            |.....+.+ +|    +.|+++    +
T Consensus       365 --~~v~g~v~~~t~~g----~fv~l--e~gidG~vh~~d~s------------w~~~~~~~~-~~----k~Gd~v~~~vl  419 (541)
T COG0539         365 --DVVEGKVKSITDFG----AFVEL--EGGIDGLVHLSDLS------------WDRPGEEAE-KY----KKGDEVEAKVL  419 (541)
T ss_pred             --CeEEEEEeeecccc----eEEcc--CCCccceEEHHhcC------------ccccCcHHH-hh----ccCcEEEEEEE
Confidence              44999999999999    99888  889999995 5555            665555444 45    999999    8


Q ss_pred             EEecccchhhhhhchhhhhhhHHhhhhcccC
Q 024995          228 EIQLSHSLIRKASKRHCNEYWNVFHETAIVN  258 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~~~~~p~~~~~~~~~~~  258 (259)
                      .||.++++|||++|||.++||+.+.+.|+.|
T Consensus       420 ~vd~~~~~isLgiKql~~~p~~~~~~~~~~~  450 (541)
T COG0539         420 AVDKEKERISLGIKQLEESPWEEFSEKYKKG  450 (541)
T ss_pred             EEecccceeeeehhhhccCchhhhHhhccCC
Confidence            9999999999999999999999999999987

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=3.3e-36  Score=303.07  Aligned_cols=202  Identities=28%  Similarity=0.500  Sum_probs=180.9

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc
Q 024995           22 TGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW   93 (259)
Q Consensus        22 vG~~v~~~Vl~id~~~~~v~lS~k~~---~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~   93 (259)
                      +||+++|+|+.+|++++++.||+|+.   +|+.+.+.+++|+++.|+     +||+||+++     .|++||+|+||++|
T Consensus       539 vGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~-----~gveGLvhiSEls~  613 (863)
T PRK12269        539 KGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELA-----EGIEGLAHISEFSW  613 (863)
T ss_pred             CCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEEec-----CCceeeeEHHHhcC
Confidence            89999999999999999999999975   588888899999999999     999999997     48999999999999


Q ss_pred             -ccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccc
Q 024995           94 -DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA  172 (259)
Q Consensus        94 -~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~  172 (259)
                       .++.+|.+.|++||+|+|+|+++|++++|++||+|++.+|||....++ +++        |++++|+|+++++||    
T Consensus       614 ~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~-~~v--------G~~v~G~V~~i~~~G----  680 (863)
T PRK12269        614 VKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEAR-YPV--------GARFTRRIVKVTNAG----  680 (863)
T ss_pred             ccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHh-CCC--------CCEEEEEEEEEecce----
Confidence             578899999999999999999999999999999999999999876554 554        566999999999999    


Q ss_pred             eeeeecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhhhh
Q 024995          173 IFEELLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCNEY  247 (259)
Q Consensus       173 ~fv~l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~~p  247 (259)
                      +||+|  .+||+||+| |+++            |.....+++.    .+++||.|    ++||+++++|+||+|++.++|
T Consensus       681 ~fV~l--~~gV~GlIh~sels------------~~~~~~~~~~----~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dp  742 (863)
T PRK12269        681 AFIEM--EEGIDGFLHVDDLS------------WVKRTRPADH----ELEVGKEIECMVIECDPQARRIRLGVKQLSDNP  742 (863)
T ss_pred             EEEEe--CCCcEEEEEhHHhh------------ccccccchhh----ccCCCCEEEEEEEEEeccCCEEEEEecccccCh
Confidence            99999  899999994 5555            6554444444    45999999    799999999999999999999


Q ss_pred             hHHhhhhcccCC
Q 024995          248 WNVFHETAIVNN  259 (259)
Q Consensus       248 ~~~~~~~~~~~~  259 (259)
                      |+.+.++|++|.
T Consensus       743 w~~~~~~~~vG~  754 (863)
T PRK12269        743 WQVFANAYGVGS  754 (863)
T ss_pred             HHHHHhhCCCCC
Confidence            999999999884

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=5.9e-34  Score=273.96  Aligned_cols=204  Identities=25%  Similarity=0.439  Sum_probs=178.2

Q ss_pred             cCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEE
Q 024995           20 GLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH   87 (259)
Q Consensus        20 ~~vG~~v~~~Vl~id~~~~~v~lS~k~~-------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~   87 (259)
                      .++|++++|+|+.+|++++++.+|+|..       .|+.++..+++|+++.|+     +||+||+++     .|++||||
T Consensus       157 ~~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~-----~gv~g~v~  231 (491)
T PRK13806        157 SYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELA-----PGVEGMVH  231 (491)
T ss_pred             HcCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcC-----CCcEEEEE
Confidence            4699999999999999999999999875       356667789999999999     899999997     38999999


Q ss_pred             ceecCcccccChhhhcCCCCeEEEEEEEEeCCC----CeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceee
Q 024995           88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK----SRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNT  163 (259)
Q Consensus        88 isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~----~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~  163 (259)
                      +++++|.++.++.+.|++||.|+|+|+++|.++    +||.||+|++.++||....++ ++.        |+++.|+|++
T Consensus       232 ~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~-~~~--------G~~v~G~V~~  302 (491)
T PRK13806        232 ISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDR-LKA--------GDKVTGKVVR  302 (491)
T ss_pred             HHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhcc-CCC--------CCEEEEEEEE
Confidence            999999999999999999999999999999866    479999999999999765544 444        6669999999


Q ss_pred             eccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhh
Q 024995          164 IEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRK  238 (259)
Q Consensus       164 i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~l  238 (259)
                      +++||    +|++|  .+|++||+ .|+++            |..+...+..    .+++||.|    +++|.++++|+|
T Consensus       303 v~~~G----~fV~l--~~gv~Glvh~sels------------~~~~~~~~~~----~~~~Gd~v~vkVl~iD~e~~ri~L  360 (491)
T PRK13806        303 LAPFG----AFVEI--LPGIEGLVHVSEMS------------WTRRVNKPED----VVAPGDAVAVKIKDIDPAKRRISL  360 (491)
T ss_pred             EeCce----EEEEe--CCCcEEEEEHHHcC------------cccccCCHHH----cCCCCCEEEEEEEEEEccCCEEEE
Confidence            99999    99988  78999999 57766            4333333333    56999999    789999999999


Q ss_pred             hhchhhhhhhHHhhhhcccCC
Q 024995          239 ASKRHCNEYWNVFHETAIVNN  259 (259)
Q Consensus       239 s~k~~~~~p~~~~~~~~~~~~  259 (259)
                      |+|++..+||+.+.++|++|.
T Consensus       361 s~K~~~~~p~~~~~~~~~vG~  381 (491)
T PRK13806        361 SLRDAEGDPWADVAERFAPGT  381 (491)
T ss_pred             EEeecccChhHHhhhhCCCCC
Confidence            999999999999999999984

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=2.2e-33  Score=270.06  Aligned_cols=195  Identities=27%  Similarity=0.479  Sum_probs=169.9

Q ss_pred             CCCEEEEEEEEEeCCC----CEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEce
Q 024995           22 TGSIISVKVIQANEEM----KKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVS   89 (259)
Q Consensus        22 vG~~v~~~Vl~id~~~----~~v~lS~k~~---~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~is   89 (259)
                      +||.|+|+|+.+|.++    +++.||+|++   +|+.+...+++|+++.|+     +||+||+++     .|++||+|+|
T Consensus       249 vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~-----~gv~Glvh~s  323 (491)
T PRK13806        249 VGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEIL-----PGIEGLVHVS  323 (491)
T ss_pred             CCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCceEEEEeC-----CCcEEEEEHH
Confidence            9999999999999876    4799999986   588888899999999999     999999997     4899999999


Q ss_pred             ecCc-ccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCC
Q 024995           90 EVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLP  168 (259)
Q Consensus        90 els~-~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G  168 (259)
                      +|+| .++.++.+.|++||.|+|+|+++|+++++|.||+|++.++||....++ +++        |++++|+|+++++||
T Consensus       324 els~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~-~~v--------G~~v~G~V~~i~~~G  394 (491)
T PRK13806        324 EMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAER-FAP--------GTTVTGTVEKRAQFG  394 (491)
T ss_pred             HcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhh-CCC--------CCEEEEEEEEEecCc
Confidence            9999 477899999999999999999999999999999999999999876554 454        666999999999999


Q ss_pred             CccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchh
Q 024995          169 GLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRH  243 (259)
Q Consensus       169 ~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~  243 (259)
                          +|+++  ++|++||| +|++++++            . ..+..    .+++||.|    +++|.+++||+||+|++
T Consensus       395 ----~FV~l--~~gv~Gli~~se~s~~~------------~-~~~~~----~~~~Gd~v~~~V~~id~e~~ri~Ls~~~~  451 (491)
T PRK13806        395 ----LFVNL--APGVTGLLPASVISRAG------------K-PATYE----KLKPGDSVTLVVEEIDTAKRKISLAPAGA  451 (491)
T ss_pred             ----eEEEc--CCCcEEEEEHHHcCccc------------c-cchhh----cCCCCCEEEEEEEEEeCCCCEEEEEeehh
Confidence                99988  78999999 67777332            1 22223    45999999    79999999999999987


Q ss_pred             -----hhhhhHHhhh
Q 024995          244 -----CNEYWNVFHE  253 (259)
Q Consensus       244 -----~~~p~~~~~~  253 (259)
                           ..+||+.+..
T Consensus       452 ~~~~~~~~~~~~~~~  466 (491)
T PRK13806        452 AGSGADDDDWKQFAP  466 (491)
T ss_pred             hhhhhhhhHHHhhcc
Confidence                 4589999854

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=2.7e-33  Score=282.04  Aligned_cols=206  Identities=23%  Similarity=0.460  Sum_probs=179.1

Q ss_pred             hcccCCCCEEEEEEEEEeC-----CCCEEEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCC
Q 024995           17 IAKGLTGSIISVKVIQANE-----EMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGL   79 (259)
Q Consensus        17 ~~~~~vG~~v~~~Vl~id~-----~~~~v~lS~k~~~-------~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~   79 (259)
                      +++.++|++++|+|+.+|.     +++++++|+|...       .+++++.+++|+++.|+     +||+||+++     
T Consensus       440 ~~~~~vG~~ie~~V~~~~~~~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~-----  514 (863)
T PRK12269        440 APESLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLG-----  514 (863)
T ss_pred             chHHhCCCeEEEEEEEEecccccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEEC-----
Confidence            3456799999999999975     3469999998742       34567889999999998     899999996     


Q ss_pred             ccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCcccc
Q 024995           80 YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSS  159 (259)
Q Consensus        80 ~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G  159 (259)
                       |++||||+|+++|.++.+|.+.|++||+++|+|+++|++++++.||+|++.++||....++ +++        |++++|
T Consensus       515 -Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~-~~v--------G~iV~G  584 (863)
T PRK12269        515 -GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENK-FGV--------NDVVKG  584 (863)
T ss_pred             -CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhcc-CCC--------CCEEEE
Confidence             8999999999999999999999999999999999999999999999999999999765544 454        666999


Q ss_pred             ceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccc
Q 024995          160 NSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHS  234 (259)
Q Consensus       160 ~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~  234 (259)
                      +|+++++||    +|++|  .+|++||+ +|+++            |.....++..    .+++||.|    +.+|.+++
T Consensus       585 ~V~~I~~fG----~fVeL--~~gveGLvhiSEls------------~~~~~~~p~~----~~kvGd~V~vkVl~iD~e~~  642 (863)
T PRK12269        585 RVTKIADFG----AFIEL--AEGIEGLAHISEFS------------WVKKTSKPSD----MVKIGDEVECMILGYDIQAG  642 (863)
T ss_pred             EEEEEeCCe----EEEEe--cCCceeeeEHHHhc------------CccccCCHHH----cCCCCCEEEEEEEEEecccC
Confidence            999999999    99988  78999999 57776            5433443443    56999999    79999999


Q ss_pred             hhhhhhchhhhhhhHHhhhhcccCC
Q 024995          235 LIRKASKRHCNEYWNVFHETAIVNN  259 (259)
Q Consensus       235 ~i~ls~k~~~~~p~~~~~~~~~~~~  259 (259)
                      +|+||+|++.++||+.+.++|++|.
T Consensus       643 rIsLS~K~l~~~Pw~~~~~~~~vG~  667 (863)
T PRK12269        643 RVSLGLKQVTANPWEEIEARYPVGA  667 (863)
T ss_pred             ceEEEehhcccCchHHHHHhCCCCC
Confidence            9999999999999999999999984

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.98  E-value=6.6e-32  Score=258.04  Aligned_cols=192  Identities=24%  Similarity=0.452  Sum_probs=166.5

Q ss_pred             cccCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEE
Q 024995           18 AKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL   85 (259)
Q Consensus        18 ~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~-------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~gl   85 (259)
                      ++.++|++|+|+|+++|.+++++.+|+|..       .|+.++..+++|+++.|+     +||+||+|+      |++||
T Consensus       161 ~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlg------gv~Gl  234 (486)
T PRK07899        161 LQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG------GVDGL  234 (486)
T ss_pred             hhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEE
Confidence            345799999999999999999999999852       366778899999999999     999999996      79999


Q ss_pred             EEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeec
Q 024995           86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE  165 (259)
Q Consensus        86 v~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~  165 (259)
                      ||+|+++|.++.+|.+.|++||.|+|+|+++|++++||.||+|++.++||..+... ++.        |+++.|+|+++.
T Consensus       235 v~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~-~~v--------G~vv~G~V~~I~  305 (486)
T PRK07899        235 VHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFART-HAI--------GQIVPGKVTKLV  305 (486)
T ss_pred             EEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHh-cCC--------CCEEEEEEEEEe
Confidence            99999999999999999999999999999999999999999999999999766554 343        566999999999


Q ss_pred             cCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhh
Q 024995          166 PLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKAS  240 (259)
Q Consensus       166 ~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~  240 (259)
                      +||    +|++|  .+|++||+ +|+++.+.             ...+..    .+++||.|    ++||.++++|+||+
T Consensus       306 ~fG----vFVeL--~~gieGLvh~SeLs~~~-------------v~~~~~----~~kvGd~V~VkIi~ID~e~rrI~LSl  362 (486)
T PRK07899        306 PFG----AFVRV--EEGIEGLVHISELAERH-------------VEVPEQ----VVQVGDEVFVKVIDIDLERRRISLSL  362 (486)
T ss_pred             ccE----EEEEe--CCCcEEEEEHHHcCccc-------------ccCccc----eeCCCCEEEEEEEEEECCCCEEEEEE
Confidence            999    99998  78999999 67776331             111222    56999999    68999999999999


Q ss_pred             chhhhhh
Q 024995          241 KRHCNEY  247 (259)
Q Consensus       241 k~~~~~p  247 (259)
                      |++.++.
T Consensus       363 K~~~~~~  369 (486)
T PRK07899        363 KQANEGV  369 (486)
T ss_pred             EEcccCC
Confidence            9987654

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.97  E-value=2.3e-31  Score=260.19  Aligned_cols=203  Identities=30%  Similarity=0.536  Sum_probs=178.1

Q ss_pred             cCCCCEEEEEEEEEeCCCCEEEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEE
Q 024995           20 GLTGSIISVKVIQANEEMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH   87 (259)
Q Consensus        20 ~~vG~~v~~~Vl~id~~~~~v~lS~k~~~-------~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~   87 (259)
                      .++|++++|+|+.+|.+++++.+|+|.+.       |+.++..+++|+++.|+     +||+||+++      |++||+|
T Consensus       156 ~~vG~~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~------g~~glv~  229 (565)
T PRK06299        156 PLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLG------GVDGLLH  229 (565)
T ss_pred             HhCCCEEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC------CEEEEEE
Confidence            56999999999999999999999999753       55677899999999999     999999997      7999999


Q ss_pred             ceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccC
Q 024995           88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL  167 (259)
Q Consensus        88 isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~  167 (259)
                      +++++|.++.++.+.|++||.|+|+|+++|++++++.||+|++.++||....+. ++.        |+++.|+|+++++|
T Consensus       230 ~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~-~~~--------G~~v~g~V~~i~~~  300 (565)
T PRK06299        230 ITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKK-YPV--------GSKVKGKVTNITDY  300 (565)
T ss_pred             HHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhh-CCC--------CCEEEEEEEEEeCC
Confidence            999999999999999999999999999999999999999999999999865444 454        66699999999999


Q ss_pred             CCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhch
Q 024995          168 PGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKR  242 (259)
Q Consensus       168 G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~  242 (259)
                      |    +|++|  .+|+.||+ .|+++            |.....++..    .+++||.|    +++|.++++|+||+|+
T Consensus       301 G----~fV~l--~~~v~Glv~~sel~------------~~~~~~~~~~----~~~~G~~v~v~V~~id~~~~~i~ls~k~  358 (565)
T PRK06299        301 G----AFVEL--EEGIEGLVHVSEMS------------WTKKNKHPSK----VVSVGQEVEVMVLEIDEEKRRISLGLKQ  358 (565)
T ss_pred             e----EEEEe--CCCCEEEEEHHHcC------------ccccccCHHH----hcCCCCEEEEEEEEEcCCCCEEEEehHH
Confidence            9    99988  78999999 57765            3332333332    45899998    7999999999999999


Q ss_pred             hhhhhhHHhhhhcccCC
Q 024995          243 HCNEYWNVFHETAIVNN  259 (259)
Q Consensus       243 ~~~~p~~~~~~~~~~~~  259 (259)
                      +..+||..+.++|++|.
T Consensus       359 ~~~~p~~~~~~~~~~G~  375 (565)
T PRK06299        359 CKENPWEEFAEKYPVGD  375 (565)
T ss_pred             hccchhhhHHHhCCCCC
Confidence            99999999999999874

>TIGR00717 rpsA ribosomal protein S1

Probab=99.97  E-value=9.9e-31  Score=253.08  Aligned_cols=202  Identities=29%  Similarity=0.504  Sum_probs=175.6

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc
Q 024995           22 TGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW   93 (259)
Q Consensus        22 vG~~v~~~Vl~id~~~~~v~lS~k~~---~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~   93 (259)
                      +|+++.|+|+.+|++++++.+|+|..   +|+.+...+++|+++.|+     ++|+||+++     .+++||+|+++++|
T Consensus       233 vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~-----~~v~g~v~~sels~  307 (516)
T TIGR00717       233 VGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIE-----EGIEGLVHVSEMSW  307 (516)
T ss_pred             CCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeC-----CCCEEEEEHHHcCC
Confidence            89999999999999999999999965   588888889999999999     999999997     48999999999998


Q ss_pred             c-cccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccc
Q 024995           94 D-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA  172 (259)
Q Consensus        94 ~-~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~  172 (259)
                      . ...++.+.|++||.|+|+|+++|++++++.||+|++..+||....+. +..        |+.+.|+|+++.+||    
T Consensus       308 ~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~-~~~--------G~~v~g~V~~v~~~G----  374 (516)
T TIGR00717       308 VKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEK-HPV--------GDRVTGKIKKITDFG----  374 (516)
T ss_pred             ccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHh-CCC--------CCEEEEEEEEEecce----
Confidence            6 46678888999999999999999999999999999999999866554 343        667999999999999    


Q ss_pred             eeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhhhh
Q 024995          173 IFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCNEY  247 (259)
Q Consensus       173 ~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~~p  247 (259)
                      +|++|  .+|++||+ .++++            |.....++..    .+++||.|    +++|.++++|.||+|++..+|
T Consensus       375 ~fV~l--~~~v~glv~~s~ls------------~~~~~~~~~~----~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p  436 (516)
T TIGR00717       375 AFVEL--EGGIDGLIHLSDIS------------WDKDGREADH----LYKKGDEIEAVVLAVDKEKKRISLGVKQLTENP  436 (516)
T ss_pred             EEEEC--CCCCEEEEEHHHCc------------CcccCCCHhH----ccCCCCEEEEEEEEEeCcCCEEEEeeccccCCc
Confidence            99888  78999999 67766            3322222223    45999997    899999999999999999999


Q ss_pred             hHHhhhhcccCC
Q 024995          248 WNVFHETAIVNN  259 (259)
Q Consensus       248 ~~~~~~~~~~~~  259 (259)
                      |..+.+.|++|.
T Consensus       437 ~~~~~~~~~~G~  448 (516)
T TIGR00717       437 WEKFAAKYKVGS  448 (516)
T ss_pred             hhhhhhccCcce
Confidence            999999898874

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=99.97  E-value=1.3e-30  Score=244.41  Aligned_cols=197  Identities=24%  Similarity=0.404  Sum_probs=170.8

Q ss_pred             cCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEE
Q 024995           20 GLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH   87 (259)
Q Consensus        20 ~~vG~~v~~~Vl~id~~~~~v~lS~k~~-------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~   87 (259)
                      .++|+++.|+|+++|++++++.+|+|..       .|..++..+++|+++.|+     ++|+||+++      +++||||
T Consensus       147 ~~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~------~v~g~v~  220 (390)
T PRK06676        147 DFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG------GVDGLVH  220 (390)
T ss_pred             HcCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC------CeEEEEE
Confidence            4599999999999999999999999874       245567789999999999     899999996      7999999


Q ss_pred             ceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccC
Q 024995           88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL  167 (259)
Q Consensus        88 isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~  167 (259)
                      +++++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++.++||....+. +.        +|+.+.|+|+++.+|
T Consensus       221 ~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~-~~--------~G~~v~g~V~~i~~~  291 (390)
T PRK06676        221 ISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEK-LP--------EGDVIEGTVKRLTDF  291 (390)
T ss_pred             HHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhh-hc--------CCcEEEEEEEEEeCc
Confidence            999999999999999999999999999999999999999999999999765443 33        366699999999999


Q ss_pred             CCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhch
Q 024995          168 PGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKR  242 (259)
Q Consensus       168 G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~  242 (259)
                      |    +|+++  .+|+.||+ +|+++...             ...++.    .+++||.|    +++|.++++|+||+|+
T Consensus       292 G----~fV~l--~~gi~Glv~~se~~~~~-------------~~~~~~----~~~~Gd~v~v~V~~id~e~~~i~ls~k~  348 (390)
T PRK06676        292 G----AFVEV--LPGVEGLVHISQISHKH-------------IATPSE----VLEEGQEVKVKVLEVNEEEKRISLSIKA  348 (390)
T ss_pred             e----EEEEE--CCCCeEEEEhHHcCccc-------------cCChhh----ccCCCCEEEEEEEEEECCCCEEEEEEEe
Confidence            9    99988  78999999 67765221             122222    56999999    7999999999999999


Q ss_pred             hhhhhhHHhhhh
Q 024995          243 HCNEYWNVFHET  254 (259)
Q Consensus       243 ~~~~p~~~~~~~  254 (259)
                      +..+||+.+.++
T Consensus       349 ~~~~~~~~~~~~  360 (390)
T PRK06676        349 LEEAPAEEEDRR  360 (390)
T ss_pred             cccChhhhhhhh
Confidence            999999998765

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.97  E-value=5.1e-30  Score=250.70  Aligned_cols=202  Identities=29%  Similarity=0.481  Sum_probs=175.4

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc
Q 024995           22 TGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW   93 (259)
Q Consensus        22 vG~~v~~~Vl~id~~~~~v~lS~k~~---~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~   93 (259)
                      +||+|.|+|+.+|++++++.||++..   +|+.+...+++|+++.|+     ++|+||+++     .|++||+|+++++|
T Consensus       247 vG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~-----~~v~Glv~~sel~~  321 (565)
T PRK06299        247 VGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELE-----EGIEGLVHVSEMSW  321 (565)
T ss_pred             CCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeC-----CCCEEEEEHHHcCc
Confidence            89999999999999999999999964   588888889999999999     999999998     58999999999998


Q ss_pred             c-cccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccc
Q 024995           94 D-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA  172 (259)
Q Consensus        94 ~-~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~  172 (259)
                      . +..+|.+.|++||.|+|+|+++|++++++.||+|++..+||....+. ++.        |+++.|+|.++.++|    
T Consensus       322 ~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~-~~~--------G~~v~g~V~~v~~~G----  388 (565)
T PRK06299        322 TKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEK-YPV--------GDVVEGKVKNITDFG----  388 (565)
T ss_pred             cccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHh-CCC--------CCEEEEEEEEEecce----
Confidence            6 46788888999999999999999999999999999999999866554 443        666999999999999    


Q ss_pred             eeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhhhh
Q 024995          173 IFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCNEY  247 (259)
Q Consensus       173 ~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~~p  247 (259)
                      +|++|  .+|++|++ .|++++.            .....+..    .+++||.|    +++|.++++|.||+|++..+|
T Consensus       389 ~fV~l--~~~v~g~i~~s~l~~~------------~~~~~~~~----~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p  450 (565)
T PRK06299        389 AFVGL--EGGIDGLVHLSDISWD------------KKGEEAVE----LYKKGDEVEAVVLKVDVEKERISLGIKQLEEDP  450 (565)
T ss_pred             EEEEC--CCCCEEEEEHHHcCcc------------ccccChHh----hCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCc
Confidence            99988  77999999 6776622            11122222    55999999    789999999999999999999


Q ss_pred             hHHhhhhcccCC
Q 024995          248 WNVFHETAIVNN  259 (259)
Q Consensus       248 ~~~~~~~~~~~~  259 (259)
                      |..+.+.+++|.
T Consensus       451 ~~~~~~~~~~G~  462 (565)
T PRK06299        451 FEEFAKKHKKGS  462 (565)
T ss_pred             hhHHHhhcCCCC
Confidence            999999888874

>TIGR00717 rpsA ribosomal protein S1

Probab=99.97  E-value=1.6e-29  Score=244.72  Aligned_cols=205  Identities=27%  Similarity=0.525  Sum_probs=176.4

Q ss_pred             cccCCCCEEEEEEEEEeCCCCEEEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEE
Q 024995           18 AKGLTGSIISVKVIQANEEMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL   85 (259)
Q Consensus        18 ~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~~-------~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~gl   85 (259)
                      ...++|++++|+|+.+|..++++.+|+|...       ++..+..+++|++++|+     ++|+||+++      |++||
T Consensus       140 ~~~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~------g~~g~  213 (516)
T TIGR00717       140 LDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLG------GVDGL  213 (516)
T ss_pred             hhhhCCCEEEEEEEEEECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEE
Confidence            3457999999999999999999999998752       44567789999999999     899999996      79999


Q ss_pred             EEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeec
Q 024995           86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE  165 (259)
Q Consensus        86 v~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~  165 (259)
                      +|.++++|.+..++.+.|++||.+.|+|+++|++++++.||+|.+.++||....+. +.        +|++++|+|+++.
T Consensus       214 lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~-~~--------~G~i~~g~V~~v~  284 (516)
T TIGR00717       214 LHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKK-FP--------VGDKITGRVTNLT  284 (516)
T ss_pred             EEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhh-cc--------CCCEEEEEEEEee
Confidence            99999999999999999999999999999999999999999999999999865443 34        3677999999999


Q ss_pred             cCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhh
Q 024995          166 PLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKAS  240 (259)
Q Consensus       166 ~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~  240 (259)
                      ++|    +|++|  .+|+.||+ .|+++            |.....++.    ..+++||.|    +++|.++++|.||+
T Consensus       285 ~~G----~fV~l--~~~v~g~v~~sels------------~~~~~~~~~----~~~~vG~~v~v~V~~id~~~~~i~lS~  342 (516)
T TIGR00717       285 DYG----VFVEI--EEGIEGLVHVSEMS------------WVKKNSHPS----KVVKKGDEVEVMILDIDPERRRLSLGL  342 (516)
T ss_pred             CCc----EEEEe--CCCCEEEEEHHHcC------------CccccCCHH----HhccCCCEEEEEEEEEcCCCCEEEEEe
Confidence            999    99988  78999999 57765            322122222    246899999    68899999999999


Q ss_pred             chhhhhhhHHhhhhcccCC
Q 024995          241 KRHCNEYWNVFHETAIVNN  259 (259)
Q Consensus       241 k~~~~~p~~~~~~~~~~~~  259 (259)
                      |++.++||..+.+.+++|.
T Consensus       343 k~~~~~p~~~~~~~~~~G~  361 (516)
T TIGR00717       343 KQCKANPWEQFEEKHPVGD  361 (516)
T ss_pred             hhcccCcHHHHHHhCCCCC
Confidence            9999999999999998874

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.

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.96  E-value=5.1e-29  Score=238.20  Aligned_cols=196  Identities=19%  Similarity=0.405  Sum_probs=165.8

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC
Q 024995           22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (259)
Q Consensus        22 vG~~v~~~Vl~id~~~~~v~lS~k~~----~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels   92 (259)
                      +|++|+|+|+.+|.+++++.||+|.+    .|+.+...++.|+++.|+     ++|+||++       |++||||.|+++
T Consensus        82 vGd~Ie~~V~~~~~~~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl-------Gi~gflP~Sel~  154 (486)
T PRK07899         82 VGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-------GLRGFLPASLVE  154 (486)
T ss_pred             CCCEEEEEEEEEECCCCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEE-------CCEEEEEhhHhc
Confidence            99999999999999999999999975    366666667899999999     88999999       489999999999


Q ss_pred             cccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecccc----CcchHhhhhhcCCCCccccCCCCccccceeeeccCC
Q 024995           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE----DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLP  168 (259)
Q Consensus        93 ~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~----~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G  168 (259)
                      +.++.++..+  +||.|+|+|+++|++++++.||+|....    .+|..+... ++        +|+++.|+|+++++||
T Consensus       155 ~~~~~~~~~~--vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~-lk--------~G~iv~G~V~~i~~~G  223 (486)
T PRK07899        155 MRRVRDLQPY--IGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQ-LQ--------KGQVRKGVVSSIVNFG  223 (486)
T ss_pred             ccccCChhhc--CCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHh-cc--------CCCEEEEEEEEEECCe
Confidence            9888887763  8999999999999999999999996443    567655443 33        4777999999999999


Q ss_pred             CccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchh
Q 024995          169 GLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRH  243 (259)
Q Consensus       169 ~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~  243 (259)
                          +|++|   +|++||+ .|+++            |-. +.+++.    .+++||.|    +++|.++++|+||+|++
T Consensus       224 ----~FVdl---ggv~Glv~~Sels------------~~~-v~~~~~----~~kvGd~V~vkVl~iD~e~~rI~LSlK~~  279 (486)
T PRK07899        224 ----AFVDL---GGVDGLVHVSELS------------WKH-IDHPSE----VVEVGQEVTVEVLDVDMDRERVSLSLKAT  279 (486)
T ss_pred             ----EEEEE---CCEEEEEEHHHCC------------Ccc-cCCHHH----hcCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence                99998   5899999 67777            322 232333    56999999    78999999999999999


Q ss_pred             hhhhhHHhhhhcccCC
Q 024995          244 CNEYWNVFHETAIVNN  259 (259)
Q Consensus       244 ~~~p~~~~~~~~~~~~  259 (259)
                      .++||+.+.++|++|.
T Consensus       280 ~~dPw~~~~~~~~vG~  295 (486)
T PRK07899        280 QEDPWQQFARTHAIGQ  295 (486)
T ss_pred             cccchhhhHHhcCCCC
Confidence            9999999999998873

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.96  E-value=1.1e-28  Score=225.40  Aligned_cols=189  Identities=15%  Similarity=0.266  Sum_probs=156.7

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC
Q 024995           22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (259)
Q Consensus        22 vG~~v~~~Vl~id~~~~~v~lS~k~~----~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels   92 (259)
                      +|++++|+|+++|.+++++.||+|..    .|+.+....+.|+++.|+     ++|+||+++      |++||||+|+++
T Consensus        78 ~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~------Gv~gfip~s~ls  151 (318)
T PRK07400         78 PNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIE------GLRGFIPGSHIS  151 (318)
T ss_pred             CCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHcC
Confidence            89999999999999999999999875    477777778889999998     899999996      899999999999


Q ss_pred             cccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccc
Q 024995           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA  172 (259)
Q Consensus        93 ~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~  172 (259)
                      |.+..   +.+ +|+.+.++|+++|+++++|.||+|.+...+   .... ++        +|+++.|+|+++++||    
T Consensus       152 ~~~~~---~~~-vG~~i~~kVl~id~~~~~i~lS~K~~~~~~---~~~~-~k--------~G~vv~G~V~~I~~~G----  211 (318)
T PRK07400        152 TRKPK---EEL-VGEELPLKFLEVDEERNRLVLSHRRALVER---KMNR-LE--------VGEVVVGTVRGIKPYG----  211 (318)
T ss_pred             ccCCc---ccc-CCCEEEEEEEEEEcccCEEEEEhhHhhhhh---hhcc-CC--------CCCEEEEEEEEEECCe----
Confidence            96433   334 899999999999999999999999765432   1222 33        4777999999999999    


Q ss_pred             eeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhhhh
Q 024995          173 IFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCNEY  247 (259)
Q Consensus       173 ~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~~p  247 (259)
                      +|+++   +|+.||+ +|++++.+             ...    ....+++||.|    +++|.++++|+||+|++.++|
T Consensus       212 ~fV~i---~gv~Gllhisels~~~-------------~~~----~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P  271 (318)
T PRK07400        212 AFIDI---GGVSGLLHISEISHEH-------------IET----PHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEP  271 (318)
T ss_pred             EEEEE---CCEEEEEEHHHccccc-------------ccC----hhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccCh
Confidence            99988   5899999 67776331             111    22356999999    688999999999999999999


Q ss_pred             hHHhhhhcc
Q 024995          248 WNVFHETAI  256 (259)
Q Consensus       248 ~~~~~~~~~  256 (259)
                      |+.+.....
T Consensus       272 ~~~~~~~~~  280 (318)
T PRK07400        272 GDMLKDPQK  280 (318)
T ss_pred             hhhhhhHHH
Confidence            988876644

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

Probab=99.95  E-value=5.6e-27  Score=232.37  Aligned_cols=191  Identities=30%  Similarity=0.519  Sum_probs=165.5

Q ss_pred             ccCCCCEEEEEEEEEeCCCCE-EEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEE
Q 024995           19 KGLTGSIISVKVIQANEEMKK-LVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL   85 (259)
Q Consensus        19 ~~~vG~~v~~~Vl~id~~~~~-v~lS~k~~~-------~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~gl   85 (259)
                      +.++|+++.|+|+++|+++++ +.+|+|...       ++..+..+++|+++.|+     ++|+||+++      +++||
T Consensus       430 ~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~------gv~Gl  503 (647)
T PRK00087        430 SEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIG------GVDGL  503 (647)
T ss_pred             HHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEEC------CEEEE
Confidence            346999999999999999888 999998763       44567789999999999     899999995      89999


Q ss_pred             EEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeec
Q 024995           86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE  165 (259)
Q Consensus        86 v~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~  165 (259)
                      +|+++++|.++.++.+.|++||.|+|+|+++|++++++.||+|++.++||.....+ +..        |+.+.|+|+++.
T Consensus       504 l~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~-~~~--------G~~v~g~V~~i~  574 (647)
T PRK00087        504 LHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEK-YPV--------GSIVLGKVVRIA  574 (647)
T ss_pred             EEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhh-ccC--------CeEEEEEEEEEE
Confidence            99999999999999999999999999999999999999999999999999765444 343        666999999999


Q ss_pred             cCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhh
Q 024995          166 PLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKAS  240 (259)
Q Consensus       166 ~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~  240 (259)
                      +||    +|++|  .+|+.||+ .++++++.             ...+..    .+++||.|    +++|.++++|+||+
T Consensus       575 ~~G----~fV~l--~~~i~Gli~~sel~~~~-------------~~~~~~----~~kvGd~V~vkV~~id~e~~rI~lsl  631 (647)
T PRK00087        575 PFG----AFVEL--EPGVDGLVHISQISWKR-------------IDKPED----VLSEGEEVKAKILEVDPEEKRIRLSI  631 (647)
T ss_pred             CCe----EEEEE--CCCCEEEEEhhhcCccc-------------cCCHhh----cCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence            999    99988  78999999 67766331             122222    56999999    79999999999999


Q ss_pred             chhhhhh
Q 024995          241 KRHCNEY  247 (259)
Q Consensus       241 k~~~~~p  247 (259)
                      |++.++|
T Consensus       632 k~~~~~~  638 (647)
T PRK00087        632 KEVEEEP  638 (647)
T ss_pred             eecccCc
Confidence            9999998

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.95  E-value=3.8e-27  Score=220.91  Aligned_cols=197  Identities=20%  Similarity=0.360  Sum_probs=166.3

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC
Q 024995           22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (259)
Q Consensus        22 vG~~v~~~Vl~id~~~~~v~lS~k~~----~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels   92 (259)
                      +|++|+|+|+.+|.+++++.||++..    .|+.+...++.|+++.|+     ++|+||+++      |++||||+++++
T Consensus        65 vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~------G~~gflp~~el~  138 (390)
T PRK06676         65 VGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVE------GVRGFIPASLIS  138 (390)
T ss_pred             CCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHcC
Confidence            99999999999999999999999974    477777788999999999     899999996      789999999999


Q ss_pred             cccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccC----cchHhhhhhcCCCCccccCCCCccccceeeeccCC
Q 024995           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED----PLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLP  168 (259)
Q Consensus        93 ~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~----p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G  168 (259)
                      +.+..++.++  +||.+.|+|+++|.+++++.||+|.+...    +|...... +.        +|++++|+|.++.++|
T Consensus       139 ~~~~~~~~~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~-~~--------~G~~v~g~V~~v~~~G  207 (390)
T PRK06676        139 TRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSS-LK--------EGDVVEGTVARLTDFG  207 (390)
T ss_pred             CccCCChHHc--CCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhh-CC--------CCCEEEEEEEEEecce
Confidence            9988888764  89999999999999999999999987653    55443333 23        4777999999999999


Q ss_pred             CccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchh
Q 024995          169 GLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRH  243 (259)
Q Consensus       169 ~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~  243 (259)
                          +|+.+   +|++||+ .|++++.          +   ..    ++...+++||.|    +++|.++++|.||+|++
T Consensus       208 ----~fV~l---~~v~g~v~~sels~~----------~---~~----~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~  263 (390)
T PRK06676        208 ----AFVDI---GGVDGLVHISELSHE----------R---VE----KPSEVVSVGQEVEVKVLSIDWETERISLSLKDT  263 (390)
T ss_pred             ----EEEEe---CCeEEEEEHHHcCcc----------c---cC----CHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence                99988   5899999 5776632          1   12    133356999999    68899999999999999


Q ss_pred             hhhhhHHhhhhcccCC
Q 024995          244 CNEYWNVFHETAIVNN  259 (259)
Q Consensus       244 ~~~p~~~~~~~~~~~~  259 (259)
                      ..+||+.+.+.|.+|.
T Consensus       264 ~~~~~~~~~~~~~~G~  279 (390)
T PRK06676        264 LPGPWEGVEEKLPEGD  279 (390)
T ss_pred             ccCccccchhhhcCCc
Confidence            9999999998888873

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

Probab=99.93  E-value=3.4e-25  Score=219.72  Aligned_cols=197  Identities=19%  Similarity=0.369  Sum_probs=166.2

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC
Q 024995           22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (259)
Q Consensus        22 vG~~v~~~Vl~id~~~~~v~lS~k~~----~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels   92 (259)
                      +|++++|+|+.+|.+++++.||++..    .|+.+...+++|+++.|+     ++|+||+++      |++||||.++++
T Consensus       349 vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lg------gi~gfiP~sel~  422 (647)
T PRK00087        349 VGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYG------GVRAFLPASHVE  422 (647)
T ss_pred             CCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHhC
Confidence            99999999999999999999999875    377777788999999999     889999997      799999999999


Q ss_pred             cccccChhhhcCCCCeEEEEEEEEeCCCCe-eEEEEecccc----CcchHhhhhhcCCCCccccCCCCccccceeeeccC
Q 024995           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSR-ITLSIKQLEE----DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL  167 (259)
Q Consensus        93 ~~~~~~~~~~~~~Gd~V~vkVl~id~~~~r-i~lS~K~~~~----~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~  167 (259)
                      +.+..++.++  +|+.++|+|+++|.++++ +.+|+|....    .+|....++ +.        +|+.+.|+|.++.++
T Consensus       423 ~~~~~d~~~~--vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~-l~--------~G~iV~g~V~~v~~~  491 (647)
T PRK00087        423 LGYVEDLSEY--KGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNS-LE--------EGDVVEGEVKRLTDF  491 (647)
T ss_pred             ccccCCHHHh--CCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHh-CC--------CCCEEEEEEEEEeCC
Confidence            9988888764  899999999999998888 9999998753    455444333 23        477799999999999


Q ss_pred             CCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhch
Q 024995          168 PGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKR  242 (259)
Q Consensus       168 G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~  242 (259)
                      |    +|+++   +|++||+ +|++++.            . ...    .+..+++||.|    +++|.++++|.||+|+
T Consensus       492 G----~fV~l---~gv~Gll~~sels~~------------~-~~~----~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~  547 (647)
T PRK00087        492 G----AFVDI---GGVDGLLHVSEISWG------------R-VEK----PSDVLKVGDEIKVYILDIDKENKKLSLSLKK  547 (647)
T ss_pred             c----EEEEE---CCEEEEEEHHHcCcc------------c-cCC----HHHhcCCCCEEEEEEEEEECCCCEEEEEeec
Confidence            9    99888   7999999 5776632            1 121    23356999999    6889999999999999


Q ss_pred             hhhhhhHHhhhhcccCC
Q 024995          243 HCNEYWNVFHETAIVNN  259 (259)
Q Consensus       243 ~~~~p~~~~~~~~~~~~  259 (259)
                      +.++||..+.++|++|.
T Consensus       548 ~~~~p~~~~~~~~~~G~  564 (647)
T PRK00087        548 LLPDPWENVEEKYPVGS  564 (647)
T ss_pred             cccChhhhhhhhccCCe
Confidence            99999999999998873

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.85  E-value=1.3e-20  Score=172.41  Aligned_cols=165  Identities=15%  Similarity=0.199  Sum_probs=134.0

Q ss_pred             HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCee
Q 024995           49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRI  123 (259)
Q Consensus        49 ~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri  123 (259)
                      ++++...++.|+++.|+     ++|+||+|+     .+.+||||.+|++|.++.++.+.|++||.++|+|+++|.+++++
T Consensus        22 le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig-----~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i   96 (318)
T PRK07400         22 LDKYDYHFKPGDIVNGTVFSLEPRGALIDIG-----AKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQL   96 (318)
T ss_pred             HHhhHhhcCCCCEEEEEEEEEECCEEEEEEC-----CCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeE
Confidence            44444568999999999     799999997     47899999999999999999999999999999999999999999


Q ss_pred             EEEEecccc-CcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccceeeeecccCCeeEEE-Eccccccccccchh
Q 024995          124 TLSIKQLEE-DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQD  201 (259)
Q Consensus       124 ~lS~K~~~~-~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~  201 (259)
                      .||+|++.. ++|.... ..+..        |+.++|+|.++.++|    +|+.|   +|++||+ .|++++.       
T Consensus        97 ~lS~k~~~~~~~w~~l~-~~~~~--------~~~V~g~V~~~~~~G----~~V~l---~Gv~gfip~s~ls~~-------  153 (318)
T PRK07400         97 TLSIRRIEYMRAWERVR-QLQKE--------DATVRSEVFATNRGG----ALVRI---EGLRGFIPGSHISTR-------  153 (318)
T ss_pred             EEehhhhhhhhHHHHHH-HhccC--------CCEEEEEEEEEECCe----EEEEE---CCEEEEEEHHHcCcc-------
Confidence            999998764 8897543 33443        556999999999999    99988   5999999 6776521       


Q ss_pred             hhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhhhhhHHhhhhcccC
Q 024995          202 LQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCNEYWNVFHETAIVN  258 (259)
Q Consensus       202 ~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~~p~~~~~~~~~~~  258 (259)
                           . ..   . .    .+|+.+    +++|+++++|.||+|++..+   ....+|++|
T Consensus       154 -----~-~~---~-~----~vG~~i~~kVl~id~~~~~i~lS~K~~~~~---~~~~~~k~G  197 (318)
T PRK07400        154 -----K-PK---E-E----LVGEELPLKFLEVDEERNRLVLSHRRALVE---RKMNRLEVG  197 (318)
T ss_pred             -----C-Cc---c-c----cCCCEEEEEEEEEEcccCEEEEEhhHhhhh---hhhccCCCC
Confidence                 0 00   1 1    388887    89999999999999986643   345566766

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.75  E-value=4.2e-18  Score=154.38  Aligned_cols=116  Identities=23%  Similarity=0.304  Sum_probs=99.6

Q ss_pred             CCC-CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           55 RVN-VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        55 ~l~-~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      .+. +|+++.|+     +||+||+|.+|+   |++||||+|||||.++.++++.+++||.+.|+|+++|+++++|.||+|
T Consensus        13 ~~P~~GdvV~g~V~~I~d~GafV~L~EY~---gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K   89 (319)
T PTZ00248         13 KFPEEDDLVMVKVVRITEMGAYVSLLEYD---DIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKK   89 (319)
T ss_pred             hCCCCCCEEEEEEEEEeCCeEEEEecCCC---CcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEee
Confidence            455 89999998     999999996432   799999999999999999999999999999999999999999999999


Q ss_pred             ccccCcchHhhhhhcCCCCccccCCCCccccceeeecc-CCCccceeee-----ecccCCeeEEE
Q 024995          129 QLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEP-LPGLGAIFEE-----LLQEDGIDDVR  187 (259)
Q Consensus       129 ~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~-~G~~~~~fv~-----l~~~~gv~gl~  187 (259)
                      ++.++||.....+ ++.        |..++|+|.++.+ ||    +|++     + ..|++.++-
T Consensus        90 ~v~~~pw~~~~e~-~~~--------g~~v~~~V~~ia~~~g----~~~eely~~i-~~pl~~~~g  140 (319)
T PTZ00248         90 RVSPEDIEACEEK-FSK--------SKKVHSIMRHIAQKHG----MSVEELYTKI-IWPLYKKYG  140 (319)
T ss_pred             ecccchHHHHHHh-CcC--------CCEEEEEEEEchhhcC----CCHHHHHHHH-HHHHHHhcC
Confidence            9999999876665 555        5559999999954 99    6654     1 247778876

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

Probab=99.67  E-value=4.6e-17  Score=126.96  Aligned_cols=76  Identities=45%  Similarity=0.732  Sum_probs=71.3

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      .+++|++++|+     +|||||+|++     |-.|||||||+++.|+.++.+++++||+|.|+|+++|. +++|+||+|.
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~-----g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~   75 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEG-----GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRK   75 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecC-----CCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHH
Confidence            57899999999     9999999983     89999999999999999999999999999999999997 9999999999


Q ss_pred             cccCcch
Q 024995          130 LEEDPLL  136 (259)
Q Consensus       130 ~~~~p~~  136 (259)
                      +...|-.
T Consensus        76 ~~e~pe~   82 (129)
T COG1098          76 LEEEPEK   82 (129)
T ss_pred             hhhCccc
Confidence            9888753

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=99.58  E-value=2.6e-14  Score=146.11  Aligned_cols=190  Identities=20%  Similarity=0.229  Sum_probs=151.2

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechhh-----------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEE
Q 024995           22 TGSIISVKVIQANEEMKKLVFSEKDAV-----------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL   85 (259)
Q Consensus        22 vG~~v~~~Vl~id~~~~~v~lS~k~~~-----------~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~gl   85 (259)
                      .++.+.++++.++..++.+.+|.|...           -....++++.|+++.|+     +.|+|+.+.     +++++|
T Consensus      1115 ~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls-----~~v~a~ 1189 (1710)
T KOG1070|consen 1115 KIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALS-----RKVEAF 1189 (1710)
T ss_pred             cccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEEEEEc-----cceEEE
Confidence            679999999999999888999998421           12346789999999999     889999998     699999


Q ss_pred             EEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeec
Q 024995           86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE  165 (259)
Q Consensus        86 v~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~  165 (259)
                      +|+|++++.+...|+..|++||.+.++|++++...+|+.|++|.....--...+.. +     .....|+...|+|.++.
T Consensus      1190 v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~-~-----~~l~~gd~~~g~v~~~~ 1263 (1710)
T KOG1070|consen 1190 VPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKD-S-----KDLKKGDREDGTVEVVD 1263 (1710)
T ss_pred             EEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEeccccCCchhhhhh-h-----hhhhccccccceEEEec
Confidence            99999999999999999999999999999999999999999998654322221111 1     11245777999999999


Q ss_pred             cCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhh
Q 024995          166 PLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKAS  240 (259)
Q Consensus       166 ~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~  240 (259)
                      |||    .|+.+.....+.|+| +++++..+.          .       .++.....|+.|    ++++.+.++|++++
T Consensus      1264 ~~G----~fi~l~~tv~~~g~~~~~e~~d~~~----------e-------~it~~~~~~~~V~a~~lk~~~ek~rIsl~~ 1322 (1710)
T KOG1070|consen 1264 PFG----LFIKLDVTVNMVGLCHISEEADDRG----------E-------NITALYYAGDRVKACVLKEDSEKKRISLGL 1322 (1710)
T ss_pred             CCc----eEEEecCcceecccccceeecchhh----------h-------hcccceeccceeeeEeeeccchhhhhhhhh
Confidence            999    999995545569999 777774431          1       122233677777    89999999999999


Q ss_pred             chh
Q 024995          241 KRH  243 (259)
Q Consensus       241 k~~  243 (259)
                      |..
T Consensus      1323 k~s 1325 (1710)
T KOG1070|consen 1323 KSS 1325 (1710)
T ss_pred             hhh
Confidence            973

>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=99.55  E-value=1.6e-14  Score=105.01  Aligned_cols=66  Identities=26%  Similarity=0.423  Sum_probs=60.6

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccCh---hhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~---~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      +++|+++.|+     +||+||+++     ++++||+|++++||.++.++   .+.|++||.++|+|+++|+++++|.||
T Consensus         1 ~k~G~~V~g~V~~i~~~G~fV~l~-----~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS   74 (74)
T cd05705           1 IKEGQLLRGYVSSVTKQGVFFRLS-----SSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeC-----CCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            5789999999     999999998     58999999999999987765   588999999999999999999999886

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.

>PRK08582 hypothetical protein; Provisional

Probab=99.52  E-value=4.8e-14  Score=114.50  Aligned_cols=77  Identities=40%  Similarity=0.679  Sum_probs=71.7

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      .+++|++|.|+     +||+||+|+     .+++||||++++++.++.++.+.|++||.|+|+|+++|. .++|.||+|+
T Consensus         2 ~~kvG~iv~G~V~~I~~fG~fV~L~-----~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~   75 (139)
T PRK08582          2 SIEVGSKLQGKVTGITNFGAFVELP-----EGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKK   75 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEEC-----CCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence            47899999999     999999998     489999999999999999999999999999999999997 5999999999


Q ss_pred             cccCcchH
Q 024995          130 LEEDPLLE  137 (259)
Q Consensus       130 ~~~~p~~~  137 (259)
                      +.++||.+
T Consensus        76 ~~~~~~~~   83 (139)
T PRK08582         76 AKDRPKRQ   83 (139)
T ss_pred             cccCchhh
Confidence            99999964

>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=99.47  E-value=1.5e-13  Score=99.22  Aligned_cols=66  Identities=20%  Similarity=0.305  Sum_probs=61.1

Q ss_pred             CCCCCEEEEE-----e-eeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           56 VNVEDIFVGR-----D-YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        56 l~~G~iv~G~-----~-~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      +++|+++.|+     + ||+||+++     .+.+|++|+|++++++..++.+.|++||.|+|+|+++|.  +|+.||+|
T Consensus         1 l~~G~iv~G~V~~i~~~~g~~v~l~-----~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~   72 (72)
T cd05704           1 LEEGAVTLGMVTKVIPHSGLTVQLP-----FGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR   72 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECC-----CCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence            4789999999     4 89999998     589999999999999999999999999999999999984  99999986

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.

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

Probab=99.47  E-value=1.8e-13  Score=98.63  Aligned_cols=69  Identities=43%  Similarity=0.731  Sum_probs=64.7

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      ++++|+++.|+     ++|+||+++     .+++||||++++++.+..++.+.|++||.++|+|+++|.+++++.||+|
T Consensus         1 k~~~G~iv~g~V~~v~~~g~~V~l~-----~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k   74 (74)
T PF00575_consen    1 KLKEGDIVEGKVTSVEDFGVFVDLG-----NGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             -SSTTSEEEEEEEEEETTEEEEEES-----TSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEEC-----CcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            36899999999     899999998     4899999999999999999999999999999999999999999999986

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 ....

>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=99.47  E-value=1.8e-13  Score=101.28  Aligned_cols=71  Identities=31%  Similarity=0.395  Sum_probs=66.1

Q ss_pred             hccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        52 ~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      .+.++++|+++.|+     +||+||+++     .+++||+|+++++++++.++.+.|++||.|+|+|+++|.+++++.||
T Consensus         8 ~~~~~~~G~i~~g~V~~v~~~G~fv~l~-----~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~ls   82 (83)
T cd04461           8 NFSDLKPGMVVHGYVRNITPYGVFVEFL-----GGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS   82 (83)
T ss_pred             hHHhCCCCCEEEEEEEEEeeceEEEEcC-----CCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEe
Confidence            35578999999999     999999998     38999999999999999999999999999999999999999999998


Q ss_pred             E
Q 024995          127 I  127 (259)
Q Consensus       127 ~  127 (259)
                      +
T Consensus        83 l   83 (83)
T cd04461          83 L   83 (83)
T ss_pred             C
Confidence            5

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.

>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=99.47  E-value=2.2e-13  Score=98.68  Aligned_cols=65  Identities=17%  Similarity=0.305  Sum_probs=60.4

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc--ccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~--~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      |+++.|+     ++|+||++.     .+++|+||+++++|..  ..++.+.|++||.|+|+|+++|++++||.||+|
T Consensus         1 G~~V~g~V~~i~~~g~~V~l~-----~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k   72 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTIS-----PDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeC-----CCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            7788888     899999998     4899999999999864  789999999999999999999999999999986

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.

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

Probab=99.46  E-value=3.9e-13  Score=97.15  Aligned_cols=66  Identities=33%  Similarity=0.559  Sum_probs=59.7

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      +.|+++.|+     +||+||++.+    .+.+||+|+|+++|.++.++.+.|++||.|+|+|+++|.++ |+.||+
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~~----~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~   72 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPG----CRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL   72 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEECC----CCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence            579999999     9999999962    24799999999999999999999999999999999999865 999986

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.45  E-value=1.4e-13  Score=138.80  Aligned_cols=87  Identities=28%  Similarity=0.435  Sum_probs=77.7

Q ss_pred             HhhhccCCCCCCEEE-EE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCe
Q 024995           49 WNKYSSRVNVEDIFV-GR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR  122 (259)
Q Consensus        49 ~~~~~~~l~~G~iv~-G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~r  122 (259)
                      ++.+....++|++|. |+     +||+||+|.     .|++||||+|+|+|.++.++.+.|++||.|+|+|+++|. ++|
T Consensus       744 I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~-----~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~gr  817 (891)
T PLN00207        744 ISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIA-----PGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQ  817 (891)
T ss_pred             HHHHhcCcCCCcEEECcEEEEEeccEEEEEeC-----CCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCc
Confidence            445556789999995 45     999999998     489999999999999999999999999999999999997 899


Q ss_pred             eEEEEeccccCcchHhhhh
Q 024995          123 ITLSIKQLEEDPLLETLEK  141 (259)
Q Consensus       123 i~lS~K~~~~~p~~~~~~~  141 (259)
                      |.||+|++.++||.++...
T Consensus       818 I~LSlK~l~~~Pw~~~~~~  836 (891)
T PLN00207        818 LRLSRRALLPEANSEKSSQ  836 (891)
T ss_pred             EEEEEeccccCchhhhhhh
Confidence            9999999999999876543

>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=99.43  E-value=4.6e-13  Score=95.55  Aligned_cols=65  Identities=29%  Similarity=0.396  Sum_probs=60.6

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      |+++.|+     ++|+||++.     .+++||+|++++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~-----~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k   70 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFY-----NNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEEC-----CCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            6788888     999999998     3799999999999998889999999999999999999999999999986

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.

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

Probab=99.43  E-value=1.1e-12  Score=94.96  Aligned_cols=71  Identities=34%  Similarity=0.489  Sum_probs=64.1

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      ++.|+++.|+     ++|+||++.+.   .+++||+|+++++++++.++.+.|++||.|+|+|+++|.+++++.||+|+
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~---~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~   76 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEY---GNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCC---CCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence            3689999999     99999999631   15999999999999999999999999999999999999989999999874

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

>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=99.42  E-value=8.7e-13  Score=94.92  Aligned_cols=68  Identities=26%  Similarity=0.418  Sum_probs=63.1

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      +++|+++.|+     ++|+||+++     .+++|++|++++++++..++.+.|++||.++++|+++|.+++++.||+|
T Consensus         1 ~~~G~iv~g~V~~v~~~gi~v~l~-----~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~   73 (73)
T cd05706           1 LKVGDILPGRVTKVNDRYVLVQLG-----NKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeC-----CCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            4789999999     899999998     5899999999999998888889999999999999999999999999975

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.

>PHA02945 interferon resistance protein; Provisional

Probab=99.42  E-value=9.4e-13  Score=97.09  Aligned_cols=75  Identities=31%  Similarity=0.396  Sum_probs=67.6

Q ss_pred             cCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEEceec--CcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVSEV--SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        54 ~~l~~G~iv~G~----~~G~fV~l~~~~g~~gi~glv~isel--s~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      .-.++|+++.|+    +||+||.|..|+   |.+||+|+|+.  +..++++ ++++ +||++.|||+++|+.++.|.||+
T Consensus         7 ~~P~~GelvigtV~~~d~ga~v~L~EY~---g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSl   81 (88)
T PHA02945          7 SLPNVGDVLKGKVYENGYALYIDLFDYP---HSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNY   81 (88)
T ss_pred             cCCCCCcEEEEEEEecCceEEEEecccC---CcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEe
Confidence            345899999999    999999999754   79999999955  9999999 9999 99999999999999999999999


Q ss_pred             eccccC
Q 024995          128 KQLEED  133 (259)
Q Consensus       128 K~~~~~  133 (259)
                      |+..++
T Consensus        82 K~V~~~   87 (88)
T PHA02945         82 KRMCRH   87 (88)
T ss_pred             eEcccC
Confidence            987643

>PRK07252 hypothetical protein; Provisional

Probab=99.41  E-value=1.2e-12  Score=103.65  Aligned_cols=73  Identities=37%  Similarity=0.674  Sum_probs=67.8

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccc
Q 024995           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (259)
Q Consensus        57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~  131 (259)
                      ++|+++.|+     ++|+||++.     .+++||+|++++++.++.++.+.|++||.|+|+|+++|.+++++.||+|.+.
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~-----~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~   76 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALE-----NGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLE   76 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEEC-----CCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence            579999999     999999997     4799999999999999999999999999999999999999999999999988


Q ss_pred             cCc
Q 024995          132 EDP  134 (259)
Q Consensus       132 ~~p  134 (259)
                      +++
T Consensus        77 ~~~   79 (120)
T PRK07252         77 EEK   79 (120)
T ss_pred             cCc
Confidence            744

>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=99.40  E-value=1.1e-12  Score=93.56  Aligned_cols=64  Identities=22%  Similarity=0.437  Sum_probs=59.6

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      |+++.|+     ++|+||+++     .+++||+|++++++.+..++.+.|++||.++|+|+++|++++++.||+
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~-----~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls~   69 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKLS-----DHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEec-----CCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            6788888     999999997     489999999999999888999999999999999999999999999985

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.

>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=99.40  E-value=9.2e-13  Score=94.81  Aligned_cols=57  Identities=26%  Similarity=0.402  Sum_probs=53.8

Q ss_pred             eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      +||+||++.     .|++||+|+|++++.+..++.+.|++||.++|+|+++|+.++++.||+
T Consensus        15 ~~G~~V~l~-----~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~   71 (71)
T cd05696          15 DLGAVFELK-----DGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CceEEEEeC-----CCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            799999998     489999999999999988899999999999999999999999999985

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.

>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=99.39  E-value=2.3e-12  Score=93.62  Aligned_cols=68  Identities=16%  Similarity=0.166  Sum_probs=60.9

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      ++++|+++.|+     ++|+||+++-    .|++||+|.++++|.      +.+++||.+.|+|+++|++++++.||+|+
T Consensus         1 dl~~G~~v~g~V~si~d~G~~v~~g~----~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~   70 (74)
T cd05694           1 DLVEGMVLSGCVSSVEDHGYILDIGI----PGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADP   70 (74)
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEeCC----CCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            47899999999     9999999961    279999999999986      67899999999999999999999999998


Q ss_pred             ccc
Q 024995          130 LEE  132 (259)
Q Consensus       130 ~~~  132 (259)
                      ..+
T Consensus        71 ~~~   73 (74)
T cd05694          71 SKV   73 (74)
T ss_pred             ccc
Confidence            754

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.

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=99.36  E-value=3.3e-12  Score=131.06  Aligned_cols=221  Identities=21%  Similarity=0.250  Sum_probs=152.6

Q ss_pred             CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechhhHh------hhccCCCCCCEEEEE-----eeeE
Q 024995            1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWN------KYSSRVNVEDIFVGR-----DYGA   69 (259)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~~~~------~~~~~l~~G~iv~G~-----~~G~   69 (259)
                      +.++|++.+|-..+...+.  +|..+.++|+.++.+.+++.++++.+...      .-.....+|.++.|+     ++||
T Consensus       538 lp~~hlsd~~~~~p~~~f~--v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~  615 (1710)
T KOG1070|consen  538 LPKEHLSDHPLQPPLRDFK--VGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGA  615 (1710)
T ss_pred             cChHhhhhcccccccceee--eccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCe
Confidence            4678888888877765444  88888889999999999999999976432      223456799999999     8999


Q ss_pred             EEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCcc
Q 024995           70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSV  149 (259)
Q Consensus        70 fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~  149 (259)
                      ||.+.+     |++||.|.+++++.++.++++.|.+||++.++|.++|.+++||.+++|+..-  |.........  .  
T Consensus       616 ~V~F~g-----~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~--~~a~~~~~~e--~--  684 (1710)
T KOG1070|consen  616 FVTFTG-----GLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSC--ARACVKRSVE--N--  684 (1710)
T ss_pred             EEEecC-----ccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhhh--HHHHHHHHHH--H--
Confidence            999984     8999999999999999999999999999999999999999999999997642  4321111100  0  


Q ss_pred             ccCCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee--
Q 024995          150 ISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV--  226 (259)
Q Consensus       150 ~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V--  226 (259)
                       ..+|.+..+.+...+. +   .+.|++ .+.|+.|+. ..++.+....++....-.+.. ..+.  +  .+-+|+.+  
T Consensus       685 -~~~g~v~s~~~~~~tk-d---~viVei-~~~~~~~v~~~~~L~dg~v~~~~~~~~kl~~-~t~~--~--~lv~gq~~~~  753 (1710)
T KOG1070|consen  685 -FVKGGVKSLKSIDKTK-D---SVIVEI-VDQGITGVGVFGELVDGSVVVNKVLENKLRK-NTSL--L--HLVVGQVTVG  753 (1710)
T ss_pred             -hhccccccceeehhcc-c---cEEEEc-cCcceEEEEEEEEEccCceEEccchhhhhhh-cchh--h--eeeecceeEE
Confidence             0123334555555544 2   466666 133588886 666665544333332111111 1011  1  23566665  


Q ss_pred             --EEEecccchhhhhhchhhh
Q 024995          227 --QEIQLSHSLIRKASKRHCN  245 (259)
Q Consensus       227 --~~v~~~~~~i~ls~k~~~~  245 (259)
                        +.|+..++.+.+|.++=++
T Consensus       754 ~i~~isl~k~lv~~s~~~~L~  774 (1710)
T KOG1070|consen  754 VILSISLKKSLVLISLCTDLP  774 (1710)
T ss_pred             EEEEeehhhhhhhcccccccc
Confidence              6777777777777766443

>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=99.36  E-value=4.8e-12  Score=91.46  Aligned_cols=70  Identities=41%  Similarity=0.643  Sum_probs=63.8

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecc
Q 024995           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (259)
Q Consensus        57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~  130 (259)
                      ++|+++.|+     ++|+||++.+    .+.+|++|++++++.+..++.+.|++||.|+|+|+++|.+++++.||+|+.
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l~~----~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~   75 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDIDG----TNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECC----CCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            468899998     9999999972    269999999999999988899999999999999999999999999999874

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.

>PRK08059 general stress protein 13; Validated

Probab=99.36  E-value=3.9e-12  Score=101.21  Aligned_cols=76  Identities=46%  Similarity=0.813  Sum_probs=71.2

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      ..+++|+++.|+     ++|+||++.     .+++||+|++++++.++.++.+.|++||.|+|+|+++|.+++++.||+|
T Consensus         3 ~~~k~G~iv~G~V~~i~~~G~fV~i~-----~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk   77 (123)
T PRK08059          3 SQYEVGSVVTGKVTGIQPYGAFVALD-----EETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR   77 (123)
T ss_pred             ccCCCCCEEEEEEEEEecceEEEEEC-----CCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEE
Confidence            468999999999     999999998     4899999999999999989999999999999999999999999999999


Q ss_pred             ccccCc
Q 024995          129 QLEEDP  134 (259)
Q Consensus       129 ~~~~~p  134 (259)
                      .+..+|
T Consensus        78 ~~~~~~   83 (123)
T PRK08059         78 ATEEAP   83 (123)
T ss_pred             EcccCc
Confidence            998877

>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=99.36  E-value=2e-12  Score=91.86  Aligned_cols=63  Identities=29%  Similarity=0.470  Sum_probs=58.5

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      |+++.|+     ++|+||++.     .+++||+|++++++.+..++.+.|++||.++|+|+++|++++++.||
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~-----~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls   68 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLG-----RGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeC-----CCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            6778887     999999998     48999999999999999999999999999999999999999999876

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.

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

Probab=99.35  E-value=4.2e-12  Score=90.92  Aligned_cols=67  Identities=33%  Similarity=0.553  Sum_probs=62.0

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecc
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~  130 (259)
                      |+++.|+     ++|+||++.     .+++|++|+++++++++.++.+.|++||.++|+|+++|.+++++.||+|.+
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~-----~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~   72 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLG-----DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK   72 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeC-----CCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence            6777777     899999998     489999999999999999999999999999999999999889999999875

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.

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

Probab=99.34  E-value=3.5e-12  Score=90.51  Aligned_cols=63  Identities=37%  Similarity=0.748  Sum_probs=56.8

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc-ccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~-~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      |+++.|+     +||+||++.     .+++||+|+++++| .+..++.+.|++||.|+|+|+++|.+++++.||
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~-----~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLD-----GGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeC-----CCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence            6777887     999999998     48999999999997 567888899999999999999999999999875

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.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.34  E-value=7e-13  Score=120.50  Aligned_cols=85  Identities=16%  Similarity=0.200  Sum_probs=73.1

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+++.|+|++|.+||    +||.|.-.+|++||+ +|++++.          |+   .    +++.++++||.|    ++
T Consensus        18 GdvV~g~V~~I~d~G----afV~L~EY~gvEGlIhiSElS~~----------ri---~----~i~d~vkvGd~v~vkVl~   76 (319)
T PTZ00248         18 DDLVMVKVVRITEMG----AYVSLLEYDDIEGMILMSELSKR----------RI---R----SINKLIRVGRHEVVVVLR   76 (319)
T ss_pred             CCEEEEEEEEEeCCe----EEEEecCCCCcEEEEEHHHhccc----------cc---C----CHHHhcCCCCEEEEEEEE
Confidence            667999999999999    999995457999999 7888742          23   3    244478999999    79


Q ss_pred             EecccchhhhhhchhhhhhhHHhhhhcccCC
Q 024995          229 IQLSHSLIRKASKRHCNEYWNVFHETAIVNN  259 (259)
Q Consensus       229 v~~~~~~i~ls~k~~~~~p~~~~~~~~~~~~  259 (259)
                      ||.++++|+||+|++.++||..+.++|+.|+
T Consensus        77 VD~ekg~IdLS~K~v~~~pw~~~~e~~~~g~  107 (319)
T PTZ00248         77 VDKEKGYIDLSKKRVSPEDIEACEEKFSKSK  107 (319)
T ss_pred             EeCCCCEEEEEeeecccchHHHHHHhCcCCC
Confidence            9999999999999999999999999999874

>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=99.34  E-value=7.5e-12  Score=91.58  Aligned_cols=71  Identities=35%  Similarity=0.675  Sum_probs=61.7

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc-cChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecccc
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE  132 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~-~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~  132 (259)
                      |+++.|+     +||+||++.+.-  .+.+||+|+++++|.+. .++.+.|++||.|+|+|+++|  ++++.+|+|++.+
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~--~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~   76 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLK--GRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVDQ   76 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCC--CCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEeccc
Confidence            5677777     999999997310  05899999999999986 899999999999999999999  7999999999876


Q ss_pred             C
Q 024995          133 D  133 (259)
Q Consensus       133 ~  133 (259)
                      +
T Consensus        77 ~   77 (79)
T cd05684          77 D   77 (79)
T ss_pred             C
Confidence            5

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.

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

Probab=99.34  E-value=1.5e-12  Score=113.84  Aligned_cols=77  Identities=35%  Similarity=0.623  Sum_probs=72.3

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      -..+|+++-|+     +||+||.|..|+   |++||+|+||++..|+.+..+++++||.+-|+|+++|+.++.|.||+|.
T Consensus         8 ~PeeGEiVv~tV~~V~~~GAyv~L~EY~---g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkr   84 (269)
T COG1093           8 YPEEGEIVVGTVKQVADYGAYVELDEYP---GKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKR   84 (269)
T ss_pred             CCCCCcEEEEEEEEeeccccEEEeeccC---CeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhh
Confidence            46899999999     999999999776   6999999999999999999999999999999999999999999999999


Q ss_pred             cccCc
Q 024995          130 LEEDP  134 (259)
Q Consensus       130 ~~~~p  134 (259)
                      ..++.
T Consensus        85 V~~~q   89 (269)
T COG1093          85 VTEHQ   89 (269)
T ss_pred             CCHHH
Confidence            88765

>PRK05807 hypothetical protein; Provisional

Probab=99.33  E-value=5.5e-12  Score=102.07  Aligned_cols=70  Identities=46%  Similarity=0.722  Sum_probs=65.5

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      .+++|+++.|+     +||+||+|.      +..||||++++++.++.++.+.|++||.|+|+|+++|. +++|.||+|+
T Consensus         2 ~~~vG~vv~G~Vt~i~~~GafV~L~------~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~   74 (136)
T PRK05807          2 TLKAGSILEGTVVNITNFGAFVEVE------GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQ   74 (136)
T ss_pred             CccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence            46789999999     999999995      68999999999999999999999999999999999997 7999999999


Q ss_pred             cc
Q 024995          130 LE  131 (259)
Q Consensus       130 ~~  131 (259)
                      +.
T Consensus        75 ~~   76 (136)
T PRK05807         75 AM   76 (136)
T ss_pred             cc
Confidence            76

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]

Probab=99.33  E-value=1.2e-11  Score=108.73  Aligned_cols=167  Identities=19%  Similarity=0.188  Sum_probs=120.6

Q ss_pred             CCCCEEEEEEEEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE------eeeEEEEEccCCCCccEEEEEEceecCcc
Q 024995           21 LTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD   94 (259)
Q Consensus        21 ~vG~~v~~~Vl~id~~~~~v~lS~k~~~~~~~~~~l~~G~iv~G~------~~G~fV~l~~~~g~~gi~glv~isels~~   94 (259)
                      .+||+|++. ++.|.+ +++.++.+..       ...+|+.-.++      +-|+|++.+     ...+-+||.++++..
T Consensus        45 evGdev~vF-iY~D~~-~rl~aTt~~p-------~~tvg~~g~~~Vv~v~~~lGaFlD~G-----l~KDl~vp~~elp~~  110 (287)
T COG2996          45 EVGDEVTVF-IYVDSE-DRLIATTREP-------KATVGEYGWLKVVEVNKDLGAFLDWG-----LPKDLLVPLDELPTL  110 (287)
T ss_pred             ccCcEEEEE-EEECCC-Cceeheeecc-------eEeecceeEEEEEEEcCCcceEEecC-----CCcceeeehhhcccc
Confidence            399999999 889965 7788888776       34556554444      789999997     568999999999764


Q ss_pred             cccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCcccee
Q 024995           95 LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIF  174 (259)
Q Consensus        95 ~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~f  174 (259)
                      +    +-++++||++.|.+ .+|. ++||.-.++.-   .|.+.++...-.+.     -++.+.|+|++...-|    .|
T Consensus       111 ~----~~wpq~Gd~l~v~l-~~Dk-k~Ri~g~~a~~---~~l~~l~~~~~~~l-----~nq~v~~tVYr~~~~G----~f  172 (287)
T COG2996         111 K----SLWPQKGDKLLVYL-YVDK-KGRIWGTLAIE---KILENLATPAYNNL-----KNQEVDATVYRLLESG----TF  172 (287)
T ss_pred             c----ccCCCCCCEEEEEE-EEcc-CCcEEEEecch---hHHHhcCCccchhh-----hcCeeeeEEEEEeccc----eE
Confidence            2    23588999999998 8997 66998877532   12222221111111     1566999999999999    99


Q ss_pred             eeecccCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccC
Q 024995          175 EELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARA  222 (259)
Q Consensus       175 v~l~~~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~  222 (259)
                      +.+  ++|.-||+|+..+...+.+|+.++.++...+. |+++++++++
T Consensus       173 v~~--e~~~~GfIh~sEr~~~prlG~~l~~rVi~~re-Dg~lnLSl~p  217 (287)
T COG2996         173 VIT--ENGYLGFIHKSERFAEPRLGERLTARVIGVRE-DGKLNLSLRP  217 (287)
T ss_pred             EEE--cCCeEEEEcchhhcccccCCceEEEEEEEEcc-CCeeeccccc
Confidence            877  89999999655555667777777777766663 6666666665

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

Probab=99.30  E-value=1.1e-11  Score=88.41  Aligned_cols=65  Identities=32%  Similarity=0.532  Sum_probs=60.3

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      |+++.|+     ++|+||+++     .+.+|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~-----~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIG-----YKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeC-----CCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            6788888     889999997     4799999999999999999999999999999999999988899999985

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.

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

Probab=99.29  E-value=1.5e-11  Score=86.48  Aligned_cols=64  Identities=44%  Similarity=0.830  Sum_probs=59.0

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      |+++.|+     ++|+||+++     .+.+||+|+++++++++.++.+.|++||.++|+|+++|. ++++.||+|
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~-----~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~k   69 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELG-----GGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEEC-----CCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence            6777777     999999998     489999999999999999999999999999999999998 899999986

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.

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

Probab=99.28  E-value=1.7e-11  Score=87.94  Aligned_cols=66  Identities=39%  Similarity=0.674  Sum_probs=58.4

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcc-cccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~-~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      +++|+++.|+     +||+||++.     .+++||+|+++++|. +..++.+.|++||.|+|+|+++|.+++++.++
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~-----~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELE-----EGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcC-----CCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence            4689999999     999999998     479999999999975 45577788999999999999999999998864

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.

>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=99.24  E-value=1.7e-11  Score=94.07  Aligned_cols=71  Identities=30%  Similarity=0.466  Sum_probs=62.8

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc-------------------cChhhhcCCCCeEEE
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDEVRV  111 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~-------------------~~~~~~~~~Gd~V~v  111 (259)
                      +++|+++.|+     ++|+||.++     .|++|++|+++++|.+.                   .++.+.|++||.|+|
T Consensus         1 L~~G~vV~G~V~~v~~~gl~v~L~-----~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~   75 (100)
T cd05693           1 LSEGMLVLGQVKEITKLDLVISLP-----NGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRC   75 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECC-----CCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEE
Confidence            5789999999     899999998     48999999999998753                   347789999999999


Q ss_pred             EEEEEeCC---CCeeEEEEeccc
Q 024995          112 KVIKIDRE---KSRITLSIKQLE  131 (259)
Q Consensus       112 kVl~id~~---~~ri~lS~K~~~  131 (259)
                      +|+++|++   +++|.||+|...
T Consensus        76 kVi~~d~~~~~~~~i~LSlr~~~   98 (100)
T cd05693          76 KVVSLDKSKSGKKRIELSLEPEL   98 (100)
T ss_pred             EEEEccCCcCCCcEEEEEecHHH
Confidence            99999987   789999998654

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.

>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=99.21  E-value=4.2e-11  Score=84.04  Aligned_cols=63  Identities=38%  Similarity=0.670  Sum_probs=57.4

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      |+++.|+     ++|+||++.     .+.+||+|.+++++.++.++.+.|++||.++|+|+++|.+++++.||
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~-----~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIG-----VKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcC-----CCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            5677777     999999998     47999999999999988899999999999999999999988999876

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.

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

Probab=99.21  E-value=7.1e-11  Score=83.67  Aligned_cols=62  Identities=27%  Similarity=0.545  Sum_probs=55.7

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      |+++.|+     ++|+||+++      |++||+|.+++++.+..++.+.  +||.++|+|+++|.+++++.||+|
T Consensus         1 G~iv~g~V~~v~~~G~~v~l~------g~~gfip~s~~~~~~~~~~~~~--vG~~i~~~i~~vd~~~~~i~lS~k   67 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDIE------GVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHCCCcccCChHHh--CCCEEEEEEEEEeCCCCEEEEEcC
Confidence            6788887     999999995      8999999999999887777763  899999999999999999999975

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.

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

Probab=99.19  E-value=8e-11  Score=105.06  Aligned_cols=77  Identities=36%  Similarity=0.614  Sum_probs=69.7

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      -+++|+++.|+     ++|+||+|..++   |++||+|+|+++++++.++.+.|++||.|.|+|+++|.++++|.||+|+
T Consensus         5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~---gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~   81 (262)
T PRK03987          5 WPEEGELVVGTVKEVKDFGAFVTLDEYP---GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR   81 (262)
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCCC---CcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEe
Confidence            45899999999     999999997422   7999999999999999999999999999999999999999999999998


Q ss_pred             cccCc
Q 024995          130 LEEDP  134 (259)
Q Consensus       130 ~~~~p  134 (259)
                      +.++.
T Consensus        82 v~~~e   86 (262)
T PRK03987         82 VNEHQ   86 (262)
T ss_pred             cccch
Confidence            77654

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

Probab=99.19  E-value=9.3e-11  Score=82.45  Aligned_cols=63  Identities=44%  Similarity=0.865  Sum_probs=58.0

Q ss_pred             CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        58 ~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      +|+++.|+     ++|+||+++      +.+|++|.+++++.+..++.+.|++||.|+|+|+++|.+++++.||
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~------~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLG------GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC------CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence            47888888     899999996      6999999999999888889999999999999999999989999876

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.

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

Probab=99.18  E-value=1.1e-10  Score=82.21  Aligned_cols=63  Identities=44%  Similarity=0.783  Sum_probs=57.3

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      |+++.|+     ++|+||+++     .+.+||+|++++++.++.++.+.|++||.++|+|+++|. ++++.||+
T Consensus         1 g~~~~g~V~~v~~~G~~v~l~-----~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~   68 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEIL-----PGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeC-----CCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence            5677777     999999998     479999999999999988889999999999999999998 89999884

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.

>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=99.16  E-value=9.1e-11  Score=83.21  Aligned_cols=61  Identities=20%  Similarity=0.333  Sum_probs=53.4

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      |+++.|+     ++|+||++.     .+++||+|.++++..+..  .+.|++||+++|+|+++|+++++|.||
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~-----~~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS   66 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFL-----SSFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEc-----CCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            6788888     999999997     279999999999765544  677999999999999999999999886

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.16  E-value=1.6e-10  Score=114.66  Aligned_cols=89  Identities=24%  Similarity=0.493  Sum_probs=73.9

Q ss_pred             EEEeCCCCEEEEEechhh--------Hhhhcc--CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC---
Q 024995           31 IQANEEMKKLVFSEKDAV--------WNKYSS--RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS---   92 (259)
Q Consensus        31 l~id~~~~~v~lS~k~~~--------~~~~~~--~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels---   92 (259)
                      |+++. .+.+.++.....        .+.+..  .+++|++|.|+     +||+||+|.     .|++||||+||++   
T Consensus       611 Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~-----~G~eGLvHISeisdls  684 (719)
T TIGR02696       611 ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLL-----PGKDGLLHISQIRKLA  684 (719)
T ss_pred             EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEec-----CCceEEEEhhhccccc
Confidence            77775 588887765421        233444  58999999999     999999997     4899999999996   


Q ss_pred             -cccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           93 -WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        93 -~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                       |.++.++.+.|++||.|+|+|+++|. ++||.|+
T Consensus       685 ~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~  718 (719)
T TIGR02696       685 GGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV  718 (719)
T ss_pred             cccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence             46899999999999999999999995 8999986

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.

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

Probab=99.15  E-value=1.4e-10  Score=86.07  Aligned_cols=70  Identities=23%  Similarity=0.363  Sum_probs=62.0

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc----ccccChhhhcCCCCeEEEEEEEEeCCCCeeEE
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW----DLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~----~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~l  125 (259)
                      .+++|+++.|+     ++|+||+++     .+.+|++|++++++    .+..++.+.+++||.+.|+|+++|++ +++.|
T Consensus         3 ~p~~GdiV~g~V~~i~~~g~~v~i~-----~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~L   76 (86)
T cd05789           3 IPEVGDVVIGRVTEVGFKRWKVDIN-----SPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSL   76 (86)
T ss_pred             cCCCCCEEEEEEEEECCCEEEEECC-----CCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEE
Confidence            45899999999     899999998     48999999999996    45567788899999999999999975 99999


Q ss_pred             EEecc
Q 024995          126 SIKQL  130 (259)
Q Consensus       126 S~K~~  130 (259)
                      |+|+.
T Consensus        77 S~~~~   81 (86)
T cd05789          77 HTRSL   81 (86)
T ss_pred             EeCcc
Confidence            99874

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".

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

Probab=99.14  E-value=2.2e-11  Score=95.28  Aligned_cols=76  Identities=18%  Similarity=0.189  Sum_probs=63.1

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      +.|+.++|+|+.|++||    +||+|  ++|=+||+ +|+++..          |++       +++..+++||+|    
T Consensus         4 kvG~~l~GkItgI~~yG----AFV~l--~~g~tGLVHISEIa~~----------fVk-------dI~d~L~vG~eV~vKV   60 (129)
T COG1098           4 KVGSKLKGKITGITPYG----AFVEL--EGGKTGLVHISEIADG----------FVK-------DIHDHLKVGQEVKVKV   60 (129)
T ss_pred             cccceEEEEEEeeEecc----eEEEe--cCCCcceEEehHhhhh----------hHH-------hHHHHhcCCCEEEEEE
Confidence            45788999999999999    99999  88999998 8998733          443       355688999999    


Q ss_pred             EEEecccchhhhhhchhhhhhhHHh
Q 024995          227 QEIQLSHSLIRKASKRHCNEYWNVF  251 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~~~~p~~~~  251 (259)
                      +.||. +.+|+||||.+.++|-...
T Consensus        61 l~ide-~GKisLSIr~~~e~pe~~~   84 (129)
T COG1098          61 LDIDE-NGKISLSIRKLEEEPEKQH   84 (129)
T ss_pred             Eeecc-CCCcceehHHhhhCccccc
Confidence            56666 7799999999999887654

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

Probab=99.12  E-value=3.8e-10  Score=79.25  Aligned_cols=67  Identities=43%  Similarity=0.725  Sum_probs=61.2

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      ++|+++.|+     ++|+||+++     .++.|++|.+++++.+..++.+.|++||.++|+|+++|.+++++.+|++
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~-----~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLG-----NGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeC-----CCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            368899988     899999998     4899999999999988888888999999999999999998899999975

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=99.12  E-value=3.2e-10  Score=113.70  Aligned_cols=93  Identities=34%  Similarity=0.615  Sum_probs=78.1

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc
Q 024995           31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (259)
Q Consensus        31 l~id~~~~~v~lS~k~~--------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~   97 (259)
                      ++++. ++.+.++....        ..+.+...+++|++|.|+     +||+||++.     .+.+||+|+|++++.++.
T Consensus       587 idi~d-~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~-----~~~~GllhiSels~~~v~  660 (693)
T PRK11824        587 IDIED-DGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEIL-----PGKDGLVHISEIADERVE  660 (693)
T ss_pred             cccCC-CceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEEC-----CCCEEEEEeeeccCcccc
Confidence            44443 47777765432        134455678999999999     999999998     489999999999999999


Q ss_pred             ChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecc
Q 024995           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (259)
Q Consensus        98 ~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~  130 (259)
                      ++.+.|++||.|+|+|+++|.+ +++.||+|.+
T Consensus       661 ~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~  692 (693)
T PRK11824        661 KVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV  692 (693)
T ss_pred             CccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence            9999999999999999999986 9999999975

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

Probab=99.10  E-value=4.4e-10  Score=84.30  Aligned_cols=69  Identities=26%  Similarity=0.411  Sum_probs=59.2

Q ss_pred             CCCCCCEEEEE-----ee--eEEEEEccCCCCccEEEEEEceecCc---ccccChhhhcCCCCeEEEEEEEEeCCCCeeE
Q 024995           55 RVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSW---DLIQDIRDILNEGDEVRVKVIKIDREKSRIT  124 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~--G~fV~l~~~~g~~gi~glv~isels~---~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~  124 (259)
                      .++.|++|.|+     +|  ||||+++     .|.+||||+||++|   .++.++.+.+++||.|.|+|++.....+-..
T Consensus         4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~-----~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~   78 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIG-----LGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPR   78 (88)
T ss_pred             cCCCCCEEEEEEEEeccCCcEEEEEeC-----CCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCce
Confidence            57899999999     65  9999998     48999999999999   6688889999999999999999877666555


Q ss_pred             EEEe
Q 024995          125 LSIK  128 (259)
Q Consensus       125 lS~K  128 (259)
                      ||.+
T Consensus        79 lt~~   82 (88)
T cd04453          79 LTTN   82 (88)
T ss_pred             EEEE
Confidence            5543

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

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

Probab=99.06  E-value=1.1e-09  Score=80.33  Aligned_cols=66  Identities=30%  Similarity=0.610  Sum_probs=55.8

Q ss_pred             CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc-----------ChhhhcCCCCeEEEEEEEEeCCCC
Q 024995           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREKS  121 (259)
Q Consensus        58 ~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~-----------~~~~~~~~Gd~V~vkVl~id~~~~  121 (259)
                      +|+++.|+     ++|+||+++.    ++++|++|.+++++.++.           ++.+.|++||.|+|+|.++|.+++
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~----~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~   76 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDN----LTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRR   76 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecC----CCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccC
Confidence            37788888     9999999982    379999999999876422           345789999999999999999899


Q ss_pred             eeEEEE
Q 024995          122 RITLSI  127 (259)
Q Consensus       122 ri~lS~  127 (259)
                      ++.+++
T Consensus        77 ~i~~~l   82 (83)
T cd04471          77 KIDFEL   82 (83)
T ss_pred             EEEEEE
Confidence            999986

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.

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

Probab=99.03  E-value=5.9e-10  Score=108.91  Aligned_cols=94  Identities=36%  Similarity=0.631  Sum_probs=82.1

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc
Q 024995           31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (259)
Q Consensus        31 l~id~~~~~v~lS~k~~--------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~   97 (259)
                      ++++ +.+.+..+....        .++.+...+++|++|.|+     +||+||++.     +|.+||||+|++++.++.
T Consensus       585 Idie-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~-----~gkdgl~hiS~~~~~rv~  658 (692)
T COG1185         585 IDIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELL-----PGKDGLVHISQLAKERVE  658 (692)
T ss_pred             EEec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEec-----CCcceeEEehhhhhhhhh
Confidence            6777 667777776542        245567889999999999     999999998     589999999999999999


Q ss_pred             ChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccc
Q 024995           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (259)
Q Consensus        98 ~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~  131 (259)
                      +.++.+++||.+.||++.+|. .+|+.||+|...
T Consensus       659 kv~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~~  691 (692)
T COG1185         659 KVEDVLKEGDEVKVKVIEIDK-QGRIRLSIKAVL  691 (692)
T ss_pred             cccceeecCceEEEEEeeecc-cCCccceehhcc
Confidence            999999999999999999996 899999998753

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=99.02  E-value=4.4e-10  Score=111.31  Aligned_cols=75  Identities=37%  Similarity=0.648  Sum_probs=70.2

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      +.+|++|+++.|+     +||+||+|+     .+.+|+||+|+++..++.+|.+.+++||.|+|+|+++|..++||.|||
T Consensus       653 i~dLk~Gm~leg~Vrnv~~fgafVdIg-----v~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsm  727 (780)
T COG2183         653 ITDLKPGMILEGTVRNVVDFGAFVDIG-----VHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSM  727 (780)
T ss_pred             HhhccCCCEEEEEEEEeeeccceEEec-----cccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEe
Confidence            3489999999999     999999998     689999999999999999999999999999999999999999999999


Q ss_pred             ecccc
Q 024995          128 KQLEE  132 (259)
Q Consensus       128 K~~~~  132 (259)
                      +....
T Consensus       728 r~~~~  732 (780)
T COG2183         728 RLDEE  732 (780)
T ss_pred             eccCC
Confidence            87543

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

Probab=98.97  E-value=2.6e-09  Score=78.64  Aligned_cols=69  Identities=22%  Similarity=0.212  Sum_probs=63.0

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      .+++|+++.|+     +.|++|+++     .+.+|++|+++++..+..++.+.|++||.+.|+|+++|.+ +++.||++.
T Consensus         3 ~p~~GdiV~G~V~~v~~~~~~V~i~-----~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~   76 (82)
T cd04454           3 LPDVGDIVIGIVTEVNSRFWKVDIL-----SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD   76 (82)
T ss_pred             CCCCCCEEEEEEEEEcCCEEEEEeC-----CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence            35899999999     889999998     4899999999999888888899999999999999999985 999999986

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".

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=98.95  E-value=3.5e-09  Score=90.27  Aligned_cols=101  Identities=23%  Similarity=0.319  Sum_probs=80.2

Q ss_pred             CCCEEEEEE---EEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE-----eeeEEEEEccCC--C---CccEEEEEEc
Q 024995           22 TGSIISVKV---IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPD--G---LYHLTGLVHV   88 (259)
Q Consensus        22 vG~~v~~~V---l~id~~~~~v~lS~k~~~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~--g---~~gi~glv~i   88 (259)
                      .+..+.+.+   +++|.+++++.+..    |......+++|+++.|+     ++|+||+|..++  +   ..+.+|++|+
T Consensus        29 ~~~~i~as~~G~~~id~~~~~Isv~P----~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~  104 (189)
T PRK09521         29 DNGEVYASVVGKVFIDDINRKISVIP----FKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHI  104 (189)
T ss_pred             eCCEEEEEeeEEEEEcCCCCEEEEec----CcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEh
Confidence            455666555   45577777887753    44445678999999999     899999996321  0   0268999999


Q ss_pred             eecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           89 SEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        89 sels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      +++++.+..++.+.|++||.|.|+|++++   +++.||+|+
T Consensus       105 s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~  142 (189)
T PRK09521        105 SQVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKG  142 (189)
T ss_pred             hHcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEec
Confidence            99999888889999999999999999997   789999985

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.91  E-value=4.4e-09  Score=105.42  Aligned_cols=88  Identities=34%  Similarity=0.649  Sum_probs=73.2

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc
Q 024995           31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (259)
Q Consensus        31 l~id~~~~~v~lS~k~~--------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~   97 (259)
                      ++++. ++.+.++....        .++.+...+++|++|.|+     +||+||++.     .+.+||||+|+++|.++.
T Consensus       584 I~i~d-dG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~-----~g~~GllHiSei~~~~v~  657 (684)
T TIGR03591       584 IDIED-DGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEIL-----PGKDGLVHISEIANERVE  657 (684)
T ss_pred             EEEec-CeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEEC-----CCcEEEEEHHHcCCCccc
Confidence            56664 47777775432        133455678999999999     999999998     489999999999999999


Q ss_pred             ChhhhcCCCCeEEEEEEEEeCCCCeeEE
Q 024995           98 DIRDILNEGDEVRVKVIKIDREKSRITL  125 (259)
Q Consensus        98 ~~~~~~~~Gd~V~vkVl~id~~~~ri~l  125 (259)
                      ++.+.|++||.|+|+|+++|. ++|+.|
T Consensus       658 ~~~~~~kvGD~V~VkVi~id~-~gki~L  684 (684)
T TIGR03591       658 KVEDVLKEGDEVKVKVLEIDK-QGRIKL  684 (684)
T ss_pred             ChhhccCCCCEEEEEEEEECC-CCCccC
Confidence            999999999999999999997 788764

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).

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

Probab=98.89  E-value=4.5e-09  Score=72.32  Aligned_cols=56  Identities=45%  Similarity=0.781  Sum_probs=51.8

Q ss_pred             eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      ++|+||+++     .+.+|++|.+++++.+..++.+.|++||.|+|+|+++|.+++++.||
T Consensus        10 ~~g~~v~l~-----~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164          10 KFGVFVELE-----DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             eeeEEEEec-----CCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            899999998     48999999999999888888899999999999999999988888875

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.

>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=98.87  E-value=6.3e-09  Score=74.32  Aligned_cols=57  Identities=21%  Similarity=0.256  Sum_probs=50.8

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc--ccChhhhcCCCCeEEEEEEEEeCCC
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREK  120 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~--~~~~~~~~~~Gd~V~vkVl~id~~~  120 (259)
                      |+++.|+     ++|+||+++     .+++|++|++++++++  ..++.+.|++||.|+|+|+++|.++
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~-----~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~   64 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLA-----DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK   64 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeC-----CCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence            6777887     889999998     5899999999999885  7888899999999999999999743

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.

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

Probab=98.86  E-value=1.4e-08  Score=73.99  Aligned_cols=61  Identities=34%  Similarity=0.578  Sum_probs=54.1

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      ..+++.|+.+.|+     +||+||++.     .+.+||+|.+++.        +.|++||.++++|.++ .+++++.+|+
T Consensus        11 ~~~~~~G~~~~g~V~~i~~~G~fV~l~-----~~~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~~   76 (77)
T cd04473          11 MEDLEVGKLYKGKVNGVAKYGVFVDLN-----DHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP   76 (77)
T ss_pred             hhhCCCCCEEEEEEEeEecceEEEEEC-----CCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence            3468999999999     999999998     4799999999973        4589999999999999 7899999986

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.

>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=98.85  E-value=2.7e-09  Score=77.42  Aligned_cols=68  Identities=9%  Similarity=0.154  Sum_probs=53.7

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|.++++||    +|+.|  .+|++|++ .+++++.          |...   +. ++...+++||.|    
T Consensus         2 k~G~~V~g~V~~i~~~G----~fV~l--~~~v~G~v~~~~ls~~----------~~~~---~~-~~~~~~~~G~~v~~kV   61 (74)
T cd05705           2 KEGQLLRGYVSSVTKQG----VFFRL--SSSIVGRVLFQNVTKY----------FVSD---PS-LYNKYLPEGKLLTAKV   61 (74)
T ss_pred             CCCCEEEEEEEEEeCCc----EEEEe--CCCCEEEEEHHHccCc----------cccC---hh-hHhcccCCCCEEEEEE
Confidence            46888999999999999    99988  89999999 6887743          2211   11 133466999999    


Q ss_pred             EEEecccchhhhh
Q 024995          227 QEIQLSHSLIRKA  239 (259)
Q Consensus       227 ~~v~~~~~~i~ls  239 (259)
                      +++|.++++|.||
T Consensus        62 l~id~~~~~i~LS   74 (74)
T cd05705          62 LSVNSEKNLVELS   74 (74)
T ss_pred             EEEECCCCEEecC
Confidence            7999999999886

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.

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

Probab=98.83  E-value=1.8e-08  Score=76.88  Aligned_cols=65  Identities=31%  Similarity=0.584  Sum_probs=55.9

Q ss_pred             eeeEEEEEccCCCCccEEEEEEceecCcccccC-----------hhhhcCCCCeEEEEEEEEeCCC-----CeeEEEEec
Q 024995           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-----------IRDILNEGDEVRVKVIKIDREK-----SRITLSIKQ  129 (259)
Q Consensus        66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~-----------~~~~~~~Gd~V~vkVl~id~~~-----~ri~lS~K~  129 (259)
                      ++|+||++.      +++||+|+++++++++..           +.+.|++||.|+|+|.++|.+.     .++.||+|+
T Consensus        12 ~~GifV~l~------~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~   85 (99)
T cd04460          12 DFGAFVRIG------PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIGLTMRQ   85 (99)
T ss_pred             eccEEEEEc------CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEEEEEec
Confidence            999999997      599999999999876543           3477999999999999999764     589999999


Q ss_pred             cccCcch
Q 024995          130 LEEDPLL  136 (259)
Q Consensus       130 ~~~~p~~  136 (259)
                      ....||.
T Consensus        86 ~~~g~~~   92 (99)
T cd04460          86 PGLGKLE   92 (99)
T ss_pred             CCCCcHH
Confidence            8888874

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.

>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=98.80  E-value=3.1e-09  Score=76.86  Aligned_cols=67  Identities=10%  Similarity=0.110  Sum_probs=52.6

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |++++|+|.++.++|    +|++|  .+||+|++ .++++++.           .....+..    .+++||.|    ++
T Consensus         1 G~~V~g~V~~i~~~g----~~V~l--~~~i~G~i~~~~ls~~~-----------~~~~~~~~----~~~vG~~v~~kV~~   59 (73)
T cd05703           1 GQEVTGFVNNVSKEF----VWLTI--SPDVKGRIPLLDLSDDV-----------SVLEHPEK----KFPIGQALKAKVVG   59 (73)
T ss_pred             CCEEEEEEEEEeCCE----EEEEe--CCCcEEEEEHHHcCCcc-----------ccccCHHH----hCCCCCEEEEEEEE
Confidence            567999999999999    99988  88999999 67776321           11122223    45999999    79


Q ss_pred             Eecccchhhhhhc
Q 024995          229 IQLSHSLIRKASK  241 (259)
Q Consensus       229 v~~~~~~i~ls~k  241 (259)
                      +|+++++|.||+|
T Consensus        60 id~~~~~i~Ls~k   72 (73)
T cd05703          60 VDKEHKLLRLSAR   72 (73)
T ss_pred             EeCCCCEEEEEec
Confidence            9999999999986

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.

>PRK08582 hypothetical protein; Provisional

Probab=98.77  E-value=8.4e-09  Score=83.79  Aligned_cols=75  Identities=15%  Similarity=0.152  Sum_probs=60.1

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|++|++||    +||+|  .++++||+ +|+++++          |+.   .    ....+++||.|    
T Consensus         4 kvG~iv~G~V~~I~~fG----~fV~L--~~~~~GlVhiSels~~----------~v~---~----~~~~l~vGD~VkvkV   60 (139)
T PRK08582          4 EVGSKLQGKVTGITNFG----AFVEL--PEGKTGLVHISEVADN----------YVK---D----INDHLKVGDEVEVKV   60 (139)
T ss_pred             cCCCEEEEEEEEEECCe----EEEEE--CCCCEEEEEeeccCcc----------ccc---c----cccccCCCCEEEEEE
Confidence            45888999999999999    99988  78999999 7777633          221   1    22356999999    


Q ss_pred             EEEecccchhhhhhchhhhhhhHH
Q 024995          227 QEIQLSHSLIRKASKRHCNEYWNV  250 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~~~~p~~~  250 (259)
                      +.|+. ..+|.||+|++.++||..
T Consensus        61 ~~id~-~gkI~LSlk~~~~~~~~~   83 (139)
T PRK08582         61 LNVED-DGKIGLSIKKAKDRPKRQ   83 (139)
T ss_pred             EEECC-CCcEEEEEEecccCchhh
Confidence            57776 489999999999999975

>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=98.74  E-value=9.2e-09  Score=74.65  Aligned_cols=65  Identities=8%  Similarity=0.081  Sum_probs=53.4

Q ss_pred             CCCCccccceeeeccCCCccceeeeeccc-CCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~-~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---  226 (259)
                      +.|+++.|+|.+|++||    +|+++  . +|++||++ ++++            |.           ..+++||.+   
T Consensus         3 ~~G~~v~g~V~si~d~G----~~v~~--g~~gv~Gfl~~~~~~------------~~-----------~~~~~Gq~v~~~   53 (74)
T cd05694           3 VEGMVLSGCVSSVEDHG----YILDI--GIPGTTGFLPKKDAG------------NF-----------SKLKVGQLLLCV   53 (74)
T ss_pred             CCCCEEEEEEEEEeCCE----EEEEe--CCCCcEEEEEHHHCC------------cc-----------cccCCCCEEEEE
Confidence            56888999999999999    99888  4 69999994 5544            11           145899998   


Q ss_pred             -EEEecccchhhhhhchhhh
Q 024995          227 -QEIQLSHSLIRKASKRHCN  245 (259)
Q Consensus       227 -~~v~~~~~~i~ls~k~~~~  245 (259)
                       +.||.+++++.||+|++.+
T Consensus        54 V~~vd~~~~~v~ls~k~~~~   73 (74)
T cd05694          54 VEKVKDDGRVVSLSADPSKV   73 (74)
T ss_pred             EEEEECCCCEEEEEEeeccc
Confidence             6889999999999998764

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.73  E-value=1.5e-08  Score=97.18  Aligned_cols=97  Identities=19%  Similarity=0.276  Sum_probs=78.5

Q ss_pred             ccCCCCEEEEEEEEEeCCCCEEEEEe-chh--------hHhhhccCCC--CCCEEEEE-----eeeEEEEEccCCCCccE
Q 024995           19 KGLTGSIISVKVIQANEEMKKLVFSE-KDA--------VWNKYSSRVN--VEDIFVGR-----DYGAFIHLRFPDGLYHL   82 (259)
Q Consensus        19 ~~~vG~~v~~~Vl~id~~~~~v~lS~-k~~--------~~~~~~~~l~--~G~iv~G~-----~~G~fV~l~~~~g~~gi   82 (259)
                      +..+|+.+.+.|...+  .+|+.++. |+.        .++.++..++  .|+++.|+     ++|+||+++      |+
T Consensus        86 ~~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLg------gv  157 (470)
T PRK09202         86 DAEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLG------RA  157 (470)
T ss_pred             cccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEEC------Ce
Confidence            4569999999988776  34444443 332        2345677787  99999999     899999997      79


Q ss_pred             EEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCC--eeEEEEec
Q 024995           83 TGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ  129 (259)
Q Consensus        83 ~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~--ri~lS~K~  129 (259)
                      +||||.++++      |.+.|++||.|+|+|++++++++  +|.||++.
T Consensus       158 ea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~  200 (470)
T PRK09202        158 EAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH  200 (470)
T ss_pred             EEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence            9999999985      67789999999999999999777  89999864

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

Probab=98.72  E-value=4.5e-08  Score=82.70  Aligned_cols=128  Identities=22%  Similarity=0.436  Sum_probs=85.7

Q ss_pred             CCCCCCCCCCchhHhhhcc-cCCCCEEE-----EEEEEEeC-CCCEEEEEech----hhHhhhccCCCCCCEEEEE----
Q 024995            1 MSPSHSCKEPQKSIHEIAK-GLTGSIIS-----VKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR----   65 (259)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~-~~vG~~v~-----~~Vl~id~-~~~~v~lS~k~----~~~~~~~~~l~~G~iv~G~----   65 (259)
                      +.|++|.+++...+.+.++ .+.|+.+.     +.|.++.. ..+++.-.--.    ..+..+.-+...|+++.|+    
T Consensus        13 i~P~~~~~~~~~~i~~~l~~~~~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~~gEvv~G~V~~v   92 (179)
T TIGR00448        13 IPPDQFGEDLEEVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPELGEIVEGEVIEI   92 (179)
T ss_pred             ECHHHhCccHHHHHHHHHHHHhcCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEeccCCCEEEEEEEEE
Confidence            3577777666655554443 35555433     33444433 33444311111    1123334467789999999    


Q ss_pred             -eeeEEEEEccCCCCccEEEEEEceecCccccc-----------ChhhhcCCCCeEEEEEEEEe-----CCCCeeEEEEe
Q 024995           66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKID-----REKSRITLSIK  128 (259)
Q Consensus        66 -~~G~fV~l~~~~g~~gi~glv~isels~~~~~-----------~~~~~~~~Gd~V~vkVl~id-----~~~~ri~lS~K  128 (259)
                       ++|+||+++      .++|++|.+++.+.+..           +....|+.||.|+++|.++|     ++..+|.+|+|
T Consensus        93 ~~~GifV~lg------~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~~I~lt~k  166 (179)
T TIGR00448        93 VEFGAFVSLG------PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEGSKIGLTMR  166 (179)
T ss_pred             EeeEEEEEeC------CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCcceEEEEec
Confidence             999999996      59999999999866432           23467999999999999998     56789999999


Q ss_pred             ccccCc
Q 024995          129 QLEEDP  134 (259)
Q Consensus       129 ~~~~~p  134 (259)
                      +.-..|
T Consensus       167 ~~~LG~  172 (179)
T TIGR00448       167 QPLLGK  172 (179)
T ss_pred             cCcCCc
Confidence            865444

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

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=98.71  E-value=7.5e-09  Score=105.01  Aligned_cols=78  Identities=15%  Similarity=0.249  Sum_probs=63.6

Q ss_pred             CCCCccc-cceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995          152 DSSSMSS-SNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---  226 (259)
Q Consensus       152 ~~g~~v~-G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---  226 (259)
                      +.|+++. |+|++|++||    +||+|  .+|++||+ +|++++.          |+   ..+..    ++++||.|   
T Consensus       752 ~vG~iy~~g~V~~I~~FG----aFVeL--~~g~EGLVHISeLs~~----------rv---~~~~d----v~kvGD~V~Vk  808 (891)
T PLN00207        752 TVGDIYRNCEIKSIAPYG----AFVEI--APGREGLCHISELSSN----------WL---AKPED----AFKVGDRIDVK  808 (891)
T ss_pred             CCCcEEECcEEEEEeccE----EEEEe--CCCCEEEEEhhhcCCc----------cc---cCHHH----hcCCCCEEEEE
Confidence            3588894 6999999999    99999  78999999 7888743          22   22223    56999999   


Q ss_pred             -EEEecccchhhhhhchhhhhhhHHhhh
Q 024995          227 -QEIQLSHSLIRKASKRHCNEYWNVFHE  253 (259)
Q Consensus       227 -~~v~~~~~~i~ls~k~~~~~p~~~~~~  253 (259)
                       ++||. +++|+||+|++.++||+.+.+
T Consensus       809 Vi~ID~-~grI~LSlK~l~~~Pw~~~~~  835 (891)
T PLN00207        809 LIEVND-KGQLRLSRRALLPEANSEKSS  835 (891)
T ss_pred             EEEECC-CCcEEEEEeccccCchhhhhh
Confidence             68886 689999999999999998876

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

Probab=98.66  E-value=1.1e-08  Score=89.75  Aligned_cols=77  Identities=14%  Similarity=0.197  Sum_probs=66.4

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      .|+.+-|+|.+|.+||    +|+.|+-.+|++||+ +||++          +.|+++++       ..+|.||.|    +
T Consensus        11 eGEiVv~tV~~V~~~G----Ayv~L~EY~g~Eg~ihiSEva----------s~wVknIr-------d~vkegqkvV~kVl   69 (269)
T COG1093          11 EGEIVVGTVKQVADYG----AYVELDEYPGKEGFIHISEVA----------SGWVKNIR-------DYVKEGQKVVAKVL   69 (269)
T ss_pred             CCcEEEEEEEEeeccc----cEEEeeccCCeeeeEEHHHHH----------HHHHHHHH-------HHhhcCCeEEEEEE
Confidence            3777999999999999    999999889999998 79987          24998765       267999998    8


Q ss_pred             EEecccchhhhhhchhhhhhhHH
Q 024995          228 EIQLSHSLIRKASKRHCNEYWNV  250 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~~~~~p~~~  250 (259)
                      .||++++.|.||||++.++--..
T Consensus        70 rVd~~rg~IDLSlkrV~~~q~~~   92 (269)
T COG1093          70 RVDPKRGHIDLSLKRVTEHQRRK   92 (269)
T ss_pred             EEcCCCCeEeeehhhCCHHHHHH
Confidence            99999999999999988765443

>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=98.64  E-value=3e-08  Score=71.22  Aligned_cols=64  Identities=17%  Similarity=0.187  Sum_probs=49.6

Q ss_pred             CCccc-cceeee-ccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          154 SSMSS-SNSNTI-EPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       154 g~~v~-G~V~~i-~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      |++++ |+|+++ .+||    +|++|  .+|++||+ .|+++.++             ...+..    .+++||.+    
T Consensus         1 G~v~~~g~V~~v~~~~G----~~V~l--~~gv~G~i~~s~l~~~~-------------~~~~~~----~~~vG~~v~~kV   57 (71)
T cd05696           1 GAVVDSVKVTKVEPDLG----AVFEL--KDGLLGFVHISHLSDDK-------------VPSDTG----PFKAGTTHKARI   57 (71)
T ss_pred             CcEeeeeEEEEEccCce----EEEEe--CCCCEEEEEHHHCCcch-------------hcCccc----ccCCCCEEEEEE
Confidence            45678 899998 6999    99988  78999999 57766321             121223    45999999    


Q ss_pred             EEEecccchhhhhh
Q 024995          227 QEIQLSHSLIRKAS  240 (259)
Q Consensus       227 ~~v~~~~~~i~ls~  240 (259)
                      +++|+.+++|+||+
T Consensus        58 ~~id~~~~~i~lS~   71 (71)
T cd05696          58 IGYSPMDGLLQLSL   71 (71)
T ss_pred             EEEeCCCCEEEEeC
Confidence            79999999999985

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.

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

Probab=98.62  E-value=3.7e-08  Score=69.66  Aligned_cols=64  Identities=22%  Similarity=0.421  Sum_probs=49.2

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+.+.|+|.++++||    +|++|  ++|++||+ .++++            |......+..    .+++||.|    ++
T Consensus         1 G~~~~g~V~~i~~~G----~fv~l--~~~~~Glv~~~~l~------------~~~~~~~~~~----~~~~G~~v~v~v~~   58 (69)
T cd05690           1 GTVVSGKIKSITDFG----IFVGL--DGGIDGLVHISDIS------------WTQRVRHPSE----IYKKGQEVEAVVLN   58 (69)
T ss_pred             CCEEEEEEEEEEeee----EEEEe--CCCCEEEEEHHHCC------------CccccCChhh----EECCCCEEEEEEEE
Confidence            456999999999999    99999  78999999 55554            3222222333    55999999    69


Q ss_pred             Eecccchhhhh
Q 024995          229 IQLSHSLIRKA  239 (259)
Q Consensus       229 v~~~~~~i~ls  239 (259)
                      +|.++++|+||
T Consensus        59 id~~~~~i~l~   69 (69)
T cd05690          59 IDVERERISLG   69 (69)
T ss_pred             EECCcCEEeCC
Confidence            99999999875

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.

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=98.59  E-value=4e-08  Score=94.00  Aligned_cols=77  Identities=29%  Similarity=0.457  Sum_probs=70.0

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      ++..|.+|+|+     ++|+||++.     ++..||+|+|+|+..++.+|++.+.+||.|.+|.++.|+ .+.+.+|.|.
T Consensus       665 ~l~~g~vy~~tIt~~rd~G~~V~l~-----p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~-~g~~~ls~ra  738 (760)
T KOG1067|consen  665 DLEFGGVYTATITEIRDTGVMVELY-----PMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSSRA  738 (760)
T ss_pred             ceEeeeEEEEEEeeecccceEEEec-----CCchhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehhhh
Confidence            57778888888     999999998     589999999999999999999999999999999999997 7888888899


Q ss_pred             cccCcchH
Q 024995          130 LEEDPLLE  137 (259)
Q Consensus       130 ~~~~p~~~  137 (259)
                      ++++|-..
T Consensus       739 lLp~p~~~  746 (760)
T KOG1067|consen  739 LLPDPATK  746 (760)
T ss_pred             hcCCcccC
Confidence            99988643

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.59  E-value=1.5e-07  Score=82.91  Aligned_cols=70  Identities=27%  Similarity=0.370  Sum_probs=62.9

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc----cChhhhcCCCCeEEEEEEEEeCCCCeeE
Q 024995           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRIT  124 (259)
Q Consensus        54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~----~~~~~~~~~Gd~V~vkVl~id~~~~ri~  124 (259)
                      ..+++|++|.|+     ++|+||+|+     .+.+|+||++++++.++    .++.+.|++||.|.|+|+++++ .+++.
T Consensus        59 y~P~vGDiViG~V~~i~~~~~~vdI~-----~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~-~~~~~  132 (235)
T PRK04163         59 YIPKVGDLVIGKVTDVTFSGWEVDIN-----SPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDR-TRDVV  132 (235)
T ss_pred             ccCCCCCEEEEEEEEEeCceEEEEeC-----CCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECC-CCcEE
Confidence            466999999999     899999998     47999999999999887    7889999999999999999996 56699


Q ss_pred             EEEec
Q 024995          125 LSIKQ  129 (259)
Q Consensus       125 lS~K~  129 (259)
                      ||+|+
T Consensus       133 LS~k~  137 (235)
T PRK04163        133 LTLKG  137 (235)
T ss_pred             EEEcC
Confidence            99975

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

Probab=98.56  E-value=1.9e-07  Score=79.40  Aligned_cols=126  Identities=21%  Similarity=0.432  Sum_probs=84.6

Q ss_pred             CCCCCCCCCCchhHhhhccc-CCCCEEE-----EEEEEEeC-CCCEEEEEech----hhHhhhccCCCCCCEEEEE----
Q 024995            1 MSPSHSCKEPQKSIHEIAKG-LTGSIIS-----VKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR----   65 (259)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~-~vG~~v~-----~~Vl~id~-~~~~v~lS~k~----~~~~~~~~~l~~G~iv~G~----   65 (259)
                      +.|++|.++....+.+.++. +.|+.+.     +.|++++. ..+++.-.-..    ..+..+.-....|+++.|+    
T Consensus        13 i~P~~~~~~~~~~i~~~l~~~~~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~~GEVv~g~V~~v   92 (187)
T PRK08563         13 IPPEMFGEDLEEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEVVEV   92 (187)
T ss_pred             ECHHHcCccHHHHHHHHHHHHhhCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEeccCCCEEEEEEEEE
Confidence            35777776666655554443 3454432     44455544 33444311111    1133344567899999999    


Q ss_pred             -eeeEEEEEccCCCCccEEEEEEceecCccccc-----------ChhhhcCCCCeEEEEEEEEeCCCC-----eeEEEEe
Q 024995           66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREKS-----RITLSIK  128 (259)
Q Consensus        66 -~~G~fV~l~~~~g~~gi~glv~isels~~~~~-----------~~~~~~~~Gd~V~vkVl~id~~~~-----ri~lS~K  128 (259)
                       ++|+||+++      .++|++|.+++.+.+..           +....+++||.|+++|.+++.+.+     +|.+|+|
T Consensus        93 ~~~Gi~V~lg------~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~~I~ls~~  166 (187)
T PRK08563         93 VEFGAFVRIG------PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRGSKIGLTMR  166 (187)
T ss_pred             EccEEEEEEe------CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCCEEEEEec
Confidence             899999997      59999999999876432           345678999999999999997543     8999998


Q ss_pred             cccc
Q 024995          129 QLEE  132 (259)
Q Consensus       129 ~~~~  132 (259)
                      +.-.
T Consensus       167 ~~~L  170 (187)
T PRK08563        167 QPGL  170 (187)
T ss_pred             CCCC
Confidence            7443

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

Probab=98.56  E-value=1.9e-07  Score=78.29  Aligned_cols=129  Identities=24%  Similarity=0.402  Sum_probs=86.0

Q ss_pred             CCCCCCCCCchhHhhhcc-cCCCCEEE-----EEEEEEeC-CCCEEEEEechh----hHhhhccCCCCCCEEEEE-----
Q 024995            2 SPSHSCKEPQKSIHEIAK-GLTGSIIS-----VKVIQANE-EMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----   65 (259)
Q Consensus         2 ~~~~~~~~p~~~~~~~~~-~~vG~~v~-----~~Vl~id~-~~~~v~lS~k~~----~~~~~~~~l~~G~iv~G~-----   65 (259)
                      .|+.|-.+.+....+.+. .+.|+...     +.|.++.. ..+++...--..    .+..+.-....|+++.|.     
T Consensus        14 pP~~fg~~~~~~v~~~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~   93 (183)
T COG1095          14 PPSYFGEDLEEAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVV   93 (183)
T ss_pred             CHHHcCccHHHHHHHHHHHHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEeccccEEEEEEEEEe
Confidence            566665555555544443 45565543     33344432 345555332211    234445577889999998     


Q ss_pred             eeeEEEEEccCCCCccEEEEEEceecCcccc----------cC-hhhhcCCCCeEEEEEEEEeCCC-----CeeEEEEec
Q 024995           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----------QD-IRDILNEGDEVRVKVIKIDREK-----SRITLSIKQ  129 (259)
Q Consensus        66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~----------~~-~~~~~~~Gd~V~vkVl~id~~~-----~ri~lS~K~  129 (259)
                      +||+||.++      .++||+|++++.++++          .+ ....+++||.|+++|+.+....     .+|.+++|+
T Consensus        94 ~~G~fV~ig------p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~~I~lTmrq  167 (183)
T COG1095          94 EFGAFVRIG------PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMRQ  167 (183)
T ss_pred             ecceEEEec------cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCccccceEEEEecc
Confidence            999999998      6999999999998743          12 2336999999999999998755     578999998


Q ss_pred             ccc--Ccch
Q 024995          130 LEE--DPLL  136 (259)
Q Consensus       130 ~~~--~p~~  136 (259)
                      .-.  -+|.
T Consensus       168 ~~LGklew~  176 (183)
T COG1095         168 PGLGKLEWI  176 (183)
T ss_pred             ccCCcchhh
Confidence            543  4564

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

Probab=98.55  E-value=3e-07  Score=65.19  Aligned_cols=58  Identities=17%  Similarity=0.300  Sum_probs=48.8

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCC--CeeEEE
Q 024995           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITLS  126 (259)
Q Consensus        57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~--~ri~lS  126 (259)
                      +.|++++|+     ++|+||+++      +.+|+||.+|++.      .+.|++||.+++.|++++.++  .+|.||
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig------~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS   66 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLG------KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILS   66 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcC------CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence            468999998     789999997      5999999999873      346899999999999999643  467777

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.

>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=98.54  E-value=5.6e-08  Score=69.02  Aligned_cols=65  Identities=8%  Similarity=0.055  Sum_probs=51.0

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+++.|+|.+++++|    +|++|  .++++||+ .|+++.+          +   ...+..    .+++||.+    ++
T Consensus         1 g~~~~g~V~~v~~~G----~~V~l--~~~~~gli~~s~l~~~----------~---~~~~~~----~~~~G~~i~v~v~~   57 (70)
T cd05698           1 GLKTHGTIVKVKPNG----CIVSF--YNNVKGFLPKSELSEA----------F---IKDPEE----HFRVGQVVKVKVLS   57 (70)
T ss_pred             CCEEEEEEEEEecCc----EEEEE--CCCCEEEEEHHHcChh----------h---cCCHHH----cccCCCEEEEEEEE
Confidence            566999999999999    99999  78899999 5666522          1   122222    56999999    68


Q ss_pred             Eecccchhhhhhc
Q 024995          229 IQLSHSLIRKASK  241 (259)
Q Consensus       229 v~~~~~~i~ls~k  241 (259)
                      +|.+++++.||+|
T Consensus        58 ~d~~~~~i~ls~k   70 (70)
T cd05698          58 CDPEQQRLLLSCK   70 (70)
T ss_pred             EcCCCCEEEEEeC
Confidence            9999999999986

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.

>PRK07252 hypothetical protein; Provisional

Probab=98.51  E-value=8.2e-08  Score=76.09  Aligned_cols=81  Identities=12%  Similarity=0.110  Sum_probs=62.1

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|++|+++|    +|++|  .++++||+ .|+++.+          ++   ..+.    ..+++||.|    
T Consensus         2 kvG~iv~G~V~~V~~~G----~fVei--~~~~~GllhiseLs~~----------~~---~~~~----~~~~vGD~V~VkI   58 (120)
T PRK07252          2 KIGDKLKGTITGIKPYG----AFVAL--ENGTTGLIHISEIKTG----------FI---DNIH----QLLKVGEEVLVQV   58 (120)
T ss_pred             CCCCEEEEEEEEEeCcE----EEEEE--CCCCEEEEEHHHcCCc----------cc---cChh----hccCCCCEEEEEE
Confidence            35888999999999999    99998  78899999 6776632          12   1122    256999999    


Q ss_pred             EEEecccchhhhhhchhhh-hhhHHhhhhc
Q 024995          227 QEIQLSHSLIRKASKRHCN-EYWNVFHETA  255 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~~~-~p~~~~~~~~  255 (259)
                      +++|.++++|.+|+|.+.+ .+|......|
T Consensus        59 ~~iD~~~~ri~lSlk~~~~~~~~~~~~~~~   88 (120)
T PRK07252         59 VDFDEYTGKASLSLRTLEEEKQHFPHRHRF   88 (120)
T ss_pred             EEEeCCCCEEEEEEeecccCccccCccccc
Confidence            6899999999999999887 5565444433

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

Probab=98.50  E-value=1.1e-07  Score=68.18  Aligned_cols=67  Identities=16%  Similarity=0.333  Sum_probs=53.4

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ..|++++|+|.++.++|    +|+.|  ..|++|++ .++++...             .+.+..    .+++||.|    
T Consensus         3 ~~G~iv~g~V~~v~~~g----~~V~l--~~~~~g~ip~~~l~~~~-------------~~~~~~----~~~~G~~v~v~v   59 (74)
T PF00575_consen    3 KEGDIVEGKVTSVEDFG----VFVDL--GNGIEGFIPISELSDDR-------------IDDPSE----VYKIGQTVRVKV   59 (74)
T ss_dssp             STTSEEEEEEEEEETTE----EEEEE--STSSEEEEEGGGSSSSE-------------ESSSHG----TCETTCEEEEEE
T ss_pred             CCCCEEEEEEEEEECCE----EEEEE--CCcEEEEEEeehhcCcc-------------cccccc----ccCCCCEEEEEE
Confidence            35888999999999999    99999  58999999 56666321             122333    45999999    


Q ss_pred             EEEecccchhhhhhc
Q 024995          227 QEIQLSHSLIRKASK  241 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k  241 (259)
                      +++|.+++++.+|+|
T Consensus        60 ~~vd~~~~~i~lS~k   74 (74)
T PF00575_consen   60 IKVDKEKGRIRLSLK   74 (74)
T ss_dssp             EEEETTTTEEEEEST
T ss_pred             EEEECCCCeEEEEEC
Confidence            799999999999987

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 ....

>TIGR02063 RNase_R ribonuclease R

Probab=98.45  E-value=6.7e-07  Score=90.35  Aligned_cols=69  Identities=28%  Similarity=0.549  Sum_probs=59.0

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc-----------cChhhhcCCCCeEEEEEEEEeC
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDR  118 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~-----------~~~~~~~~~Gd~V~vkVl~id~  118 (259)
                      .-+.|+++.|+     +||+||++.+    ++++||+|+++++++++           .+..+.|++||.|+|+|.++|.
T Consensus       624 ~~~iG~~~~g~V~~v~~fGifV~L~~----~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~  699 (709)
T TIGR02063       624 SEKIGEEFEGVISGVTSFGLFVELEN----NTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADL  699 (709)
T ss_pred             hccCCcEEEEEEEEEEeCCEEEEecC----CceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEec
Confidence            45789999999     9999999973    37999999999987643           2345679999999999999999


Q ss_pred             CCCeeEEEE
Q 024995          119 EKSRITLSI  127 (259)
Q Consensus       119 ~~~ri~lS~  127 (259)
                      .+++|.+++
T Consensus       700 ~~~~I~~~l  708 (709)
T TIGR02063       700 DTGKIDFEL  708 (709)
T ss_pred             ccCeEEEEE
Confidence            999999986

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.

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

Probab=98.43  E-value=2.1e-07  Score=66.95  Aligned_cols=70  Identities=14%  Similarity=0.287  Sum_probs=53.4

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      +.|+.+.|+|.++.+||    +|+++...+|++||+ .|+++...          +   .    +....+++||.|    
T Consensus         2 ~~G~~~~g~V~~v~~~g----~~v~l~~~~~~~gll~~s~l~~~~----------~---~----~~~~~~~~Gd~v~vkv   60 (76)
T cd04452           2 EEGELVVVTVKSIADMG----AYVSLLEYGNIEGMILLSELSRRR----------I---R----SIRKLVKVGRKEVVKV   60 (76)
T ss_pred             CCCCEEEEEEEEEEccE----EEEEEcCCCCeEEEEEhHHcCCcc----------c---C----CHHHeeCCCCEEEEEE
Confidence            35788999999999999    999994335799999 67766321          1   1    123356999999    


Q ss_pred             EEEecccchhhhhhch
Q 024995          227 QEIQLSHSLIRKASKR  242 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~  242 (259)
                      .++|.+++++.||+|+
T Consensus        61 ~~~d~~~~~i~ls~k~   76 (76)
T cd04452          61 IRVDKEKGYIDLSKKR   76 (76)
T ss_pred             EEEECCCCEEEEEEcC
Confidence            5888888899999885

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

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

Probab=98.43  E-value=3.8e-07  Score=65.10  Aligned_cols=65  Identities=17%  Similarity=0.318  Sum_probs=49.0

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      +|+.+.|+|.++++||    +|++|  .+|++||+ .+++.            |......+..    .++.||.|    +
T Consensus         3 ~g~~~~g~V~~i~~~G----~fv~l--~~~~~Gl~~~~~l~------------~~~~~~~~~~----~~~~Gd~v~v~v~   60 (72)
T cd05689           3 EGTRLFGKVTNLTDYG----CFVEL--EEGVEGLVHVSEMD------------WTNKNIHPSK----VVSLGDEVEVMVL   60 (72)
T ss_pred             CCCEEEEEEEEEEeeE----EEEEc--CCCCEEEEEEEecc------------CcccccCccc----EeCCCCEEEEEEE
Confidence            4677999999999999    99999  78999999 56654            2111111222    56999999    6


Q ss_pred             EEecccchhhhh
Q 024995          228 EIQLSHSLIRKA  239 (259)
Q Consensus       228 ~v~~~~~~i~ls  239 (259)
                      ++|.++++|.+|
T Consensus        61 ~id~~~~~i~~~   72 (72)
T cd05689          61 DIDEERRRISLG   72 (72)
T ss_pred             EeeCCcCEEeCC
Confidence            889998888775

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.

>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=98.42  E-value=1.8e-07  Score=66.43  Aligned_cols=64  Identities=14%  Similarity=0.148  Sum_probs=49.1

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |++++|+|.++.++|    +|++|  .+|++||+ .+++++..          .   ..+    ...+++||.+    ++
T Consensus         1 G~~v~g~V~~v~~~G----v~V~l--~~~v~g~i~~~~l~~~~----------~---~~~----~~~~~~Gd~i~~~V~~   57 (69)
T cd05697           1 GQVVKGTIRKLRPSG----IFVKL--SDHIKGLVPPMHLADVR----------L---KHP----EKKFKPGLKVKCRVLS   57 (69)
T ss_pred             CCEEEEEEEEEeccE----EEEEe--cCCcEEEEEHHHCCCcc----------c---cCH----HHcCCCCCEEEEEEEE
Confidence            567999999999999    99988  78999999 45655221          1   111    2245999999    79


Q ss_pred             Eecccchhhhhh
Q 024995          229 IQLSHSLIRKAS  240 (259)
Q Consensus       229 v~~~~~~i~ls~  240 (259)
                      +|.++++|.||+
T Consensus        58 id~~~~~i~ls~   69 (69)
T cd05697          58 VEPERKRLVLTL   69 (69)
T ss_pred             EECCCCEEEEEC
Confidence            999999988874

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=98.41  E-value=3.6e-07  Score=65.41  Aligned_cols=67  Identities=7%  Similarity=0.106  Sum_probs=51.7

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|.++.++|    +|++|  ++|++|++ .++++++          |..   .    ....+++||.|    
T Consensus         2 ~~G~iv~g~V~~v~~~g----i~v~l--~~~~~g~v~~s~l~~~----------~~~---~----~~~~~~~Gd~v~~~V   58 (73)
T cd05706           2 KVGDILPGRVTKVNDRY----VLVQL--GNKVTGPSFITDALDD----------YSE---A----LPYKFKKNDIVRACV   58 (73)
T ss_pred             CCCCEEEEEEEEEeCCe----EEEEe--CCCcEEEEEhhhccCc----------ccc---c----cccccCCCCEEEEEE
Confidence            45888999999999999    99988  88999999 5665522          111   1    12256999999    


Q ss_pred             EEEecccchhhhhhc
Q 024995          227 QEIQLSHSLIRKASK  241 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k  241 (259)
                      +++|.+++++.||++
T Consensus        59 ~~~d~~~~~i~ls~~   73 (73)
T cd05706          59 LSVDVPNKKIALSLR   73 (73)
T ss_pred             EEEeCCCCEEEEEEC
Confidence            688888889998875

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.

>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=98.40  E-value=2e-07  Score=67.06  Aligned_cols=67  Identities=9%  Similarity=0.046  Sum_probs=49.2

Q ss_pred             CCCCccccceeeecc-CCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee--E
Q 024995          152 DSSSMSSSNSNTIEP-LPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV--Q  227 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~-~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V--~  227 (259)
                      ++|+++.|+|.++.+ ||    +|++|  .+|.+|++ +|+++++          |..   .+    ...+++||.|  .
T Consensus         2 ~~G~iv~G~V~~i~~~~g----~~v~l--~~~~~Glvhis~~s~~----------~~~---~~----~~~~~~Gd~v~~k   58 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSG----LTVQL--PFGKTGLVSIFHLSDS----------YTE---NP----LEGFKPGKIVRCC   58 (72)
T ss_pred             CCCCEEEEEEEEeeCCcE----EEEEC--CCCCEEEEEHHHhcCc----------ccC---CH----HHhCCCCCEEEEE
Confidence            468889999999986 89    99888  89999999 6777633          222   12    2256999999  2


Q ss_pred             EEecccchhhhhhc
Q 024995          228 EIQLSHSLIRKASK  241 (259)
Q Consensus       228 ~v~~~~~~i~ls~k  241 (259)
                      -++.++++++||+|
T Consensus        59 V~~~~~~~i~LSl~   72 (72)
T cd05704          59 ILSKKDGKYQLSLR   72 (72)
T ss_pred             EEEecCCEEEEEeC
Confidence            23333488999875

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.

>PHA02945 interferon resistance protein; Provisional

Probab=98.40  E-value=3e-07  Score=68.08  Aligned_cols=70  Identities=11%  Similarity=0.199  Sum_probs=58.1

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-Eccc--cccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQ--GFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---  226 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---  226 (259)
                      +|+.+.|+|.. .+||    +|+.|+-.+|.+||+ +|+.  +          +.|+++ +   +    .+ .|+.|   
T Consensus        11 ~GelvigtV~~-~d~g----a~v~L~EY~g~eg~i~~seveva----------~~wvK~-r---d----~l-~GqkvV~K   66 (88)
T PHA02945         11 VGDVLKGKVYE-NGYA----LYIDLFDYPHSEAILAESVQMHM----------NRYFKY-R---D----KL-VGKTVKVK   66 (88)
T ss_pred             CCcEEEEEEEe-cCce----EEEEecccCCcEEEEEeehhhhc----------cceEee-e---e----Ee-cCCEEEEE
Confidence            58889999999 9999    999998889999999 7854  5          238876 3   1    45 99988   


Q ss_pred             -EEEecccchhhhhhchhhhh
Q 024995          227 -QEIQLSHSLIRKASKRHCNE  246 (259)
Q Consensus       227 -~~v~~~~~~i~ls~k~~~~~  246 (259)
                       +.||+.++.|-||+|+..++
T Consensus        67 VirVd~~kg~IDlSlK~V~~~   87 (88)
T PHA02945         67 VIRVDYTKGYIDVNYKRMCRH   87 (88)
T ss_pred             EEEECCCCCEEEeEeeEcccC
Confidence             78899999999999997653

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=98.38  E-value=9.6e-07  Score=64.74  Aligned_cols=69  Identities=25%  Similarity=0.340  Sum_probs=63.1

Q ss_pred             cCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEE-ceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        54 ~~l~~G~iv~G~----~~G~fV~l~~~~g~~gi~glv~-isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      .-.++|+++.|.    +.|+||.|..    ++++|++. .+|++.+++....+.+ +|..+.|+|+++|+++|.|.||.
T Consensus        12 ~~P~v~dvv~~Vv~i~d~~~YV~Lle----Y~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         12 VFPNINEVTKGIVFVKDNIFYVKLID----YGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             ecCCCCeEEEEEEEEeccEEEEEEec----CccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence            456899999877    8999999986    67999998 9999999999999999 99999999999999999999985

>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=98.36  E-value=3.2e-07  Score=67.60  Aligned_cols=66  Identities=12%  Similarity=0.188  Sum_probs=51.1

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+.+.|+|.++.+||    +|++|  .+|++||+ .++++.+          +.   .++.    ..+++||.|    
T Consensus        13 ~~G~i~~g~V~~v~~~G----~fv~l--~~~~~g~v~~~el~~~----------~~---~~~~----~~~~~Gd~v~vkV   69 (83)
T cd04461          13 KPGMVVHGYVRNITPYG----VFVEF--LGGLTGLAPKSYISDE----------FV---TDPS----FGFKKGQSVTAKV   69 (83)
T ss_pred             CCCCEEEEEEEEEeece----EEEEc--CCCCEEEEEHHHCCcc----------cc---cCHH----HhcCCCCEEEEEE
Confidence            35788999999999999    99888  78999999 5666532          11   1222    356999999    


Q ss_pred             EEEecccchhhhhh
Q 024995          227 QEIQLSHSLIRKAS  240 (259)
Q Consensus       227 ~~v~~~~~~i~ls~  240 (259)
                      .++|.++++|.|||
T Consensus        70 ~~id~~~~~i~lsl   83 (83)
T cd04461          70 TSVDEEKQRFLLSL   83 (83)
T ss_pred             EEEcCCCCEEEEeC
Confidence            58888899999886

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.

>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=98.36  E-value=5.6e-07  Score=63.67  Aligned_cols=61  Identities=8%  Similarity=0.069  Sum_probs=47.2

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |++++|+|.++.++|    +|++|  .+|++|++ .++++..          +.     ...+    +++|+.+    +.
T Consensus         1 G~~V~g~V~~i~~~G----~~v~l--~~~v~g~v~~~~l~~~----------~~-----~~~~----~~~G~~i~~kVi~   55 (66)
T cd05695           1 GMLVNARVKKVLSNG----LILDF--LSSFTGTVDFLHLDPE----------KS-----SKST----YKEGQKVRARILY   55 (66)
T ss_pred             CCEEEEEEEEEeCCc----EEEEE--cCCceEEEEHHHcCCc----------cC-----cccC----cCCCCEEEEEEEE
Confidence            566999999999999    99988  67999999 4555411          11     1233    4999999    79


Q ss_pred             Eecccchhhhh
Q 024995          229 IQLSHSLIRKA  239 (259)
Q Consensus       229 v~~~~~~i~ls  239 (259)
                      +|+++++|.||
T Consensus        56 id~~~~~i~LS   66 (66)
T cd05695          56 VDPSTKVVGLS   66 (66)
T ss_pred             EeCCCCEEecC
Confidence            99999998886

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.

>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=98.34  E-value=4.9e-07  Score=63.93  Aligned_cols=63  Identities=17%  Similarity=0.199  Sum_probs=48.4

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+++.|+|+++.++|    +|++|  .++++||+ .++++.+          |..   .+..    .+++||.|    ++
T Consensus         1 G~~v~g~V~~v~~~G----v~V~l--~~~~~G~v~~s~l~~~----------~~~---~~~~----~~~~Gd~v~~~v~~   57 (68)
T cd05707           1 GDVVRGFVKNIANNG----VFVTL--GRGVDARVRVSELSDS----------YLK---DWKK----RFKVGQLVKGKIVS   57 (68)
T ss_pred             CCEEEEEEEEEECcc----EEEEe--CCCCEEEEEHHHCCch----------hhc---CHhh----ccCCCCEEEEEEEE
Confidence            566999999999999    99988  78999999 5666522          222   1222    45999999    68


Q ss_pred             Eecccchhhhh
Q 024995          229 IQLSHSLIRKA  239 (259)
Q Consensus       229 v~~~~~~i~ls  239 (259)
                      +|.++++|.||
T Consensus        58 ~d~~~~~i~ls   68 (68)
T cd05707          58 IDPDNGRIEMT   68 (68)
T ss_pred             EeCCCCEEecC
Confidence            89988888775

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.

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

Probab=98.33  E-value=4.2e-07  Score=64.72  Aligned_cols=67  Identities=13%  Similarity=0.170  Sum_probs=52.1

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+++.|+|+++.++|    +|++|  .++++|++ .++++..          +.   ..    ....+++||.+    ++
T Consensus         1 G~~v~g~V~~v~~~g----~~v~l--~~~~~g~i~~~~~~~~----------~~---~~----~~~~~~~Gd~v~~~v~~   57 (73)
T cd05691           1 GSIVTGKVTEVDAKG----ATVKL--GDGVEGFLRAAELSRD----------RV---ED----ATERFKVGDEVEAKITN   57 (73)
T ss_pred             CCEEEEEEEEEECCe----EEEEe--CCCCEEEEEHHHCCCc----------cc---cC----HHHccCCCCEEEEEEEE
Confidence            566999999999999    99988  78999999 5665522          11   11    22245999999    68


Q ss_pred             Eecccchhhhhhchh
Q 024995          229 IQLSHSLIRKASKRH  243 (259)
Q Consensus       229 v~~~~~~i~ls~k~~  243 (259)
                      +|.+++++.||+|++
T Consensus        58 ~d~~~~~i~ls~k~~   72 (73)
T cd05691          58 VDRKNRKISLSIKAK   72 (73)
T ss_pred             EeCCCCEEEEEEEEc
Confidence            899899999999875

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.

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

Probab=98.32  E-value=6.6e-07  Score=64.42  Aligned_cols=64  Identities=5%  Similarity=0.063  Sum_probs=47.6

Q ss_pred             CCCccccceeeeccCCCccceeeeecccC-CeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~-gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      .|+.+.|+|+++++||    +|++|  .+ +++||+ +|++++..             ...+    ...+++||.|    
T Consensus         3 ~g~~~~g~V~~i~~fG----~fv~l--~~~~~eGlvh~sel~~~~-------------~~~~----~~~~~~Gd~v~vkv   59 (73)
T cd05686           3 LYQIFKGEVASVTEYG----AFVKI--PGCRKQGLVHKSHMSSCR-------------VDDP----SEVVDVGEKVWVKV   59 (73)
T ss_pred             CCCEEEEEEEEEEeee----EEEEE--CCCCeEEEEEchhhCCCc-------------ccCH----hhEECCCCEEEEEE
Confidence            4788999999999999    99998  22 379999 67776321             1222    2356999999    


Q ss_pred             EEEecccchhhhhh
Q 024995          227 QEIQLSHSLIRKAS  240 (259)
Q Consensus       227 ~~v~~~~~~i~ls~  240 (259)
                      +++|.++ +|+||+
T Consensus        60 ~~vd~~~-ki~ls~   72 (73)
T cd05686          60 IGREMKD-KMKLSL   72 (73)
T ss_pred             EEECCCC-cEEEEe
Confidence            5778876 888876

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.

>PRK11642 exoribonuclease R; Provisional

Probab=98.31  E-value=2.1e-06  Score=87.70  Aligned_cols=69  Identities=29%  Similarity=0.518  Sum_probs=59.4

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc-----------ChhhhcCCCCeEEEEEEEEeCCC
Q 024995           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREK  120 (259)
Q Consensus        57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~-----------~~~~~~~~Gd~V~vkVl~id~~~  120 (259)
                      ++|+++.|+     +||+||+|..    .+++||||+++|+++++.           +....|++||.|+|+|.++|.++
T Consensus       642 ~iGe~f~G~Is~V~~fGifVeL~~----~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~  717 (813)
T PRK11642        642 QVGNVFKGVISSVTGFGFFVRLDD----LFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDE  717 (813)
T ss_pred             cCCcEEEEEEEEeecCceEEEECC----CCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCC
Confidence            789999999     9999999973    369999999999876432           23467999999999999999999


Q ss_pred             CeeEEEEec
Q 024995          121 SRITLSIKQ  129 (259)
Q Consensus       121 ~ri~lS~K~  129 (259)
                      ++|.|++..
T Consensus       718 rkI~f~l~~  726 (813)
T PRK11642        718 RKIDFSLIS  726 (813)
T ss_pred             CeEEEEEec
Confidence            999999854

>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=98.31  E-value=5.8e-07  Score=65.53  Aligned_cols=71  Identities=17%  Similarity=0.182  Sum_probs=52.4

Q ss_pred             CCccccceeeeccCCCccceeeeeccc-CCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~-~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      |+++.|+|+++++||    +|++|... +|++||+ .++++++          |.  ...+.    ..+++||.|    .
T Consensus         1 G~~~~g~V~~v~~~G----~fv~l~~~~~~~~gll~~s~l~~~----------~~--~~~~~----~~~~~Gd~v~v~v~   60 (79)
T cd05684           1 GKIYKGKVTSIMDFG----CFVQLEGLKGRKEGLVHISQLSFE----------GR--VANPS----DVVKRGQKVKVKVI   60 (79)
T ss_pred             CCEEEEEEEEEEeee----EEEEEeCCCCCcEEEEEhHhccCC----------CC--cCChh----heeCCCCEEEEEEE
Confidence            456899999999999    99999322 4799999 6776633          21  12222    256999999    5


Q ss_pred             EEecccchhhhhhchhhhh
Q 024995          228 EIQLSHSLIRKASKRHCNE  246 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~~~~~  246 (259)
                      ++|  ++++.+|+|++.++
T Consensus        61 ~vd--~~~i~~s~k~~~~~   77 (79)
T cd05684          61 SIQ--NGKISLSMKDVDQD   77 (79)
T ss_pred             EEe--CCEEEEEEEecccC
Confidence            777  78999999998764

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.

>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=98.29  E-value=5e-07  Score=69.34  Aligned_cols=79  Identities=15%  Similarity=0.119  Sum_probs=56.6

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-Eccccccccccchhhhhhccc---------CCCCCcceeeecc
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSN---------APPSGKKFTLLAR  221 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~r  221 (259)
                      ++|+++.|+|.++.++|    +|+.|  ++|++|++ .++++++       +..|+..         ...........++
T Consensus         2 ~~G~vV~G~V~~v~~~g----l~v~L--~~g~~G~v~~seis~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~f~   68 (100)
T cd05693           2 SEGMLVLGQVKEITKLD----LVISL--PNGLTGYVPITNISDA-------YTERLEELDEESEEEDDEEELPDLEDLFS   68 (100)
T ss_pred             CCCCEEEEEEEEEcCCC----EEEEC--CCCcEEEEEHHHhhHH-------HHHHHHHhhhhccccccccccCCHHHhcc
Confidence            46888999999999999    99888  88999999 6777632       2223221         0011112334669


Q ss_pred             CCCee----EEEecc---cchhhhhhchh
Q 024995          222 AGRQV----QEIQLS---HSLIRKASKRH  243 (259)
Q Consensus       222 ~G~~V----~~v~~~---~~~i~ls~k~~  243 (259)
                      +||.|    +.++.+   +++|.||+|.-
T Consensus        69 vGd~V~~kVi~~d~~~~~~~~i~LSlr~~   97 (100)
T cd05693          69 VGQLVRCKVVSLDKSKSGKKRIELSLEPE   97 (100)
T ss_pred             CCCEEEEEEEEccCCcCCCcEEEEEecHH
Confidence            99999    688887   67899999964

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.

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

Probab=98.28  E-value=2.7e-06  Score=85.22  Aligned_cols=68  Identities=26%  Similarity=0.485  Sum_probs=58.3

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc-----------cChhhhcCCCCeEEEEEEEEeCC
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDRE  119 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~-----------~~~~~~~~~Gd~V~vkVl~id~~  119 (259)
                      -+.|++++|+     +||+||+|..    .+++||||++++.++++           .+....|++||.|+|+|.++|.+
T Consensus       570 ~~iG~~~~g~I~~v~~~GifV~L~~----~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~  645 (654)
T TIGR00358       570 DKVGTEFSGEISSVTRFGMFVRLDD----NGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNME  645 (654)
T ss_pred             hCCCcEEEEEEEeEEcCcEEEEecC----CceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecc
Confidence            3679999999     9999999973    58999999999998742           22346799999999999999999


Q ss_pred             CCeeEEEE
Q 024995          120 KSRITLSI  127 (259)
Q Consensus       120 ~~ri~lS~  127 (259)
                      +++|.+++
T Consensus       646 ~~~I~f~l  653 (654)
T TIGR00358       646 TRSIIFEL  653 (654)
T ss_pred             cCeEEEEE
Confidence            99999985

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.

>PRK05807 hypothetical protein; Provisional

Probab=98.27  E-value=8.8e-07  Score=71.69  Aligned_cols=68  Identities=15%  Similarity=0.176  Sum_probs=53.5

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      .+|++++|+|+.+++||    +||+|   +|..||+ +|+++..          |+..       +...+++||.|    
T Consensus         4 ~vG~vv~G~Vt~i~~~G----afV~L---~~~~Glvhiseis~~----------~v~~-------~~~~~kvGd~V~VkV   59 (136)
T PRK05807          4 KAGSILEGTVVNITNFG----AFVEV---EGKTGLVHISEVADT----------YVKD-------IREHLKEQDKVKVKV   59 (136)
T ss_pred             cCCCEEEEEEEEEECCe----EEEEE---CCEEEEEEhhhcccc----------cccC-------ccccCCCCCEEEEEE
Confidence            35788999999999999    99988   5789999 7777632          3322       22356999999    


Q ss_pred             EEEecccchhhhhhchhh
Q 024995          227 QEIQLSHSLIRKASKRHC  244 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~~  244 (259)
                      ++++. .++|+||+|++.
T Consensus        60 ~~id~-~gkI~LSlk~~~   76 (136)
T PRK05807         60 ISIDD-NGKISLSIKQAM   76 (136)
T ss_pred             EEECC-CCcEEEEEEecc
Confidence            56776 689999999986

>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=98.24  E-value=1.1e-06  Score=63.16  Aligned_cols=68  Identities=13%  Similarity=0.192  Sum_probs=52.7

Q ss_pred             CCCccccceeeeccCCCccceeeeeccc-CCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~-~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      +|+.+.|+|.+++++|    +|++|  . .+++|++ .++++.+.          .   ..    ....+++||.|    
T Consensus         2 ~g~~v~g~V~~i~~~g----~~v~l--~~~~~~g~i~~~~l~~~~----------~---~~----~~~~~~~Gd~v~v~i   58 (77)
T cd05708           2 VGQKIDGTVRRVEDYG----VFIDI--DGTNVSGLCHKSEISDNR----------V---AD----ASKLFRVGDKVRAKV   58 (77)
T ss_pred             CCCEEEEEEEEEEcce----EEEEE--CCCCeEEEEEHHHCCCCc----------c---CC----HhHeecCCCEEEEEE
Confidence            4788999999999999    99998  4 3799999 56665321          1   11    22356999999    


Q ss_pred             EEEecccchhhhhhchh
Q 024995          227 QEIQLSHSLIRKASKRH  243 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~  243 (259)
                      .+++.+++++.+++|+.
T Consensus        59 ~~vd~~~~~i~ls~k~~   75 (77)
T cd05708          59 LKIDAEKKRISLGLKAS   75 (77)
T ss_pred             EEEeCCCCEEEEEEEee
Confidence            68899999999999874

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.

>PRK08059 general stress protein 13; Validated

Probab=98.23  E-value=9.3e-07  Score=70.27  Aligned_cols=73  Identities=12%  Similarity=0.195  Sum_probs=57.8

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|.++.++|    +|++|  .++++|++ .++++.+          |.   ..    ....+++||.|    
T Consensus         6 k~G~iv~G~V~~i~~~G----~fV~i--~~~~~Gli~~sel~~~----------~~---~~----~~~~~~vGD~I~vkI   62 (123)
T PRK08059          6 EVGSVVTGKVTGIQPYG----AFVAL--DEETQGLVHISEITHG----------FV---KD----IHDFLSVGDEVKVKV   62 (123)
T ss_pred             CCCCEEEEEEEEEecce----EEEEE--CCCCEEEEEHHHCCcc----------cc---cC----HHHcCCCCCEEEEEE
Confidence            35778999999999999    99988  78999999 5666522          11   11    12256999999    


Q ss_pred             EEEecccchhhhhhchhhhhh
Q 024995          227 QEIQLSHSLIRKASKRHCNEY  247 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~~~~p  247 (259)
                      .++|.+++++.+|+|++..+|
T Consensus        63 ~~id~~~~~i~lslk~~~~~~   83 (123)
T PRK08059         63 LSVDEEKGKISLSIRATEEAP   83 (123)
T ss_pred             EEEECCCCeEEEEEEEcccCc
Confidence            588888999999999998888

>TIGR01953 NusA transcription termination factor NusA

Probab=98.23  E-value=1.9e-06  Score=79.80  Aligned_cols=98  Identities=16%  Similarity=0.273  Sum_probs=72.5

Q ss_pred             cccCCCCEEEEEEEEEeCCCCEEEEEe-ch--------hhHhhhccCC--CCCCEEEEE-----eee-EEEEEccCCCCc
Q 024995           18 AKGLTGSIISVKVIQANEEMKKLVFSE-KD--------AVWNKYSSRV--NVEDIFVGR-----DYG-AFIHLRFPDGLY   80 (259)
Q Consensus        18 ~~~~vG~~v~~~Vl~id~~~~~v~lS~-k~--------~~~~~~~~~l--~~G~iv~G~-----~~G-~fV~l~~~~g~~   80 (259)
                      .+..+|+++++.|...+  -++..++. |+        ..++.++..+  +.|++++|+     +.| +||+++      
T Consensus        82 ~~~~vGD~I~~~I~~~~--fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG------  153 (341)
T TIGR01953        82 PDVQIGDEVKKEIPPEN--FGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG------  153 (341)
T ss_pred             cccccCCEEEEEecccC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC------
Confidence            44569999999874333  24444443 32        1244566666  599999999     556 699997      


Q ss_pred             cEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCC--CCeeEEEEec
Q 024995           81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDRE--KSRITLSIKQ  129 (259)
Q Consensus        81 gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~--~~ri~lS~K~  129 (259)
                      +++|++|.+|..      |.+.|++||.++|.|++++..  ..+|.||++.
T Consensus       154 ~~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~  198 (341)
T TIGR01953       154 KTEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTH  198 (341)
T ss_pred             CeEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence            799999999987      345699999999999999954  3579999865

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.

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]

Probab=98.23  E-value=1.1e-05  Score=71.53  Aligned_cols=96  Identities=14%  Similarity=0.206  Sum_probs=76.4

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechhh-HhhhccCCCC---CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC
Q 024995           22 TGSIISVKVIQANEEMKKLVFSEKDAV-WNKYSSRVNV---EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (259)
Q Consensus        22 vG~~v~~~Vl~id~~~~~v~lS~k~~~-~~~~~~~l~~---G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels   92 (259)
                      +||.+-|. +.+|+++ |+...++... .+........   ++.+.|+     ..|.||-+.     .+.-||||-||..
T Consensus       117 ~Gd~l~v~-l~~Dkk~-Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e-----~~~~GfIh~sEr~  189 (287)
T COG2996         117 KGDKLLVY-LYVDKKG-RIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITE-----NGYLGFIHKSERF  189 (287)
T ss_pred             CCCEEEEE-EEEccCC-cEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEc-----CCeEEEEcchhhc
Confidence            89999999 8999764 8888877643 4444444444   8888888     789999997     3899999999863


Q ss_pred             cccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccC
Q 024995           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED  133 (259)
Q Consensus        93 ~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~  133 (259)
                              ..++.|+.+.++|+.+.. .++|.||++....+
T Consensus       190 --------~~prlG~~l~~rVi~~re-Dg~lnLSl~p~~~E  221 (287)
T COG2996         190 --------AEPRLGERLTARVIGVRE-DGKLNLSLRPRAHE  221 (287)
T ss_pred             --------ccccCCceEEEEEEEEcc-CCeeecccccccHH
Confidence                    236789999999999996 89999999876443

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.22  E-value=1.6e-06  Score=80.85  Aligned_cols=98  Identities=16%  Similarity=0.243  Sum_probs=71.1

Q ss_pred             cccCCCCEEEEEEEEEeCCCCEEEEEechh--------hHhhhccCC--CCCCEEEEE-----eeeEEEEEccCCCCccE
Q 024995           18 AKGLTGSIISVKVIQANEEMKKLVFSEKDA--------VWNKYSSRV--NVEDIFVGR-----DYGAFIHLRFPDGLYHL   82 (259)
Q Consensus        18 ~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~--------~~~~~~~~l--~~G~iv~G~-----~~G~fV~l~~~~g~~gi   82 (259)
                      .+..+|+.+.+.+...+-. +....+.|+.        .++..+..+  +.|+++.|+     ++|+||+++      ++
T Consensus        85 ~~~~vGD~i~~~I~~~~fg-R~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg------~v  157 (362)
T PRK12327         85 PAYELGDVIEIEVTPKDFG-RIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG------KI  157 (362)
T ss_pred             ccccCCCEEEEecCcCCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC------Ce
Confidence            3456899999886544322 2222222221        244566777  999999999     789999997      79


Q ss_pred             EEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCC--eeEEEEe
Q 024995           83 TGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIK  128 (259)
Q Consensus        83 ~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~--ri~lS~K  128 (259)
                      +||||.+++..      .+.|++||.++|.|++++.+++  +|.||+.
T Consensus       158 Ea~LP~~E~ip------~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt  199 (362)
T PRK12327        158 EAVLPPAEQIP------GETYKHGDRIKVYVVKVEKTTKGPQIFVSRT  199 (362)
T ss_pred             EEEecHHHcCC------CCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence            99999888743      5679999999999999996544  5777763

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

Probab=98.19  E-value=5.7e-06  Score=62.50  Aligned_cols=73  Identities=22%  Similarity=0.276  Sum_probs=56.8

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCC---CccEEEEEEceecCccccc--ChhhhcCCCCeEEEEEEEEeCCCCeeEE
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRITL  125 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g---~~gi~glv~isels~~~~~--~~~~~~~~Gd~V~vkVl~id~~~~ri~l  125 (259)
                      +++|+++.|+     ...++|++...++   .....|++|++++...+..  ++.+.|++||.|+|+|++++. .+.+.|
T Consensus         4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~~~L   82 (92)
T cd05791           4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASSYYL   82 (92)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCCcEE
Confidence            5788888888     5568888821111   0367999999999877665  788999999999999999985 577889


Q ss_pred             EEec
Q 024995          126 SIKQ  129 (259)
Q Consensus       126 S~K~  129 (259)
                      |+++
T Consensus        83 st~~   86 (92)
T cd05791          83 STAE   86 (92)
T ss_pred             EecC
Confidence            9875

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".

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

Probab=98.17  E-value=1.5e-06  Score=77.67  Aligned_cols=74  Identities=15%  Similarity=0.223  Sum_probs=58.5

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      +|+.+.|+|.++.+||    +|++|...+|++||+ .|+++..          |+..       ....+++||.|    +
T Consensus         8 ~GdiV~G~V~~I~~~G----~fV~L~e~~gieGlI~iSEls~~----------~i~~-------i~~~~kvGd~V~vkVi   66 (262)
T PRK03987          8 EGELVVGTVKEVKDFG----AFVTLDEYPGKEGFIHISEVASG----------WVKN-------IRDHVKEGQKVVCKVI   66 (262)
T ss_pred             CCCEEEEEEEEEECCE----EEEEECCCCCcEEEEEHHHcCcc----------cccC-------HHHhCCCCCEEEEEEE
Confidence            5788999999999999    999995435999999 6777632          3322       12256999999    6


Q ss_pred             EEecccchhhhhhchhhhhh
Q 024995          228 EIQLSHSLIRKASKRHCNEY  247 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~~~~~p  247 (259)
                      ++|.++++|.||+|++.++-
T Consensus        67 ~VD~~k~~I~LSlK~v~~~e   86 (262)
T PRK03987         67 RVDPRKGHIDLSLKRVNEHQ   86 (262)
T ss_pred             EEecccCeEEEEEEecccch
Confidence            89999999999999887654

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

Probab=98.06  E-value=3.3e-06  Score=58.93  Aligned_cols=64  Identities=20%  Similarity=0.321  Sum_probs=47.4

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+++.|+|.+++++|    +|+.+  .++++||+ .++++.+.          .   ..+.    ..+++||.+    .+
T Consensus         1 G~~~~g~V~~i~~~g----~~v~i--~~~~~g~l~~~~l~~~~----------~---~~~~----~~~~~Gd~v~v~v~~   57 (69)
T cd05692           1 GSVVEGTVTRLKPFG----AFVEL--GGGISGLVHISQIAHKR----------V---KDVK----DVLKEGDKVKVKVLS   57 (69)
T ss_pred             CCEEEEEEEEEEeee----EEEEE--CCCCEEEEEhHHcCCcc----------c---CCHH----HccCCCCEEEEEEEE
Confidence            566999999999999    99988  78999999 56665321          1   1122    245999999    46


Q ss_pred             Eecccchhhhhhc
Q 024995          229 IQLSHSLIRKASK  241 (259)
Q Consensus       229 v~~~~~~i~ls~k  241 (259)
                      ++. .+++.||+|
T Consensus        58 ~~~-~~~i~ls~k   69 (69)
T cd05692          58 IDA-RGRISLSIK   69 (69)
T ss_pred             ECC-CCcEEEEEC
Confidence            776 678888875

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.

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

Probab=98.02  E-value=5.1e-06  Score=58.88  Aligned_cols=65  Identities=5%  Similarity=0.053  Sum_probs=49.2

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+++.|+|.++.++|    +|++|  ..+++|++ .++++...             ...    +...+++||.+    ++
T Consensus         1 G~iv~g~V~~i~~~~----~~v~l--~~~~~g~l~~~e~~~~~-------------~~~----~~~~~~~Gd~i~~~i~~   57 (70)
T cd05687           1 GDIVKGTVVSVDDDE----VLVDI--GYKSEGIIPISEFSDDP-------------IEN----GEDEVKVGDEVEVYVLR   57 (70)
T ss_pred             CCEEEEEEEEEeCCE----EEEEe--CCCceEEEEHHHhCccc-------------cCC----HhHcCCCCCEEEEEEEE
Confidence            567999999999999    99888  77899999 56655221             111    22356999999    68


Q ss_pred             Eecccchhhhhhc
Q 024995          229 IQLSHSLIRKASK  241 (259)
Q Consensus       229 v~~~~~~i~ls~k  241 (259)
                      ++.+..+|.||+|
T Consensus        58 ~~~~~~~i~lS~~   70 (70)
T cd05687          58 VEDEEGNVVLSKR   70 (70)
T ss_pred             EECCCCeEEEEeC
Confidence            8877788988875

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.01  E-value=4.7e-06  Score=83.37  Aligned_cols=68  Identities=12%  Similarity=0.065  Sum_probs=51.2

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ..|+++.|+|++|++||    +|++|  .+|++||+ +|+++.        + .|..++.++    ..++++||.|    
T Consensus       646 ~vG~i~~GkV~~I~dfG----aFVel--~~G~eGLvHISeisd--------l-s~~~rv~~~----~dv~kvGd~V~VKV  706 (719)
T TIGR02696       646 EVGERFLGTVVKTTAFG----AFVSL--LPGKDGLLHISQIRK--------L-AGGKRVENV----EDVLSVGQKIQVEI  706 (719)
T ss_pred             CCCCEEEEEEEEEECce----EEEEe--cCCceEEEEhhhccc--------c-ccccCcCCH----HHcCCCCCEEEEEE
Confidence            46888999999999999    99998  79999999 677751        1 133333433    3367999999    


Q ss_pred             EEEecccchhhhh
Q 024995          227 QEIQLSHSLIRKA  239 (259)
Q Consensus       227 ~~v~~~~~~i~ls  239 (259)
                      ++||. ++||+|+
T Consensus       707 l~ID~-~gKI~L~  718 (719)
T TIGR02696       707 ADIDD-RGKLSLV  718 (719)
T ss_pred             EEECC-CCCeeec
Confidence            67773 6788875

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.

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

Probab=98.00  E-value=4.5e-06  Score=61.69  Aligned_cols=72  Identities=6%  Similarity=0.034  Sum_probs=51.6

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|.++.++|    +++++  .++++|++ .|+++..+      .+.+.       ......+++||.+    
T Consensus         5 ~~GdiV~g~V~~i~~~g----~~v~i--~~~~~G~l~~se~~~~~------~~~~~-------~~~~~~l~vGd~i~~~V   65 (86)
T cd05789           5 EVGDVVIGRVTEVGFKR----WKVDI--NSPYDAVLPLSEVNLPR------TDEDE-------LNMRSYLDEGDLIVAEV   65 (86)
T ss_pred             CCCCEEEEEEEEECCCE----EEEEC--CCCeEEEEEHHHccCCC------Cccch-------HHHHhhCCCCCEEEEEE
Confidence            46888999999999999    99888  78999999 56655210      00011       1122356999999    


Q ss_pred             EEEecccchhhhhhchh
Q 024995          227 QEIQLSHSLIRKASKRH  243 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~  243 (259)
                      ++++.+ +++.||+|+.
T Consensus        66 ~~~~~~-~~i~LS~~~~   81 (86)
T cd05789          66 QSVDSD-GSVSLHTRSL   81 (86)
T ss_pred             EEECCC-CCEEEEeCcc
Confidence            577665 7899999874

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".

>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=97.97  E-value=7.2e-06  Score=57.05  Aligned_cols=63  Identities=13%  Similarity=0.143  Sum_probs=46.9

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+.+.|+|++++++|    +|+++  .+++.|++ .++++.+          |..   .+    ...+++||.+    ++
T Consensus         1 g~~~~g~V~~i~~~G----~fv~l--~~~~~g~~~~~~l~~~----------~~~---~~----~~~~~~Gd~v~v~i~~   57 (68)
T cd05685           1 GMVLEGVVTNVTDFG----AFVDI--GVKQDGLIHISKMADR----------FVS---HP----SDVVSVGDIVEVKVIS   57 (68)
T ss_pred             CCEEEEEEEEEeccc----EEEEc--CCCCEEEEEHHHCCCc----------ccc---CH----HHhcCCCCEEEEEEEE
Confidence            456899999999999    99888  78899999 5555422          221   11    2245999999    68


Q ss_pred             Eecccchhhhh
Q 024995          229 IQLSHSLIRKA  239 (259)
Q Consensus       229 v~~~~~~i~ls  239 (259)
                      +|.+++++.||
T Consensus        58 vd~~~~~i~ls   68 (68)
T cd05685          58 IDEERGRISLS   68 (68)
T ss_pred             EECCCCEEecC
Confidence            88888888765

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.

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

Probab=97.92  E-value=1.5e-05  Score=58.04  Aligned_cols=75  Identities=13%  Similarity=0.130  Sum_probs=49.3

Q ss_pred             CCccccceeeeccCCCccceeeeecccC-CeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~-gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      |+.++|+|++++++|    +|++|  .+ |++|++ .+++..+.-  ..+-..|......    ....+++||.|    .
T Consensus         2 g~~~~g~V~~v~~~G----~fv~l--~~~~~~G~v~~~~l~~~~~--~~d~~~~~~~~~~----~~~~~~~gd~v~v~v~   69 (83)
T cd04471           2 GEEFDGVISGVTSFG----LFVEL--DNLTVEGLVHVSTLGDDYY--EFDEENHALVGER----TGKVFRLGDKVKVRVV   69 (83)
T ss_pred             CCEEEEEEEeEEeee----EEEEe--cCCCEEEEEEEEecCCCcE--EEcccceEEEecc----CCCEEcCCCEEEEEEE
Confidence            667999999999999    99999  66 899999 666552210  0000000001111    12356999999    6


Q ss_pred             EEecccchhhhhh
Q 024995          228 EIQLSHSLIRKAS  240 (259)
Q Consensus       228 ~v~~~~~~i~ls~  240 (259)
                      ++|.++++|.+++
T Consensus        70 ~vd~~~~~i~~~l   82 (83)
T cd04471          70 RVDLDRRKIDFEL   82 (83)
T ss_pred             EeccccCEEEEEE
Confidence            8888888888775

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.

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

Probab=97.91  E-value=1e-05  Score=56.93  Aligned_cols=62  Identities=8%  Similarity=0.161  Sum_probs=46.4

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |++++|+|.++.++|    +|+++   +|++||+ .|+++...          .   ..+..      .+||.+    ++
T Consensus         1 G~iv~g~V~~v~~~G----~~v~l---~g~~gfip~s~~~~~~----------~---~~~~~------~vG~~i~~~i~~   54 (67)
T cd04465           1 GEIVEGKVTEKVKGG----LIVDI---EGVRAFLPASQVDLRP----------V---EDLDE------YVGKELKFKIIE   54 (67)
T ss_pred             CCEEEEEEEEEECCe----EEEEE---CCEEEEEEHHHCCCcc----------c---CChHH------hCCCEEEEEEEE
Confidence            566999999999999    99888   6899999 56665221          1   11111      478888    79


Q ss_pred             Eecccchhhhhhc
Q 024995          229 IQLSHSLIRKASK  241 (259)
Q Consensus       229 v~~~~~~i~ls~k  241 (259)
                      +|.++++|.||.|
T Consensus        55 vd~~~~~i~lS~k   67 (67)
T cd04465          55 IDRERNNIVLSRR   67 (67)
T ss_pred             EeCCCCEEEEEcC
Confidence            9998899999875

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.88  E-value=1.3e-05  Score=80.87  Aligned_cols=69  Identities=20%  Similarity=0.216  Sum_probs=55.3

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|+++.+||    +|++|  .+|++||+ +|+++++.          +   ..+.    ..+++||.|    
T Consensus       620 ~vG~v~~G~V~~I~~fG----afVei--~~~~~GllhiSels~~~----------v---~~~~----~v~kvGD~V~VkV  676 (693)
T PRK11824        620 EVGEIYEGKVVRIVDFG----AFVEI--LPGKDGLVHISEIADER----------V---EKVE----DVLKEGDEVKVKV  676 (693)
T ss_pred             cCCeEEEEEEEEEECCe----EEEEE--CCCCEEEEEeeeccCcc----------c---cCcc----ceeCCCCEEEEEE
Confidence            56889999999999999    99999  78999999 78877331          2   2222    366999999    


Q ss_pred             EEEecccchhhhhhchhh
Q 024995          227 QEIQLSHSLIRKASKRHC  244 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~~  244 (259)
                      +++|.+ ++|+||+|.+.
T Consensus       677 ~~iD~~-grI~LS~k~~~  693 (693)
T PRK11824        677 LEIDKR-GRIRLSRKAVL  693 (693)
T ss_pred             EEECCC-CcEEEEEEecC
Confidence            678877 89999999763

>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=97.87  E-value=1.2e-05  Score=70.68  Aligned_cols=80  Identities=26%  Similarity=0.456  Sum_probs=71.5

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecc
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~  130 (259)
                      ..++++|-+.     +.|+||.|-.|+   .++|++-.||||..++....+..++|..=.|.|+++|+++|.|.||.+.+
T Consensus        14 Pev~e~VmvnV~sIaemGayv~LlEYn---niEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrV   90 (304)
T KOG2916|consen   14 PEVEEIVMVNVRSIAEMGAYVKLLEYN---NIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRV   90 (304)
T ss_pred             CCcccEEEEEeeEehhccceEeeeecC---CcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccC
Confidence            5778888777     899999998766   69999999999999999999999999999999999999999999999998


Q ss_pred             ccCcchHh
Q 024995          131 EEDPLLET  138 (259)
Q Consensus       131 ~~~p~~~~  138 (259)
                      .++.-.+.
T Consensus        91 s~ed~~kC   98 (304)
T KOG2916|consen   91 SPEDKEKC   98 (304)
T ss_pred             CHHHHHHH
Confidence            87655443

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

Probab=97.78  E-value=2.4e-05  Score=54.59  Aligned_cols=63  Identities=17%  Similarity=0.194  Sum_probs=46.3

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+.+.|+|.++.+||    +|+++  .+++.||+ .++++..          |+.   .+.    ..+++||.|    .+
T Consensus         1 g~~~~g~V~~v~~~G----~~v~l--~~~~~g~l~~~~l~~~----------~~~---~~~----~~~~~Gd~v~v~v~~   57 (68)
T cd04472           1 GKIYEGKVVKIKDFG----AFVEI--LPGKDGLVHISELSDE----------RVE---KVE----DVLKVGDEVKVKVIE   57 (68)
T ss_pred             CCEEEEEEEEEEEeE----EEEEe--CCCCEEEEEhHHcCCc----------ccc---CHH----HccCCCCEEEEEEEE
Confidence            456899999999999    99988  67899999 5665522          121   111    256999999    57


Q ss_pred             Eecccchhhhhh
Q 024995          229 IQLSHSLIRKAS  240 (259)
Q Consensus       229 v~~~~~~i~ls~  240 (259)
                      +|. ++++.+|+
T Consensus        58 ~d~-~~~i~ls~   68 (68)
T cd04472          58 VDD-RGRISLSR   68 (68)
T ss_pred             ECC-CCcEEeeC
Confidence            787 77887774

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.

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

Probab=97.73  E-value=4.5e-05  Score=53.11  Aligned_cols=62  Identities=16%  Similarity=0.283  Sum_probs=46.3

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+.+.|+|.++.++|    +|+++  . +++|++ .++++..            . ...+.    ..+++||.|    .+
T Consensus         2 g~~~~g~V~~v~~~g----~~v~l--~-~~~g~l~~~e~~~~------------~-~~~~~----~~~~~Gd~v~v~i~~   57 (68)
T cd05688           2 GDVVEGTVKSITDFG----AFVDL--G-GVDGLLHISDMSWG------------R-VKHPS----EVVNVGDEVEVKVLK   57 (68)
T ss_pred             CCEEEEEEEEEEeee----EEEEE--C-CeEEEEEhHHCCCc------------c-ccCHh----HEECCCCEEEEEEEE
Confidence            677999999999999    99988  3 799999 5554411            1 11122    256999999    68


Q ss_pred             Eecccchhhhh
Q 024995          229 IQLSHSLIRKA  239 (259)
Q Consensus       229 v~~~~~~i~ls  239 (259)
                      +|.+++++.||
T Consensus        58 vd~~~~~i~ls   68 (68)
T cd05688          58 IDKERKRISLG   68 (68)
T ss_pred             EECCCCEEecC
Confidence            88888888775

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.

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

Probab=97.72  E-value=3.4e-05  Score=53.58  Aligned_cols=66  Identities=15%  Similarity=0.232  Sum_probs=49.7

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      +|+.+.|+|.++.++|    +|+++  .+++.|++ .+++...          +   ..    +....+++||.+    .
T Consensus         2 ~G~~v~g~V~~v~~~g----~~v~i--~~~~~g~l~~~~~~~~----------~---~~----~~~~~~~~G~~v~~~V~   58 (72)
T smart00316        2 VGDVVEGTVTEITPFG----AFVDL--GNGVEGLIPISELSDK----------R---VK----DPEEVLKVGDEVKVKVL   58 (72)
T ss_pred             CCCEEEEEEEEEEccE----EEEEe--CCCCEEEEEHHHCCcc----------c---cC----CHHHeecCCCEEEEEEE
Confidence            4788999999999999    99888  77999999 5555522          1   11    122256999999    6


Q ss_pred             EEecccchhhhhhc
Q 024995          228 EIQLSHSLIRKASK  241 (259)
Q Consensus       228 ~v~~~~~~i~ls~k  241 (259)
                      .++.+++++.+|++
T Consensus        59 ~~~~~~~~i~ls~~   72 (72)
T smart00316       59 SVDEEKGRIILSLK   72 (72)
T ss_pred             EEeCCCCEEEEEeC
Confidence            88888888888764

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

Probab=97.70  E-value=3.4e-05  Score=57.74  Aligned_cols=54  Identities=11%  Similarity=0.158  Sum_probs=39.6

Q ss_pred             CCCccccceeeeccC--CCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee
Q 024995          153 SSSMSSSNSNTIEPL--PGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV  226 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~--G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V  226 (259)
                      .|+++.|+|+++.+|  |    +|++|  .+|.+||+ .|++++..          ..++.+    ....+++||.|
T Consensus         7 ~G~iy~g~V~~i~~~~~G----aFV~l--~~g~~Gllh~seis~~~----------~~~v~~----~~~~~~~Gd~v   63 (88)
T cd04453           7 VGNIYLGRVKKIVPGLQA----AFVDI--GLGKNGFLHLSDILPAY----------FKKHKK----IAKLLKEGQEI   63 (88)
T ss_pred             CCCEEEEEEEEeccCCcE----EEEEe--CCCCEEEEEhHHcCchh----------ccccCC----HHHcCCCCCEE
Confidence            578899999999997  8    99988  78999999 67776210          011222    22367999999

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

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

Probab=97.62  E-value=7.5e-05  Score=54.25  Aligned_cols=56  Identities=14%  Similarity=0.193  Sum_probs=43.0

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      .|+.+.|+|+++++||    +|+++  .++++||++ |++.                     .    .++.||.+    +
T Consensus        16 ~G~~~~g~V~~i~~~G----~fV~l--~~~~~Glv~~se~~---------------------~----~~~iGd~v~v~I~   64 (77)
T cd04473          16 VGKLYKGKVNGVAKYG----VFVDL--NDHVRGLIHRSNLL---------------------R----DYEVGDEVIVQVT   64 (77)
T ss_pred             CCCEEEEEEEeEecce----EEEEE--CCCcEEEEEchhcc---------------------C----cCCCCCEEEEEEE
Confidence            4677999999999999    99998  788999995 4421                     1    24888888    5


Q ss_pred             EEecccchhhhhh
Q 024995          228 EIQLSHSLIRKAS  240 (259)
Q Consensus       228 ~v~~~~~~i~ls~  240 (259)
                      ++ .++++|.+++
T Consensus        65 ~i-~e~~~i~l~~   76 (77)
T cd04473          65 DI-PENGNIDLIP   76 (77)
T ss_pred             EE-CCCCcEEEEE
Confidence            66 6777777764

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.

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=97.62  E-value=3e-05  Score=77.57  Aligned_cols=72  Identities=10%  Similarity=0.115  Sum_probs=59.2

Q ss_pred             ccCCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee--
Q 024995          150 ISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV--  226 (259)
Q Consensus       150 ~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V--  226 (259)
                      +.++|+.+.|+|+++++||    +||.|  .-..+||+ +|+++..       |      ++.|..    ++++||.|  
T Consensus       655 dLk~Gm~leg~Vrnv~~fg----afVdI--gv~qDglvHis~ls~~-------f------v~~P~~----vv~vGdiV~v  711 (780)
T COG2183         655 DLKPGMILEGTVRNVVDFG----AFVDI--GVHQDGLVHISQLSDK-------F------VKDPNE----VVKVGDIVKV  711 (780)
T ss_pred             hccCCCEEEEEEEEeeecc----ceEEe--ccccceeeeHHHhhhh-------h------cCChHH----hcccCCEEEE
Confidence            3678999999999999999    99988  67889998 7887733       1      343444    77999999  


Q ss_pred             --EEEecccchhhhhhchhh
Q 024995          227 --QEIQLSHSLIRKASKRHC  244 (259)
Q Consensus       227 --~~v~~~~~~i~ls~k~~~  244 (259)
                        ++||..+++|+|||+.-.
T Consensus       712 ~V~~vD~~r~rI~Lsmr~~~  731 (780)
T COG2183         712 KVIEVDTARKRIALSMRLDE  731 (780)
T ss_pred             EEEEEecccCeeeeEeeccC
Confidence              799999999999999643

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=97.55  E-value=0.00013  Score=62.13  Aligned_cols=100  Identities=13%  Similarity=0.140  Sum_probs=65.3

Q ss_pred             cCCCCeEEEEEE---EEeCCCCeeEEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccceeeeecc
Q 024995          103 LNEGDEVRVKVI---KIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (259)
Q Consensus       103 ~~~Gd~V~vkVl---~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~  179 (259)
                      |..++.+.+.+.   ++|.++++|.+       +||..... .+.        +|+++.|+|+++.++|    +|++|..
T Consensus        27 y~~~~~i~as~~G~~~id~~~~~Isv-------~P~~~~~~-~~~--------~GdiV~GkV~~i~~~g----~~V~I~~   86 (189)
T PRK09521         27 YEDNGEVYASVVGKVFIDDINRKISV-------IPFKKTPP-LLK--------KGDIVYGRVVDVKEQR----ALVRIVS   86 (189)
T ss_pred             EeeCCEEEEEeeEEEEEcCCCCEEEE-------ecCcCCCC-CCC--------CCCEEEEEEEEEcCCe----EEEEEEE
Confidence            445666776554   44766777776       47753221 122        4777999999999999    9998832


Q ss_pred             --------cCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhch
Q 024995          180 --------EDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKR  242 (259)
Q Consensus       180 --------~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~  242 (259)
                              .+++.|++ .++++...          .   .    +....+++||.|    +.++   +++.||+|.
T Consensus        87 ~~~~~~~l~~~~~G~l~~s~i~~~~----------~---~----~~~~~~~~GD~V~akV~~i~---~~i~LS~k~  142 (189)
T PRK09521         87 IEGSERELATSKLAYIHISQVSDGY----------V---E----SLTDAFKIGDIVRAKVISYT---DPLQLSTKG  142 (189)
T ss_pred             ecccccccCCCceeeEEhhHcChhh----------h---h----hHHhccCCCCEEEEEEEecC---CcEEEEEec
Confidence                    35799999 55554211          1   1    122356999999    3444   789999886

>PRK05054 exoribonuclease II; Provisional

Probab=97.53  E-value=0.00027  Score=70.88  Aligned_cols=65  Identities=14%  Similarity=0.114  Sum_probs=52.7

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc--c-c--C-------hhhhcCCCCeEEEEEEEEeCCCC
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--I-Q--D-------IRDILNEGDEVRVKVIKIDREKS  121 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~--~-~--~-------~~~~~~~Gd~V~vkVl~id~~~~  121 (259)
                      |+.+.|.     +||+||+|..    .+++||||++.|...+  . -  +       -...|++||.|+|+|.++|.+++
T Consensus       562 ~~~f~g~I~~v~~~G~fV~l~~----~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~  637 (644)
T PRK05054        562 DTRFAAEIIDISRGGMRVRLLE----NGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR  637 (644)
T ss_pred             CeEEEEEEEeeecCcEEEEEeC----CceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence            4588888     9999999974    5899999999996531  1 1  1       12469999999999999999999


Q ss_pred             eeEEEE
Q 024995          122 RITLSI  127 (259)
Q Consensus       122 ri~lS~  127 (259)
                      +|.+++
T Consensus       638 ~i~~~~  643 (644)
T PRK05054        638 SIIARP  643 (644)
T ss_pred             eEEEEE
Confidence            998875

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

Probab=97.53  E-value=0.0003  Score=59.36  Aligned_cols=122  Identities=16%  Similarity=0.205  Sum_probs=74.4

Q ss_pred             CCCCCCCCCchhHhhhcc-cCCCCEEE-----EEEEEEeC-CCCEEEEEechh----hHhhhccCCCCCCEEEEE-----
Q 024995            2 SPSHSCKEPQKSIHEIAK-GLTGSIIS-----VKVIQANE-EMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----   65 (259)
Q Consensus         2 ~~~~~~~~p~~~~~~~~~-~~vG~~v~-----~~Vl~id~-~~~~v~lS~k~~----~~~~~~~~l~~G~iv~G~-----   65 (259)
                      .|++|..+....+.+.++ .+.|+.+.     +.|.+++. ..+++.=.--.+    .+..+.-+...|++++|.     
T Consensus        14 ~P~~f~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf~gEVv~g~V~~v~   93 (176)
T PTZ00162         14 KPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVN   93 (176)
T ss_pred             CHHHcCccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecCCCCEEEEEEEEEe
Confidence            467776655555544443 34454332     33344433 234443221111    133345578999999999     


Q ss_pred             eeeEEEEEccCCCCccEEEEEEceecCcccc------------cChhhhcCCCCeEEEEEEEEeCCCCe--eEEEEec
Q 024995           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI------------QDIRDILNEGDEVRVKVIKIDREKSR--ITLSIKQ  129 (259)
Q Consensus        66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~------------~~~~~~~~~Gd~V~vkVl~id~~~~r--i~lS~K~  129 (259)
                      ++|+||.++      .+++|+|.++|.....            .+-...++.|+.|++||..+..+.+.  ...|+|+
T Consensus        94 ~~G~~v~~G------p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~i~T~~~  165 (176)
T PTZ00162         94 KLGFFAQAG------PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAIATINS  165 (176)
T ss_pred             cceEEEEee------CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEEEEEecC
Confidence            899999998      5889999999974321            11234589999999999888654433  3445543

>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=97.46  E-value=0.00019  Score=50.90  Aligned_cols=60  Identities=10%  Similarity=0.183  Sum_probs=42.6

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+++.|+|+++.++|    +|++|  .+|++|++ .++++.+          |.. ...+..    .+++||.|    ++
T Consensus         1 G~iV~g~V~~i~~~g----i~v~l--~~~i~g~i~~~~i~~~----------~~~-~~~~~~----~~~~Gd~i~~kVl~   59 (70)
T cd05702           1 GDLVKAKVKSVKPTQ----LNVQL--ADNVHGRIHVSEVFDE----------WPD-GKNPLS----KFKIGQKIKARVIG   59 (70)
T ss_pred             CCEEEEEEEEEECCc----EEEEe--CCCcEEEEEHHHhccc----------ccc-ccChhH----hCCCCCEEEEEEEE
Confidence            567999999999999    99888  78999999 5666532          211 111222    45999999    56


Q ss_pred             Eecccc
Q 024995          229 IQLSHS  234 (259)
Q Consensus       229 v~~~~~  234 (259)
                      ++.+++
T Consensus        60 ~d~~~~   65 (70)
T cd05702          60 GHDAKT   65 (70)
T ss_pred             EeCccc
Confidence            666554

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.

>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=97.44  E-value=0.00052  Score=49.33  Aligned_cols=64  Identities=19%  Similarity=0.222  Sum_probs=50.3

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccC--hhhhcCCCCeE-EEEEEEEeCCCCeeEEEEe
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD--IRDILNEGDEV-RVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~--~~~~~~~Gd~V-~vkVl~id~~~~ri~lS~K  128 (259)
                      |++++|+     +-+++|++.+    .|+.|++|..++|++.-+.  .-..+++||++ .+.|+  |...+.|.+|.|
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~----~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K   72 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILP----EEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecC----CCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence            5677777     5679999985    5899999999999943222  34558999999 99998  777888888865

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.

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

Probab=97.41  E-value=0.00024  Score=54.05  Aligned_cols=86  Identities=10%  Similarity=0.075  Sum_probs=57.3

Q ss_pred             ccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEe
Q 024995          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQ  230 (259)
Q Consensus       156 ~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~  230 (259)
                      ++.|+|..+.++|    +|++|  . +++|++ .++++.+.-..-+.-..|...      +....+++||.|    .++|
T Consensus         2 vv~g~V~~i~~~G----ifV~l--~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~------~~~~~~~~Gd~v~vkI~~vd   68 (99)
T cd04460           2 VVEGEVVEVVDFG----AFVRI--G-PVDGLLHISQIMDDYISYDPKNKRLIGE------ETKRVLKVGDVVRARIVAVS   68 (99)
T ss_pred             EEEEEEEEEEecc----EEEEE--c-CeEEEEEEEEccCCceEechhheeeccc------CcCCEECCCCEEEEEEEEEe
Confidence            4789999999999    99999  4 599999 566653321000000011110      112356999999    5777


Q ss_pred             ccc-----chhhhhhchhhhhhhHHhhhh
Q 024995          231 LSH-----SLIRKASKRHCNEYWNVFHET  254 (259)
Q Consensus       231 ~~~-----~~i~ls~k~~~~~p~~~~~~~  254 (259)
                      .+.     .++.||+|+----||+-+.+.
T Consensus        69 ~~~~~~~~~~i~ls~k~~~~g~~~~~~~~   97 (99)
T cd04460          69 LKERRPRESKIGLTMRQPGLGKLEWIEEE   97 (99)
T ss_pred             HHHCcCCCceEEEEEecCCCCcHHHhhhh
Confidence            764     479999999888888877664

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.

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

Probab=97.40  E-value=0.0018  Score=56.71  Aligned_cols=71  Identities=27%  Similarity=0.414  Sum_probs=61.1

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc----ccChhhhcCCCCeEEEEEEEEeCCCCeeE
Q 024995           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL----IQDIRDILNEGDEVRVKVIKIDREKSRIT  124 (259)
Q Consensus        54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~----~~~~~~~~~~Gd~V~vkVl~id~~~~ri~  124 (259)
                      ...+.||.|.|.     ..+..|+|+     ....+++|+|++.+..    ..+++.+|++||.|.|+|..+|+ .+...
T Consensus        60 YiP~~gD~VIG~I~~v~~~~W~VDI~-----sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~  133 (239)
T COG1097          60 YIPEVGDVVIGKIIEVGPSGWKVDIG-----SPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVE  133 (239)
T ss_pred             ccCCCCCEEEEEEEEEcccceEEEcC-----CccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceE
Confidence            467899999999     789999998     3699999999996654    35778899999999999999997 79999


Q ss_pred             EEEecc
Q 024995          125 LSIKQL  130 (259)
Q Consensus       125 lS~K~~  130 (259)
                      |++|..
T Consensus       134 L~~k~~  139 (239)
T COG1097         134 LTLKDE  139 (239)
T ss_pred             EEeecC
Confidence            998643

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

Probab=97.33  E-value=0.0019  Score=54.56  Aligned_cols=74  Identities=28%  Similarity=0.344  Sum_probs=58.1

Q ss_pred             hccCCCCCCEEEEE-----eeeEEEEEccCCC-----CccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCC
Q 024995           52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDG-----LYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS  121 (259)
Q Consensus        52 ~~~~l~~G~iv~G~-----~~G~fV~l~~~~g-----~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~  121 (259)
                      ....++.|++|.|.     ...+.|++-+.++     .....|-+|+|+.+..++.+.++.|++||.|+++|++.-   -
T Consensus        58 ~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~---~  134 (188)
T COG1096          58 TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG---D  134 (188)
T ss_pred             CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC---C
Confidence            34578999999999     5567777765433     012568899999999999999999999999999999973   4


Q ss_pred             eeEEEEe
Q 024995          122 RITLSIK  128 (259)
Q Consensus       122 ri~lS~K  128 (259)
                      .+.||.+
T Consensus       135 ~~~Lst~  141 (188)
T COG1096         135 PIQLSTK  141 (188)
T ss_pred             CeEEEec
Confidence            5666654

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

Probab=97.32  E-value=0.0014  Score=49.06  Aligned_cols=59  Identities=17%  Similarity=0.230  Sum_probs=46.1

Q ss_pred             CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccCh-----------hhhcCCCCeEEEEEEEEeCCCC
Q 024995           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----------RDILNEGDEVRVKVIKIDREKS  121 (259)
Q Consensus        58 ~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~-----------~~~~~~Gd~V~vkVl~id~~~~  121 (259)
                      .|++++|+     ++|+||.++      ++++|+|.+.+......++           ...++.|+.|++||+.+..+.+
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G------pl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~   74 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG------PLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT   74 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc------CceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence            47888888     899999998      7999999999976543332           3348899999999998876544


Q ss_pred             e
Q 024995          122 R  122 (259)
Q Consensus       122 r  122 (259)
                      .
T Consensus        75 ~   75 (88)
T cd04462          75 D   75 (88)
T ss_pred             c
Confidence            3

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=97.31  E-value=8.7e-05  Score=71.54  Aligned_cols=115  Identities=17%  Similarity=0.182  Sum_probs=75.5

Q ss_pred             EEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEE-EEeccccCcch-----HhhhhhcCCCCccccCCCCcc
Q 024995           84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL-SIKQLEEDPLL-----ETLEKVIPQDGSVISDSSSMS  157 (259)
Q Consensus        84 glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~l-S~K~~~~~p~~-----~~~~~~~~~g~~~~~~~g~~v  157 (259)
                      +.+++++....   +|  .+++||.+.+.|...+.  +|+.+ +.|+....-|.     ...+.+ .      .+.|+++
T Consensus        73 ~eI~L~eAk~~---~~--~~~vGD~ie~~I~~~~f--gRia~q~aKq~i~Qkire~ere~i~~ey-k------~~~GeIV  138 (470)
T PRK09202         73 KEISLEEARKI---DP--DAEVGDYIEEEIESVDF--GRIAAQTAKQVIVQKIREAERERVYEEY-K------DRVGEII  138 (470)
T ss_pred             ceeeHHHHhhh---Cc--cccCCCeEEEEEccccC--ChHHHHHHHHHHHHHHHHHHHHHHHHHH-H------hhcCCEE
Confidence            55555554321   22  37899999999988874  44443 33444333343     233332 2      1247789


Q ss_pred             ccceeeeccCCCccceeeeecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecc
Q 024995          158 SSNSNTIEPLPGLGAIFEELLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLS  232 (259)
Q Consensus       158 ~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~  232 (259)
                      +|+|.++..+|    +|+.|   +|++||++ +++.                   +...|    ++||.|    ++|+.+
T Consensus       139 ~G~V~ri~~~g----iiVDL---ggvea~LP~sE~i-------------------p~E~~----~~GdrIka~I~~Vd~~  188 (470)
T PRK09202        139 TGVVKRVERGN----IIVDL---GRAEAILPRKEQI-------------------PRENF----RPGDRVRAYVYEVRKE  188 (470)
T ss_pred             EEEEEEEecCC----EEEEE---CCeEEEecHHHcC-------------------CCccC----CCCCEEEEEEEEEecC
Confidence            99999999999    99888   79999995 4432                   22334    899998    788888


Q ss_pred             cc--hhhhhhch
Q 024995          233 HS--LIRKASKR  242 (259)
Q Consensus       233 ~~--~i~ls~k~  242 (259)
                      ++  .|-||.+.
T Consensus       189 ~kg~qIilSRt~  200 (470)
T PRK09202        189 ARGPQIILSRTH  200 (470)
T ss_pred             CCCCeEEEEeCc
Confidence            77  67777653

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

Probab=97.25  E-value=0.00026  Score=69.98  Aligned_cols=70  Identities=21%  Similarity=0.258  Sum_probs=54.3

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee--EE
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV--QE  228 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V--~~  228 (259)
                      .+|+++.|+|+++.+||    +|++|  .||-+||| +|+++.++             +.    +...+++.||.|  ..
T Consensus       618 evg~iy~G~V~ri~~fG----aFv~l--~~gkdgl~hiS~~~~~r-------------v~----kv~dvlk~Gd~v~Vkv  674 (692)
T COG1185         618 EVGEVYEGTVVRIVDFG----AFVEL--LPGKDGLVHISQLAKER-------------VE----KVEDVLKEGDEVKVKV  674 (692)
T ss_pred             ccccEEEEEEEEEeecc----eEEEe--cCCcceeEEehhhhhhh-------------hh----cccceeecCceEEEEE
Confidence            35888999999999999    99999  89999999 78887442             12    233477999999  45


Q ss_pred             Eeccc-chhhhhhchhh
Q 024995          229 IQLSH-SLIRKASKRHC  244 (259)
Q Consensus       229 v~~~~-~~i~ls~k~~~  244 (259)
                      ++.++ .|++|++|...
T Consensus       675 ~~iD~~Gri~ls~~~~~  691 (692)
T COG1185         675 IEIDKQGRIRLSIKAVL  691 (692)
T ss_pred             eeecccCCccceehhcc
Confidence            55555 58999998654

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.24  E-value=0.00076  Score=64.18  Aligned_cols=57  Identities=28%  Similarity=0.472  Sum_probs=47.6

Q ss_pred             CCCCCCEEEEE-----ee--eEEEEEccCCCCccEEEEEEceecCcc------------cccChhhhcCCCCeEEEEEEE
Q 024995           55 RVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVIK  115 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~--G~fV~l~~~~g~~gi~glv~isels~~------------~~~~~~~~~~~Gd~V~vkVl~  115 (259)
                      ...+|++|.|+     ++  ||||+++     .+..||+|++++.+.            +..++.+.+++||.|.|.|.+
T Consensus        22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG-----~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K   96 (414)
T TIGR00757        22 RQLKGNIYKGRVTRILPSLQAAFVDIG-----LEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK   96 (414)
T ss_pred             cCCCCCEEEEEEeeecCCCceEEEEcC-----CCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee
Confidence            56799999999     66  8999998     489999999999753            234566789999999999988


Q ss_pred             E
Q 024995          116 I  116 (259)
Q Consensus       116 i  116 (259)
                      -
T Consensus        97 e   97 (414)
T TIGR00757        97 E   97 (414)
T ss_pred             C
Confidence            3

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.

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

Probab=97.23  E-value=0.00033  Score=51.26  Aligned_cols=67  Identities=4%  Similarity=-0.099  Sum_probs=50.0

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      .+|+++.|+|.++.+.+    +++.+  ..+.+|++ .++++...          .       .+....+++||.+    
T Consensus         5 ~~GdiV~G~V~~v~~~~----~~V~i--~~~~~g~l~~~~~~~~~----------~-------~~~~~~~~~GD~i~~~V   61 (82)
T cd04454           5 DVGDIVIGIVTEVNSRF----WKVDI--LSRGTARLEDSSATEKD----------K-------KEIRKSLQPGDLILAKV   61 (82)
T ss_pred             CCCCEEEEEEEEEcCCE----EEEEe--CCCceEEeechhccCcc----------h-------HHHHhcCCCCCEEEEEE
Confidence            46888999999999999    99888  77899999 66665220          1       1122256999999    


Q ss_pred             EEEecccchhhhhhch
Q 024995          227 QEIQLSHSLIRKASKR  242 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~  242 (259)
                      ++++.+ +++.||++.
T Consensus        62 ~~~~~~-~~i~LS~~~   76 (82)
T cd04454          62 ISLGDD-MNVLLTTAD   76 (82)
T ss_pred             EEeCCC-CCEEEEECC
Confidence            566765 789999875

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".

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.16  E-value=0.00039  Score=70.14  Aligned_cols=63  Identities=19%  Similarity=0.226  Sum_probs=47.6

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|+++.+||    +|++|  .+|++||+ +|+++++          |+   ..    +...+++||.|    
T Consensus       617 ~~G~i~~G~V~~I~~~G----afVei--~~g~~GllHiSei~~~----------~v---~~----~~~~~kvGD~V~VkV  673 (684)
T TIGR03591       617 EVGKIYEGKVVRIMDFG----AFVEI--LPGKDGLVHISEIANE----------RV---EK----VEDVLKEGDEVKVKV  673 (684)
T ss_pred             ccCcEEEEEEEEEeCCE----EEEEE--CCCcEEEEEHHHcCCC----------cc---cC----hhhccCCCCEEEEEE
Confidence            46888999999999999    99999  78999999 6887633          22   21    23356999999    


Q ss_pred             EEEecccchhhh
Q 024995          227 QEIQLSHSLIRK  238 (259)
Q Consensus       227 ~~v~~~~~~i~l  238 (259)
                      +++|. +++|+|
T Consensus       674 i~id~-~gki~L  684 (684)
T TIGR03591       674 LEIDK-QGRIKL  684 (684)
T ss_pred             EEECC-CCCccC
Confidence            56665 566654

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).

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

Probab=97.01  E-value=0.00081  Score=45.59  Aligned_cols=60  Identities=20%  Similarity=0.340  Sum_probs=42.5

Q ss_pred             cccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEec
Q 024995          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQL  231 (259)
Q Consensus       157 v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~  231 (259)
                      +.|+|.++.++|    +|+++  .+|++|++ .++++..          +.   .    +....+++||.|    .++|.
T Consensus         1 v~g~V~~v~~~g----~~v~l--~~~~~g~~~~~~~~~~----------~~---~----~~~~~~~~G~~v~~~v~~~d~   57 (65)
T cd00164           1 VTGKVVSITKFG----VFVEL--EDGVEGLVHISELSDK----------FV---K----DPSEVFKVGDEVEVKVLEVDP   57 (65)
T ss_pred             CEEEEEEEEeee----EEEEe--cCCCEEEEEHHHCCCc----------cc---c----CHhhEeCCCCEEEEEEEEEcC
Confidence            368999999999    99888  68999999 5555422          11   1    112256999999    57777


Q ss_pred             ccchhhhh
Q 024995          232 SHSLIRKA  239 (259)
Q Consensus       232 ~~~~i~ls  239 (259)
                      +++++.||
T Consensus        58 ~~~~i~ls   65 (65)
T cd00164          58 EKGRISLS   65 (65)
T ss_pred             CcCEEecC
Confidence            77777664

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.

>TIGR02062 RNase_B exoribonuclease II

Probab=96.98  E-value=0.002  Score=64.64  Aligned_cols=64  Identities=13%  Similarity=0.136  Sum_probs=50.6

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc--ccc-cC--h-------hhhcCCCCeEEEEEEEEeCCCC
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI-QD--I-------RDILNEGDEVRVKVIKIDREKS  121 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~--~~~-~~--~-------~~~~~~Gd~V~vkVl~id~~~~  121 (259)
                      |+.+.|.     +||+||+|..    .|++||||++.|..  ++. -+  .       ...|+.||.|+|+|.++|.+++
T Consensus       558 ~~~f~g~I~~v~~~g~~v~l~~----~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~  633 (639)
T TIGR02062       558 NTRFAAEIVDISRGGMRVRLLE----NGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETR  633 (639)
T ss_pred             CcEEEEEEEeeeCCcEEEEEec----CceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccC
Confidence            4478888     8999999973    58999999999965  221 11  1       1259999999999999999999


Q ss_pred             eeEEE
Q 024995          122 RITLS  126 (259)
Q Consensus       122 ri~lS  126 (259)
                      +|.+.
T Consensus       634 ~i~~~  638 (639)
T TIGR02062       634 SIIAR  638 (639)
T ss_pred             cEeee
Confidence            98864

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.

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

Probab=96.97  E-value=0.0036  Score=46.65  Aligned_cols=68  Identities=19%  Similarity=0.079  Sum_probs=54.3

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      ..++||.|.|+     ....+|+|+     ....|++|.+++... .++.+..|++||.|.|+|..+|+ .....||+..
T Consensus         3 ~P~~gD~VIG~V~~~~~~~~~VdI~-----s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~-~~~~eLtc~~   75 (86)
T cd05790           3 VPAKGDHVIGIVVAKAGDFFKVDIG-----GSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANR-DMEPELSCVD   75 (86)
T ss_pred             cCCCCCEEEEEEEEEcCCeEEEEcC-----CCcceEechHHcccc-cccccccCCCCCEEEEEEEecCC-CCCeEEEEeC
Confidence            35789999999     457899998     367899999887543 34456679999999999999997 4678888765

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".

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=96.94  E-value=0.0021  Score=65.18  Aligned_cols=70  Identities=31%  Similarity=0.529  Sum_probs=57.8

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc-----------ChhhhcCCCCeEEEEEEEEeC
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDR  118 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~-----------~~~~~~~~Gd~V~vkVl~id~  118 (259)
                      .-.+|+.+.|+     .||+||.+.+    .+++|++|++.+...++.           .....|+.||.|++++.++|.
T Consensus       619 ~~~vg~~f~g~V~~v~~~g~~V~l~~----~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~  694 (706)
T COG0557         619 KKRVGEEFDGVVTGVTSFGFFVELPE----LGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDL  694 (706)
T ss_pred             HHhcCCEEEEEEEEEEeccEEEEecc----cccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcc
Confidence            45788888888     8999999984    579999999999965321           223458999999999999999


Q ss_pred             CCCeeEEEEe
Q 024995          119 EKSRITLSIK  128 (259)
Q Consensus       119 ~~~ri~lS~K  128 (259)
                      ..+++.+++-
T Consensus       695 ~~~~i~~~~v  704 (706)
T COG0557         695 DERKIDFELV  704 (706)
T ss_pred             cccceEEEec
Confidence            9999998763

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=96.78  E-value=0.0048  Score=42.86  Aligned_cols=48  Identities=33%  Similarity=0.409  Sum_probs=32.5

Q ss_pred             eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      ++|+|++.+     .+-+-|+|.++++.        .+++||.|.|-| ..|. .+|+..|+|
T Consensus        14 ~~g~fL~~~-----~~~~vlLp~~e~~~--------~~~~Gd~v~VFv-Y~D~-~~rl~AT~k   61 (61)
T PF13509_consen   14 EFGYFLDDG-----EGKEVLLPKSEVPE--------PLKVGDEVEVFV-YLDK-EGRLVATTK   61 (61)
T ss_dssp             SSEEEEEET-----T-EEEEEEGGG--------------TTSEEEEEE-EE-T-TS-EEEE--
T ss_pred             CCEEEEECC-----CCCEEEechHHcCC--------CCCCCCEEEEEE-EECC-CCCEEEecC
Confidence            899999987     36899999998753        378999999887 7886 678888875

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=96.69  E-value=0.00093  Score=64.75  Aligned_cols=76  Identities=13%  Similarity=0.056  Sum_probs=57.4

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCeeE---
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQ---  227 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V~---  227 (259)
                      -.|.+++++|+.+.|||    +||+|  .||..||+ .|+++.+          |+..   +..    ++.+||+++   
T Consensus       667 ~~g~vy~~tIt~~rd~G----~~V~l--~p~~~~Llh~sqL~~e----------~iak---psd----~levGq~I~vk~  723 (760)
T KOG1067|consen  667 EFGGVYTATITEIRDTG----VMVEL--YPMQQGLLHNSQLDQE----------KIAK---PSD----LLEVGQEIQVKY  723 (760)
T ss_pred             EeeeEEEEEEeeecccc----eEEEe--cCCchhhccchhcccc----------cccC---hHH----HHhhcceeEEEE
Confidence            45888999999999999    99999  99999999 7887744          5532   333    679999993   


Q ss_pred             -EEecccchhhhhhchhhhhhhHHh
Q 024995          228 -EIQLSHSLIRKASKRHCNEYWNVF  251 (259)
Q Consensus       228 -~v~~~~~~i~ls~k~~~~~p~~~~  251 (259)
                       +.|+.. .+.++.|.++++|....
T Consensus       724 ie~d~~g-~~~ls~ralLp~p~~~~  747 (760)
T KOG1067|consen  724 IERDPRG-GIMLSSRALLPDPATKE  747 (760)
T ss_pred             EeecCcc-ceeehhhhhcCCcccCC
Confidence             444433 46677777888887544

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

Probab=96.68  E-value=0.0021  Score=54.30  Aligned_cols=83  Identities=10%  Similarity=0.052  Sum_probs=53.5

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |++++|+|++++++|    +|+++  . .++|++ .+++..+.-..-++-..|...  ..    ...++.||.|    .+
T Consensus        82 gEvv~G~V~~v~~~G----ifV~l--g-~~~gi~~~~~l~~~~~~~d~~~~~~~~~--~~----~~~~~~Gd~VrvrV~~  148 (179)
T TIGR00448        82 GEIVEGEVIEIVEFG----AFVSL--G-PFDGLFHVSQVTDDYCYYDPKESALIGK--ET----KKVLDEGDKVRARIVA  148 (179)
T ss_pred             CCEEEEEEEEEEeeE----EEEEe--C-CceEEEEcHHhCCCceEEccccceEEEc--cC----CeEEcCCCEEEEEEEE
Confidence            667999999999999    99998  3 499998 555543321111111223321  11    2356999999    56


Q ss_pred             Ee-----cccchhhhhhchhhhhhhH
Q 024995          229 IQ-----LSHSLIRKASKRHCNEYWN  249 (259)
Q Consensus       229 v~-----~~~~~i~ls~k~~~~~p~~  249 (259)
                      ++     ++.++|.++||+----|++
T Consensus       149 v~~~~~~~~~~~I~lt~k~~~LG~~~  174 (179)
T TIGR00448       149 LSLKDRRPEGSKIGLTMRQPLLGKLE  174 (179)
T ss_pred             EEccCCCCCcceEEEEeccCcCCccc
Confidence            66     5667899999984333433

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

>TIGR02063 RNase_R ribonuclease R

Probab=96.66  E-value=0.0024  Score=64.78  Aligned_cols=71  Identities=18%  Similarity=0.216  Sum_probs=50.9

Q ss_pred             CCCccccceeeeccCCCccceeeeecccC-CeeEEE-Eccccccccccchhhhhhccc-----CCCCCcceeeeccCCCe
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR-ITRQGFEKRVVSQDLQLWLSN-----APPSGKKFTLLARAGRQ  225 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~-gv~gl~-~s~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~r~G~~  225 (259)
                      .|+.++|+|++|++||    +||+|  .+ |++||+ +|++..+.       -.|...     ......    .++.||.
T Consensus       627 iG~~~~g~V~~v~~fG----ifV~L--~~~~~eGlvhis~l~~d~-------~~~d~~~~~l~g~~~~~----~~~lGd~  689 (709)
T TIGR02063       627 IGEEFEGVISGVTSFG----LFVEL--ENNTIEGLVHISTLKDDY-------YVFDEKGLALVGERTGK----VFRLGDR  689 (709)
T ss_pred             CCcEEEEEEEEEEeCC----EEEEe--cCCceEEEEEeeecCCCc-------EEEcccceEEEeccCCc----EECCCCE
Confidence            4888999999999999    99999  56 899999 67765221       011110     011112    4599999


Q ss_pred             e----EEEecccchhhhhh
Q 024995          226 V----QEIQLSHSLIRKAS  240 (259)
Q Consensus       226 V----~~v~~~~~~i~ls~  240 (259)
                      |    .+||.++++|.+++
T Consensus       690 V~Vkv~~vd~~~~~I~~~l  708 (709)
T TIGR02063       690 VKVRVVKADLDTGKIDFEL  708 (709)
T ss_pred             EEEEEEEEecccCeEEEEE
Confidence            9    68899999998875

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.

>PRK11642 exoribonuclease R; Provisional

Probab=96.56  E-value=0.003  Score=64.97  Aligned_cols=77  Identities=13%  Similarity=0.154  Sum_probs=52.9

Q ss_pred             CCCccccceeeeccCCCccceeeeecccC-CeeEEE-EccccccccccchhhhhhcccCCC----CCcceeeeccCCCee
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR-ITRQGFEKRVVSQDLQLWLSNAPP----SGKKFTLLARAGRQV  226 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~-gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~r~G~~V  226 (259)
                      .|+.++|+|++|++||    +||+|  ++ +|+||+ .+.+..+          |+.....    ...+-...++.||.|
T Consensus       643 iGe~f~G~Is~V~~fG----ifVeL--~~~~vEGlV~vs~L~~d----------~y~~d~~~~~L~g~~~~~~~~lGD~V  706 (813)
T PRK11642        643 VGNVFKGVISSVTGFG----FFVRL--DDLFIDGLVHVSSLDND----------YYRFDQVGQRLIGESSGQTYRLGDRV  706 (813)
T ss_pred             CCcEEEEEEEEeecCc----eEEEE--CCCCeeeeEEEeecCCc----------ceEecchheEEecccCCcEECCCCEE
Confidence            4888999999999999    99999  55 599999 6666522          2221100    000111245999999


Q ss_pred             ----EEEecccchhhhhhchhhh
Q 024995          227 ----QEIQLSHSLIRKASKRHCN  245 (259)
Q Consensus       227 ----~~v~~~~~~i~ls~k~~~~  245 (259)
                          .++|.++++|.+++-....
T Consensus       707 ~VkV~~vD~~~rkI~f~l~~~~~  729 (813)
T PRK11642        707 EVRVEAVNMDERKIDFSLISSER  729 (813)
T ss_pred             EEEEEEeecCCCeEEEEEecccc
Confidence                5789999999888754333

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

Probab=96.53  E-value=0.0041  Score=43.74  Aligned_cols=32  Identities=6%  Similarity=0.164  Sum_probs=26.6

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEEE-ccc
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI-TRQ  191 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~-s~~  191 (259)
                      .|++++|+|.++.++|    +|+.+   ++++|+++ +++
T Consensus         3 ~g~iV~G~V~~~~~~~----~~vdi---g~~eg~lp~~e~   35 (67)
T cd04455           3 EGEIVTGIVKRVDRGN----VIVDL---GKVEAILPKKEQ   35 (67)
T ss_pred             CCCEEEEEEEEEcCCC----EEEEc---CCeEEEeeHHHC
Confidence            5888999999999999    99888   45999994 443

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.

>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]

Probab=96.45  E-value=0.014  Score=57.13  Aligned_cols=68  Identities=29%  Similarity=0.496  Sum_probs=58.2

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      +.+++.|..|.|+     .||+||+++     ..+.||+|-++++..      .-|.+|+.+-|.+..+-++++.|.+..
T Consensus       117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln-----~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~  185 (715)
T COG1107         117 MEDVEAGKYYKGIVSRVEKYGVFVELN-----SHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEP  185 (715)
T ss_pred             hhhcccceeeeccccchhhhcceeecC-----hhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceee
Confidence            4678999999999     999999998     589999999999862      237899999999999998889888877


Q ss_pred             eccc
Q 024995          128 KQLE  131 (259)
Q Consensus       128 K~~~  131 (259)
                      ..+.
T Consensus       186 ~~~~  189 (715)
T COG1107         186 VGLD  189 (715)
T ss_pred             cCCc
Confidence            6554

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.19  E-value=0.013  Score=54.78  Aligned_cols=62  Identities=21%  Similarity=0.353  Sum_probs=51.4

Q ss_pred             CCCCCCEEEEE----e--eeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCC---eeEE
Q 024995           55 RVNVEDIFVGR----D--YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS---RITL  125 (259)
Q Consensus        55 ~l~~G~iv~G~----~--~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~---ri~l  125 (259)
                      .-+.|+++.|+    +  .++||+++      +.+|++|.++..      |.+.|++||.++|.|.+++...+   +|.|
T Consensus       135 ~~~~Geiv~g~V~r~~~~~~i~vdlg------~~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~Iil  202 (374)
T PRK12328        135 KKKVGKIVFGTVVRVDNEENTFIEID------EIRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIEL  202 (374)
T ss_pred             HHhcCcEEEEEEEEEecCCCEEEEcC------CeEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEE
Confidence            35799999999    3  34899997      799999988864      46779999999999999998655   7888


Q ss_pred             EEe
Q 024995          126 SIK  128 (259)
Q Consensus       126 S~K  128 (259)
                      |+.
T Consensus       203 SRt  205 (374)
T PRK12328        203 SRT  205 (374)
T ss_pred             EcC
Confidence            863

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

Probab=96.17  E-value=0.0033  Score=53.02  Aligned_cols=87  Identities=10%  Similarity=0.108  Sum_probs=57.8

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+++.|.|+++..||    +|+.|   .-.+||+ .|++.++  .+..|-..|.-... +.   +..+++||.|    ..
T Consensus        82 gEVV~GeVv~~~~~G----~fV~i---gp~dglvh~sqi~dd--~~~~d~~~~~~~g~-~t---k~~i~~gd~VR~RIv~  148 (183)
T COG1095          82 GEVVEGEVVEVVEFG----AFVRI---GPLDGLVHVSQIMDD--YIDYDEKNKVLIGE-ET---KRVLKVGDKVRARIVG  148 (183)
T ss_pred             ccEEEEEEEEEeecc----eEEEe---ccccccccHhhccCc--ccccCcccceeeec-cc---ceEEecCCEEEEEEEE
Confidence            677999999999999    99999   5789998 6777655  23333333332222 22   2267999999    22


Q ss_pred             Eecc-----cchhhhhhch--hhhhhhHHhhh
Q 024995          229 IQLS-----HSLIRKASKR--HCNEYWNVFHE  253 (259)
Q Consensus       229 v~~~-----~~~i~ls~k~--~~~~p~~~~~~  253 (259)
                      +...     ..+|-++|||  |-.-+|-..+.
T Consensus       149 ~s~~~~~~~~~~I~lTmrq~~LGklew~~~~~  180 (183)
T COG1095         149 VSLKSRRPRESKIGLTMRQPGLGKLEWIEEEK  180 (183)
T ss_pred             EecccCccccceEEEEeccccCCcchhhhhhh
Confidence            2222     3568899998  55566765543

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=96.11  E-value=0.0051  Score=54.22  Aligned_cols=70  Identities=4%  Similarity=-0.023  Sum_probs=48.1

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      +|++|.|+|+++.+++    +|++|  ..+..|++ .++++..          |.   ..+..+....+++||.|    +
T Consensus        63 vGDiViG~V~~i~~~~----~~vdI--~~~~~g~L~~s~i~~~----------~~---~~d~~~~~~~~~~GDlV~akV~  123 (235)
T PRK04163         63 VGDLVIGKVTDVTFSG----WEVDI--NSPYKAYLPVSEVLGR----------PV---NVEGTDLRKYLDIGDYIIAKVK  123 (235)
T ss_pred             CCCEEEEEEEEEeCce----EEEEe--CCCceeEEEHHHcCCC----------cc---ccchhhhHhhCCCCCEEEEEEE
Confidence            4788999999999999    99888  77899999 5665522          11   00112233467999999    4


Q ss_pred             EEecccchhhhhhch
Q 024995          228 EIQLSHSLIRKASKR  242 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~  242 (259)
                      .++.+. .+.||+|+
T Consensus       124 ~i~~~~-~~~LS~k~  137 (235)
T PRK04163        124 DVDRTR-DVVLTLKG  137 (235)
T ss_pred             EECCCC-cEEEEEcC
Confidence            555443 37777765

>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=96.05  E-value=0.0024  Score=56.52  Aligned_cols=83  Identities=17%  Similarity=0.233  Sum_probs=67.0

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCe----eE
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQ----VQ  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~----V~  227 (259)
                      .+++|-+.|..|.+.|    +++.|.-.++++|++ .|++|-.          +++.       ++-+.|+|..    |+
T Consensus        16 v~e~VmvnV~sIaemG----ayv~LlEYnniEGmiLlsELSrR----------RIRS-------I~klirVGr~E~vvVl   74 (304)
T KOG2916|consen   16 VEEIVMVNVRSIAEMG----AYVKLLEYNNIEGMILLSELSRR----------RIRS-------IQKLIRVGRNEPVVVL   74 (304)
T ss_pred             cccEEEEEeeEehhcc----ceEeeeecCCcccchhhhHHHHH----------HHHH-------HHHHHhcCCcceEEEE
Confidence            3677999999999999    999998889999998 8998822          2322       3336688863    38


Q ss_pred             EEecccchhhhhhchhhhhhhHHhhhhcc
Q 024995          228 EIQLSHSLIRKASKRHCNEYWNVFHETAI  256 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~~~~~p~~~~~~~~~  256 (259)
                      .||.++.-|.||.+++.++-...-.|+|+
T Consensus        75 rVDkekGYIDLSkrrVs~ed~~kC~Er~~  103 (304)
T KOG2916|consen   75 RVDKEKGYIDLSKRRVSPEDKEKCEERFA  103 (304)
T ss_pred             EEcCCCCceechhccCCHHHHHHHHHHHH
Confidence            99999999999999999887777777664

>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]

Probab=96.04  E-value=0.0062  Score=63.29  Aligned_cols=71  Identities=24%  Similarity=0.278  Sum_probs=59.5

Q ss_pred             CCCCCCEEEEE------eeeE--EEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           55 RVNVEDIFVGR------DYGA--FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        55 ~l~~G~iv~G~------~~G~--fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      .+.+|.++.++      .+|.  =|.+.     +|++|+||.+++|...+.+|...+++||.|.++|+++|.++=-+.||
T Consensus       982 t~~~g~iV~~~V~~vt~rr~~Cv~v~ld-----~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls 1056 (1299)
T KOG1856|consen  982 TFYEGAIVPVTVTKVTHRRGICVRVRLD-----CGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELS 1056 (1299)
T ss_pred             HhccCceEEEeeeEEEecccceeEEEec-----CCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhh
Confidence            47788888866      3443  34555     59999999999999999999999999999999999999988888888


Q ss_pred             Eecc
Q 024995          127 IKQL  130 (259)
Q Consensus       127 ~K~~  130 (259)
                      .|..
T Consensus      1057 ~r~s 1060 (1299)
T KOG1856|consen 1057 CRTS 1060 (1299)
T ss_pred             hhhH
Confidence            8753

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

Probab=96.02  E-value=0.0088  Score=60.24  Aligned_cols=76  Identities=21%  Similarity=0.287  Sum_probs=50.3

Q ss_pred             CCCccccceeeeccCCCccceeeeeccc-CCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~-~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      .|+.++|+|+++++||    +|++|  + .|++||+ .+++..+.-.. ++-+.-+ .......    .++.||.|    
T Consensus       572 iG~~~~g~I~~v~~~G----ifV~L--~~~~veGlV~~s~l~~d~y~~-d~~~~~l-~g~~~~~----~~~lGD~V~Vki  639 (654)
T TIGR00358       572 VGTEFSGEISSVTRFG----MFVRL--DDNGIDGLIHISTLHNDYYVF-DQEKMAL-IGKGTGK----VYRIGDRVTVKL  639 (654)
T ss_pred             CCcEEEEEEEeEEcCc----EEEEe--cCCceEEEEEeEeCCCcceEE-eccccEE-EeccCCc----EECCCCEEEEEE
Confidence            4888999999999999    99999  5 7899999 66665321000 0000000 0011112    46999999    


Q ss_pred             EEEecccchhhhhh
Q 024995          227 QEIQLSHSLIRKAS  240 (259)
Q Consensus       227 ~~v~~~~~~i~ls~  240 (259)
                      .+||.++++|.+++
T Consensus       640 ~~vd~~~~~I~f~l  653 (654)
T TIGR00358       640 TEVNMETRSIIFEL  653 (654)
T ss_pred             EEEecccCeEEEEE
Confidence            68899999988764

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.

>TIGR01953 NusA transcription termination factor NusA

Probab=95.91  E-value=0.0028  Score=58.86  Aligned_cols=106  Identities=18%  Similarity=0.215  Sum_probs=65.0

Q ss_pred             hhhcCCCCeEEEEEEEEeCCCCeeEEEEeccc-----cCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCcccee
Q 024995          100 RDILNEGDEVRVKVIKIDREKSRITLSIKQLE-----EDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIF  174 (259)
Q Consensus       100 ~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~-----~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~f  174 (259)
                      ...+++||.+.+.+..-+. .+....+.|+..     ...+....+.+.       ...|++++|+|.++.+.|   .+|
T Consensus        81 d~~~~vGD~I~~~I~~~~f-gR~aaq~aKqvi~Qkire~ere~i~~ey~-------~k~GeiV~G~V~~v~~~g---~v~  149 (341)
T TIGR01953        81 DPDVQIGDEVKKEIPPENF-GRIAAQTAKQVILQKIREAERERVYDEFS-------SKEGEIISGTVKRVNRRG---NLY  149 (341)
T ss_pred             ccccccCCEEEEEecccCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------hhcCCEEEEEEEEEecCC---cEE
Confidence            3458899999998855543 233333344422     222333333332       134888999999999877   258


Q ss_pred             eeecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccc--hhhhhhch
Q 024995          175 EELLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHS--LIRKASKR  242 (259)
Q Consensus       175 v~l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~--~i~ls~k~  242 (259)
                      +.|   +|++|+++ +++.                   +..+|    ++||.+    ++|+.+.+  .|-+|.+.
T Consensus       150 Vdi---G~~ea~LP~~E~i-------------------p~E~~----~~Gd~ik~~V~~V~~~~kg~qIivSRt~  198 (341)
T TIGR01953       150 VEL---GKTEGILPKKEQI-------------------PGEKF----RIGDRIKAYVYEVRKTAKGPQIILSRTH  198 (341)
T ss_pred             EEE---CCeEEEecHHHcC-------------------CCcCC----CCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence            777   69999995 4433                   11224    899987    67776554  46666553

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.

>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=95.65  E-value=0.031  Score=41.25  Aligned_cols=36  Identities=25%  Similarity=0.438  Sum_probs=24.2

Q ss_pred             cEEEEEEceecCccccc--ChhhhcCCCCeEEEEEEEE
Q 024995           81 HLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKI  116 (259)
Q Consensus        81 gi~glv~isels~~~~~--~~~~~~~~Gd~V~vkVl~i  116 (259)
                      ...|.++.+++......  ++.+-|++||.|+|+|+++
T Consensus        45 ~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl   82 (82)
T PF10447_consen   45 PFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL   82 (82)
T ss_dssp             SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred             ccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence            57899999998765443  4688899999999999874

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.

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

Probab=95.25  E-value=0.022  Score=48.23  Aligned_cols=76  Identities=11%  Similarity=0.105  Sum_probs=49.7

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |+++.|+|+++.++|    +|+++  . .++|++ .+++..+.-...++=+.|+..  ..    ...++.||.|    ..
T Consensus        82 GEVv~g~V~~v~~~G----i~V~l--g-~~~g~v~~~~l~~~~~~~d~~~~~~~~~--~~----~~~i~~Gd~VrvrV~~  148 (187)
T PRK08563         82 QEVVEGEVVEVVEFG----AFVRI--G-PVDGLLHISQIMDDYISYDPKNGRLIGK--ES----KRVLKVGDVVRARIVA  148 (187)
T ss_pred             CCEEEEEEEEEEccE----EEEEE--e-CceEEEEcHHcCCCceEEccccceEEEc--cC----CeEEcCCCEEEEEEEE
Confidence            677999999999999    99998  3 499998 555543211111112234432  11    2356999999    56


Q ss_pred             Eecccc-----hhhhhhch
Q 024995          229 IQLSHS-----LIRKASKR  242 (259)
Q Consensus       229 v~~~~~-----~i~ls~k~  242 (259)
                      ++.+.+     +|.+|||+
T Consensus       149 v~~~~~~~~~~~I~ls~~~  167 (187)
T PRK08563        149 VSLKERRPRGSKIGLTMRQ  167 (187)
T ss_pred             EEcccCCCCCCEEEEEecC
Confidence            665543     78889987

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=94.86  E-value=0.0088  Score=55.96  Aligned_cols=100  Identities=13%  Similarity=0.113  Sum_probs=61.5

Q ss_pred             hcCCCCeEEEEEEEEeCCCCeeEEEEeccccCc-----chHhhhhhcCCCCccccCCCCccccceeeeccCCCccceeee
Q 024995          102 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP-----LLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEE  176 (259)
Q Consensus       102 ~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p-----~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~fv~  176 (259)
                      ..++||.+...+...+.. +.-..+.|+....-     .....+.+.       .+.|++++|+|.++.+.|    +|+.
T Consensus        86 ~~~vGD~i~~~I~~~~fg-R~aaq~akqvI~Qkire~ere~v~~ef~-------~k~GeiV~G~V~~~~~~~----~~Vd  153 (362)
T PRK12327         86 AYELGDVIEIEVTPKDFG-RIAAQTAKQVIMQRLREAEREIIYNEFS-------EREGDIVTGVVQRRDNRF----VYVN  153 (362)
T ss_pred             cccCCCEEEEecCcCCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HhcCCEEEEEEEEEeCCc----EEEE
Confidence            478999999988666542 22222233322111     111222221       235888999999999988    9988


Q ss_pred             ecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccch--hhhh
Q 024995          177 LLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSL--IRKA  239 (259)
Q Consensus       177 l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~--i~ls  239 (259)
                      |   +|++|+++ +++.                   +..    .+++||.+    ++|+.+++.  |.+|
T Consensus       154 l---g~vEa~LP~~E~i-------------------p~e----~~~~Gd~Ika~V~~V~~~~kgp~IivS  197 (362)
T PRK12327        154 L---GKIEAVLPPAEQI-------------------PGE----TYKHGDRIKVYVVKVEKTTKGPQIFVS  197 (362)
T ss_pred             e---CCeEEEecHHHcC-------------------CCC----CCCCCCEEEEEEEEEecCCCCCeEEEE
Confidence            8   67999996 4432                   122    33899998    678776664  4444

>PRK10811 rne ribonuclease E; Reviewed

Probab=94.78  E-value=0.07  Score=55.27  Aligned_cols=61  Identities=26%  Similarity=0.480  Sum_probs=46.4

Q ss_pred             CCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEceecCccccc---------ChhhhcCCCCeEEEEEEEEeCC
Q 024995           56 VNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---------DIRDILNEGDEVRVKVIKIDRE  119 (259)
Q Consensus        56 l~~G~iv~G~-------~~G~fV~l~~~~g~~gi~glv~isels~~~~~---------~~~~~~~~Gd~V~vkVl~id~~  119 (259)
                      ..+|.||.|+       =.++||+|+     .|..||+|+++.....+.         .....+++||.|.|.|.+-...
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDIG-----~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~g  110 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDYG-----AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERG  110 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEec-----CCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccC
Confidence            4689999999       357999999     489999999999644322         2245688999999999875443


Q ss_pred             CC
Q 024995          120 KS  121 (259)
Q Consensus       120 ~~  121 (259)
                      ++
T Consensus       111 tK  112 (1068)
T PRK10811        111 NK  112 (1068)
T ss_pred             CC
Confidence            33

>PRK11712 ribonuclease G; Provisional

Probab=94.56  E-value=0.14  Score=49.77  Aligned_cols=59  Identities=25%  Similarity=0.511  Sum_probs=45.1

Q ss_pred             cCCCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEceecCcc------------cccChhhhcCCCCeEEEEEE
Q 024995           54 SRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI  114 (259)
Q Consensus        54 ~~l~~G~iv~G~-------~~G~fV~l~~~~g~~gi~glv~isels~~------------~~~~~~~~~~~Gd~V~vkVl  114 (259)
                      ....+|.+|.|+       =.+|||+|+     .+..||+|++++...            ......+.+++||.|-|.|.
T Consensus        34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG-----~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~  108 (489)
T PRK11712         34 KRGIVGNIYKGRVSRVLPGMQAAFVDIG-----LDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVV  108 (489)
T ss_pred             cccccccEEEEEEeecCCCCceeEEeeC-----CCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEE
Confidence            355799999999       346999998     589999999997321            01234566999999999997


Q ss_pred             EEe
Q 024995          115 KID  117 (259)
Q Consensus       115 ~id  117 (259)
                      +--
T Consensus       109 Ke~  111 (489)
T PRK11712        109 KDP  111 (489)
T ss_pred             eCC
Confidence            753

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=93.87  E-value=0.19  Score=48.16  Aligned_cols=68  Identities=9%  Similarity=0.057  Sum_probs=50.4

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCC---CeeEEE
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK---SRITLS  126 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~---~ri~lS  126 (259)
                      .-+.|+++.|+     +.+++|+++..-|-.+++|++|.++..      |.+.|++||.++|.|.++....   -+|.||
T Consensus       149 ~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilS  222 (449)
T PRK12329        149 QDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVS  222 (449)
T ss_pred             HHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEE
Confidence            34799999999     557999983100001389999988863      4677999999999999998642   368888


Q ss_pred             Ee
Q 024995          127 IK  128 (259)
Q Consensus       127 ~K  128 (259)
                      +.
T Consensus       223 Rt  224 (449)
T PRK12329        223 RA  224 (449)
T ss_pred             cC
Confidence            63

>PRK05054 exoribonuclease II; Provisional

Probab=90.89  E-value=0.26  Score=49.68  Aligned_cols=72  Identities=13%  Similarity=0.076  Sum_probs=46.5

Q ss_pred             CccccceeeeccCCCccceeeeecccCCeeEEE-Eccccccccc--cch-hhhhhcccCCCCCcceeeeccCCCee----
Q 024995          155 SMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRV--VSQ-DLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       155 ~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~--~~~-~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      +.+.|.|+.+++||    +||+|. +.|++||+ .+.+......  ..+ +.....   . -..    .++.||.|    
T Consensus       563 ~~f~g~I~~v~~~G----~fV~l~-~~~veglV~~~~l~~~~~~y~~~~~~~~~~~---~-~~~----~~~lGd~V~V~v  629 (644)
T PRK05054        563 TRFAAEIIDISRGG----MRVRLL-ENGAVAFIPASFLHAVRDELVCNQENGTVQI---K-GET----VYKLGDVIDVTL  629 (644)
T ss_pred             eEEEEEEEeeecCc----EEEEEe-CCceEEEEEccccCCCccceEEccccceEEE---e-CCE----EEcCCCEEEEEE
Confidence            37999999999999    999995 57999998 5655421000  000 000000   0 011    45999998    


Q ss_pred             EEEecccchhhhh
Q 024995          227 QEIQLSHSLIRKA  239 (259)
Q Consensus       227 ~~v~~~~~~i~ls  239 (259)
                      .+||.++++|.+.
T Consensus       630 ~~vd~~~~~i~~~  642 (644)
T PRK05054        630 AEVRMETRSIIAR  642 (644)
T ss_pred             EEEccccCeEEEE
Confidence            5888888887654

>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=89.80  E-value=0.54  Score=33.81  Aligned_cols=68  Identities=13%  Similarity=0.070  Sum_probs=44.7

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee---EEE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---QEI  229 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---~~v  229 (259)
                      |+.++|+|..-++-+    ++++|. +.|+.|++ ...+++ .  .++.-..|-        ++    |+||.+   +-+
T Consensus         1 G~lV~~~V~EKt~D~----l~v~l~-~~~l~a~l~~~HLsD-~--~~k~~~~~~--------kl----rvG~~L~~~lvL   60 (72)
T cd05699           1 GKLVDARVLKKTLNG----LEVAIL-PEEIRAFLPTMHLSD-H--VSNCPLLWH--------CL----QEGDTIPNLMCL   60 (72)
T ss_pred             CceEEEEEEEEcCCc----EEEEec-CCCcEEEEEccccCC-c--hhhCHHHHh--------hh----hcCCCccceEEE
Confidence            456899999988877    888883 34999998 445553 1  233322233        23    889887   445


Q ss_pred             ecccchhhhhhc
Q 024995          230 QLSHSLIRKASK  241 (259)
Q Consensus       230 ~~~~~~i~ls~k  241 (259)
                      +..++.|.++.|
T Consensus        61 ~~~~r~i~lt~K   72 (72)
T cd05699          61 SNYKGRIILTKK   72 (72)
T ss_pred             eccccEEEEecC
Confidence            777777777654

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=87.46  E-value=0.2  Score=47.05  Aligned_cols=97  Identities=18%  Similarity=0.213  Sum_probs=57.9

Q ss_pred             hhcCCCCeEEEEEEEEeCCCCeeE-EEEeccccCc-----chHhhhhhcCCCCccccCCCCccccceeeeccCCCcccee
Q 024995          101 DILNEGDEVRVKVIKIDREKSRIT-LSIKQLEEDP-----LLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIF  174 (259)
Q Consensus       101 ~~~~~Gd~V~vkVl~id~~~~ri~-lS~K~~~~~p-----~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~f  174 (259)
                      ..+++||.+...+---+.  +|+. -+.|+....-     .....+.+.       .+.|++++|+|.++...|   .+|
T Consensus        89 ~~~~vGd~i~~~i~~~~f--gRiaaq~akq~i~Qkir~~er~~i~~ey~-------~~~Geiv~g~V~r~~~~~---~i~  156 (374)
T PRK12328         89 PSVEIGDELTYELSLENM--GRTAANTLFKELEYHIQRLLEESIFEKYK-------KKVGKIVFGTVVRVDNEE---NTF  156 (374)
T ss_pred             CCCCCCCEEEEecChhhC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HhcCcEEEEEEEEEecCC---CEE
Confidence            348899999987744433  3332 2233322100     011122221       235888999999998755   378


Q ss_pred             eeecccCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccc
Q 024995          175 EELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHS  234 (259)
Q Consensus       175 v~l~~~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~  234 (259)
                      +.|   ++++|+++.+.-                  .+..+|    ++||.+    .+|..+++
T Consensus       157 vdl---g~~ea~LP~~eq------------------ip~E~~----~~Gdrik~~i~~V~~~~k  195 (374)
T PRK12328        157 IEI---DEIRAVLPMKNR------------------IKGEKF----KVGDVVKAVLKRVKIDKN  195 (374)
T ss_pred             EEc---CCeEEEeCHHHc------------------CCCCcC----CCCCEEEEEEEEEecCCC
Confidence            777   589999954321                  133345    899998    67877766

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

Probab=87.37  E-value=3.2  Score=34.48  Aligned_cols=62  Identities=18%  Similarity=0.197  Sum_probs=42.1

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcc----cccC-------hhhhcCCCCeEEEEEEEEe
Q 024995           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQD-------IRDILNEGDEVRVKVIKID  117 (259)
Q Consensus        54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~----~~~~-------~~~~~~~Gd~V~vkVl~id  117 (259)
                      -+.-.|++++|+     ..|+|++++      .++.|+.---+..+    ...+       -.+.+++|..|+++|+..-
T Consensus        77 FkpfKGEVvdgvV~~Vnk~G~F~~~G------Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr  150 (170)
T KOG3298|consen   77 FKPFKGEVVDGVVTKVNKMGVFARSG------PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR  150 (170)
T ss_pred             EeecCCcEEEEEEEEEeeeeEEEecc------ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence            367789999999     889999998      57777643222211    1111       1225889999999998876


Q ss_pred             CCCC
Q 024995          118 REKS  121 (259)
Q Consensus       118 ~~~~  121 (259)
                      .+..
T Consensus       151 ~~~~  154 (170)
T KOG3298|consen  151 VDET  154 (170)
T ss_pred             Eeee
Confidence            5333

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=85.70  E-value=0.86  Score=46.46  Aligned_cols=73  Identities=18%  Similarity=0.186  Sum_probs=48.9

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCC----CCCcceeeeccCCCee-
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAP----PSGKKFTLLARAGRQV-  226 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~r~G~~V-  226 (259)
                      +|....|.|.+++.||    +|++|. ..|++|++ ++.+..+          |+....    ....+-...++.||.| 
T Consensus       622 vg~~f~g~V~~v~~~g----~~V~l~-~~~ieglV~~s~L~~d----------~y~~~~~~~~l~~~~~~~~~~lgd~v~  686 (706)
T COG0557         622 VGEEFDGVVTGVTSFG----FFVELP-ELGLEGLVHISSLPDD----------YYHFDERGQALVGEKSGKVYRLGDEVK  686 (706)
T ss_pred             cCCEEEEEEEEEEecc----EEEEec-ccccccceEcccCCCc----------eeeeccccceeeccccccccccCCEEE
Confidence            4778999999999999    999993 34699998 6666521          121111    0112233356999999 


Q ss_pred             ---EEEecccchhhhhh
Q 024995          227 ---QEIQLSHSLIRKAS  240 (259)
Q Consensus       227 ---~~v~~~~~~i~ls~  240 (259)
                         .+++...++|.+++
T Consensus       687 v~v~~v~~~~~~i~~~~  703 (706)
T COG0557         687 VKVTSVDLDERKIDFEL  703 (706)
T ss_pred             EEEEEEcccccceEEEe
Confidence               47777777776654

>COG4044 Uncharacterized protein conserved in archaea [Function unknown]

Probab=82.33  E-value=1.1  Score=38.79  Aligned_cols=74  Identities=24%  Similarity=0.376  Sum_probs=52.6

Q ss_pred             ccCCCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEceecCcccccCh-hh---hc--CCCCeEEEEEEEEeCC
Q 024995           53 SSRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-RD---IL--NEGDEVRVKVIKIDRE  119 (259)
Q Consensus        53 ~~~l~~G~iv~G~-------~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~-~~---~~--~~Gd~V~vkVl~id~~  119 (259)
                      +.++++|+++-|+       .||++|+++- .|....++|+|.-+|....-..| ++   .|  -.--.++|-|.++|..
T Consensus        70 l~~~~~Gdv~vGrl~~l~~vgyg~yvdigV-~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~  148 (247)
T COG4044          70 LSKVEEGDVYVGRLIDLGKVGYGAYVDIGV-LGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKL  148 (247)
T ss_pred             cccCCCCcEEEEEEeeeccceeEEEccccc-cCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccch
Confidence            4788999999999       7999999973 33235789999999876655444 22   22  2345677888888876


Q ss_pred             CCeeEEEE
Q 024995          120 KSRITLSI  127 (259)
Q Consensus       120 ~~ri~lS~  127 (259)
                      .+.|...+
T Consensus       149 ~~EIea~l  156 (247)
T COG4044         149 AQEIEARL  156 (247)
T ss_pred             hhhhhhhh
Confidence            66665544

>PF09876 DUF2103: Predicted metal-binding protein (DUF2103); InterPro: IPR018664 This family of various putative metal binding prokaryotic proteins has no known function

Probab=82.06  E-value=1.4  Score=33.99  Aligned_cols=54  Identities=26%  Similarity=0.343  Sum_probs=32.9

Q ss_pred             cCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccCCCeeEEEecccc
Q 024995          180 EDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQVQEIQLSHS  234 (259)
Q Consensus       180 ~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V~~v~~~~~  234 (259)
                      .++|..++++.+...+...++.+..|+.+. ...++|++++|.|-.||||-.-+.
T Consensus        32 ~~~Vk~IiPG~I~~~~~~~~~gl~lkvt~~-~~~Gn~Kllar~G~SvQEvfVVT~   85 (103)
T PF09876_consen   32 HPGVKKIIPGVISRSGGRSSGGLRLKVTRP-TRGGNFKLLARSGSSVQEVFVVTT   85 (103)
T ss_pred             CCCCCEEecccEEcCCCCCCCCeEEEEEEe-cCCCcEEEEEecCCeeEEEEEEee
Confidence            355555554444433322233455566543 356679999999999999866544

>TIGR02062 RNase_B exoribonuclease II

Probab=81.48  E-value=2  Score=43.29  Aligned_cols=70  Identities=11%  Similarity=0.077  Sum_probs=44.6

Q ss_pred             CccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCccee----eeccCCCee---
Q 024995          155 SMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFT----LLARAGRQV---  226 (259)
Q Consensus       155 ~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~r~G~~V---  226 (259)
                      ....|.|..++++|    +||+|. ..|++||+ .+.+....     +.  |. ... ....+.    -.++.||.|   
T Consensus       559 ~~f~g~I~~v~~~g----~~v~l~-~~~~~g~v~~~~l~~~~-----~~--~~-~~~-~~~~~~l~g~~~~~lgd~v~V~  624 (639)
T TIGR02062       559 TRFAAEIVDISRGG----MRVRLL-ENGAIAFIPAAFLHANR-----EE--LV-CNQ-ENGTVQIKGETVYKIGDVIDVV  624 (639)
T ss_pred             cEEEEEEEeeeCCc----EEEEEe-cCceEEEEEhhhcCCCC-----cc--eE-Ecc-cccEEEEeccEEEecCCEEEEE
Confidence            36899999999999    999995 57999998 44443210     10  10 000 000000    046899999   


Q ss_pred             -EEEecccchhhh
Q 024995          227 -QEIQLSHSLIRK  238 (259)
Q Consensus       227 -~~v~~~~~~i~l  238 (259)
                       .+||.++++|.+
T Consensus       625 v~~vd~~~~~i~~  637 (639)
T TIGR02062       625 LTEVRMETRSIIA  637 (639)
T ss_pred             EEEeccccCcEee
Confidence             588888887754

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.

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

Probab=81.42  E-value=2.1  Score=31.97  Aligned_cols=72  Identities=15%  Similarity=0.107  Sum_probs=41.8

Q ss_pred             CCCCccccceeeeccCCCccceeeeecc------cCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCC
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQ------EDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~------~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~  224 (259)
                      ++|+++.|+|+++..-.    +++++..      .....|++ +|+.+..               .....+....+++||
T Consensus         5 ~~GDiVig~V~~v~~~~----~~v~I~~v~~~~l~~~~~g~l~~~dv~~~---------------~~d~~~~~~~f~~GD   65 (92)
T cd05791           5 KVGSIVIARVTRINPRF----AKVDILCVGGRPLKESFRGVIRKEDIRAT---------------EKDKVEMYKCFRPGD   65 (92)
T ss_pred             CCCCEEEEEEEEEcCCE----EEEEEEEecCeecCCCcccEEEHHHcccc---------------ccchHHHHhhcCCCC
Confidence            56888999999998776    6666621      33456777 3443311               001012333679999


Q ss_pred             eeE-E-Eeccc-chhhhhhch
Q 024995          225 QVQ-E-IQLSH-SLIRKASKR  242 (259)
Q Consensus       225 ~V~-~-v~~~~-~~i~ls~k~  242 (259)
                      .|. + +.... +.+.||++.
T Consensus        66 iV~AkVis~~~~~~~~Lst~~   86 (92)
T cd05791          66 IVRAKVISLGDASSYYLSTAE   86 (92)
T ss_pred             EEEEEEEEcCCCCCcEEEecC
Confidence            993 2 33332 456666653

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".

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

Probab=81.20  E-value=2.3  Score=35.78  Aligned_cols=59  Identities=8%  Similarity=0.131  Sum_probs=37.9

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-Eccccccccccch--hhhhhcccCCCCCcceeeeccCCCee
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQ--DLQLWLSNAPPSGKKFTLLARAGRQV  226 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~r~G~~V  226 (259)
                      |++++|.|+++.++|    +|+.+   +=+++++ .+.+. +.-..-.  ....|...    +.  +..++.|+.|
T Consensus        82 gEVv~g~V~~v~~~G----~~v~~---Gp~~ifI~~~~l~-~~~~fd~~~~~~~~~~~----~~--~~~i~~g~~V  143 (176)
T PTZ00162         82 DEVLDAIVTDVNKLG----FFAQA---GPLKAFVSRSAIP-PDFVYDSDSAYPCYISS----DG--QIQIKPNTEV  143 (176)
T ss_pred             CCEEEEEEEEEecce----EEEEe---eCeEEEEcHHHCC-CccEECCCCCcceEecC----CC--cEEECCCCEE
Confidence            677999999999999    99888   4567888 45553 2222111  22244421    12  2367999999

>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]

Probab=80.38  E-value=2.3  Score=41.55  Aligned_cols=71  Identities=24%  Similarity=0.365  Sum_probs=52.0

Q ss_pred             ccCCCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEceecCcccccCh-----hhhcCCCCeEEEEEEEEeCCC
Q 024995           53 SSRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----RDILNEGDEVRVKVIKIDREK  120 (259)
Q Consensus        53 ~~~l~~G~iv~G~-------~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~-----~~~~~~Gd~V~vkVl~id~~~  120 (259)
                      .....+|.+|.|+       =-.+||+++     ..-.||+|.+++.+ +...+     ...++.||.+-|.+..-...+
T Consensus        32 ~~~~~~gniy~grv~~i~p~~~aafvdig-----~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~  105 (487)
T COG1530          32 AKEQIVGNIYKGRVTRVLPSLEAAFVDIG-----LERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPRGT  105 (487)
T ss_pred             CcEeeecCceEEEecccCccchhheeecc-----CCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecCcc
Confidence            4466789999999       235899998     47899999999998 43333     357999999999998776544


Q ss_pred             CeeEEEEec
Q 024995          121 SRITLSIKQ  129 (259)
Q Consensus       121 ~ri~lS~K~  129 (259)
                      +=-.||-.-
T Consensus       106 Kga~lT~~I  114 (487)
T COG1530         106 KGARLTTDI  114 (487)
T ss_pred             ccccceeEE
Confidence            433444433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	259
2k4k_A	130	Solution Structure Of Gsp13 From Bacillus Subtilis		8e-10
2aho_B	266	Structure Of The Archaeal Initiation Factor Eif2 Al		4e-06
3aev_A	275	Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex		7e-06
1yz6_A	274	Crystal Structure Of Intact Alpha Subunit Of Aif2 F		8e-06
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		1e-05
2oce_A	780	Crystal Structure Of Tex Family Protein Pa5201 From		2e-05
3bzc_A	785	Crystal Structure Of The Tex Protein From Pseudomon		2e-05
1sro_A	76	S1 Rna Binding Domain, Nmr, 20 Structures Length =		9e-05

>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis Length = 130

Iteration: 1
 Score = 60.8 bits (146), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 32/87 (36%), Positives = 52/87 (59%), Gaps = 10/87 (11%)
Query: 53  SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGD 107
           +++  V  ++ G+      YGAF+ L          GLVH+SEV+   ++DI + L+ GD
Sbjct: 2   AAKFEVGSVYTGKVTGLQAYGAFVALD-----EETQGLVHISEVTHGFVKDINEHLSVGD 56
Query: 108 EVRVKVIKIDREKSRITLSIKQLEEDP 134
           EV+VKV+ +D EK +I+LSI+  +  P
Sbjct: 57  EVQVKVLAVDEEKGKISLSIRATQAAP 83

>pdb|2AHO|B Chain B, Structure Of The Archaeal Initiation Factor Eif2 Alpha- Gamma Heterodimer From Sulfolobus Solfataricus Complexed With Gdpnp Length = 266

Iteration: 1
 Score = 48.1 bits (113), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 43/68 (63%), Gaps = 3/68 (4%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           DYG+++ L   D    L   +  SEVS   +++IRD+L E  +V VKVI++DR K  + +
Sbjct: 24  DYGSYVSL---DEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDV 80
Query: 126 SIKQLEED 133
           S+K++ +D
Sbjct: 81  SLKKVTDD 88

>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From Pyrococcus Horikoshii Ot3 Length = 275

Iteration: 1
 Score = 47.8 bits (112), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 3/65 (4%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           +YGAF+ L   D        +H+SEV+   +++IRD L EG +V  KVI++D  K  I L
Sbjct: 24  NYGAFLEL---DEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDL 80
Query: 126 SIKQL 130
           S++++
Sbjct: 81  SLRRV 85

>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From Pyrococcus Abyssi Length = 274

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 3/65 (4%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           +YGAF+ L   D        +H+SEV+   +++IRD L EG +V  KVI++D  K  I L
Sbjct: 23  NYGAFLEL---DEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDL 79
Query: 126 SIKQL 130
           S++++
Sbjct: 80  SLRRV 84

>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase Length = 723

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 49/85 (57%), Gaps = 11/85 (12%)
Query: 53  SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGD 107
           ++ + V  ++ G+     D+GAF+ +          GLVH+S+++   ++ + D L  G 
Sbjct: 622 TAEIEVGRVYTGKVTRIVDFGAFVAIGGGK-----EGLVHISQIADKRVEKVTDYLQMGQ 676
Query: 108 EVRVKVIKIDREKSRITLSIKQLEE 132
           EV VKV+++DR+  RI LSIK+  E
Sbjct: 677 EVPVKVLEVDRQ-GRIRLSIKEATE 700

>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From Pseudomonas Aeruginosa Length = 780

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 41/63 (65%), Gaps = 5/63 (7%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           ++GAF+ +       H  GLVH+S +S   ++D  +++  GD V+VKV+++D  ++R+ L
Sbjct: 668 NFGAFVDIGV-----HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGL 722
Query: 126 SIK 128
           S++
Sbjct: 723 SMR 725

>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas Aeruginosa, Crystal Form I Length = 785

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 41/63 (65%), Gaps = 5/63 (7%)
Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           ++GAF+ +       H  GLVH+S +S   ++D  +++  GD V+VKV+++D  ++R+ L
Sbjct: 667 NFGAFVDIGV-----HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGL 721
Query: 126 SIK 128
           S++
Sbjct: 722 SMR 724

>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures Length = 76

Iteration: 1
 Score = 43.9 bits (102), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 47/81 (58%), Gaps = 11/81 (13%)
Query: 54  SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 108
           + + V  ++ G+     D+GAF+ +          GLVH+S+++   ++ + D L  G E
Sbjct: 1   AEIEVGRVYTGKVTRIVDFGAFVAIGGGK-----EGLVHISQIADKRVEKVTDYLQMGQE 55
Query: 109 VRVKVIKIDREKSRITLSIKQ 129
           V VKV+++DR+  RI LSIK+
Sbjct: 56  VPVKVLEVDRQ-GRIRLSIKE 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	259
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	4e-22
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	8e-22
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	2e-21
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	2e-04
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	4e-21
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	9e-06
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	5e-19
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	1e-18
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	2e-18
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	2e-17
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	1e-16
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	1e-15
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	2e-15
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	2e-15
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	7e-15
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	9e-13
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	8e-12
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	2e-07
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	3e-07
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	4e-07
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	4e-07
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	2e-06
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	4e-05
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	7e-05
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	5e-04

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130

 Score = 87.9 bits (218), Expect = 4e-22
 Identities = 35/108 (32%), Positives = 61/108 (56%), Gaps = 10/108 (9%)

Query: 53  SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGD 107
           +++  V  ++ G+      YGAF+ L          GLVH+SEV+   ++DI + L+ GD
Sbjct: 2   AAKFEVGSVYTGKVTGLQAYGAFVAL-----DEETQGLVHISEVTHGFVKDINEHLSVGD 56

Query: 108 EVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSS 155
           EV+VKV+ +D EK +I+LSI+  +  P  +  +   P+   V  ++S+
Sbjct: 57  EVQVKVLAVDEEKGKISLSIRATQAAPEKKESKPRKPKAAQVSEEAST 104

>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 Length = 182

 Score = 88.3 bits (219), Expect = 8e-22
 Identities = 23/90 (25%), Positives = 47/90 (52%), Gaps = 8/90 (8%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
            VED+ +       + GA++ L   + +    G++ +SE+S   I+ I  ++  G    V
Sbjct: 14  EVEDVVMVNVRSIAEMGAYVSLLEYNNI---EGMILLSELSRRRIRSINKLIRIGRNECV 70

Query: 112 KVIKIDREKSRITLSIKQLEEDPLLETLEK 141
            VI++D+EK  I LS +++  +  ++  +K
Sbjct: 71  VVIRVDKEKGYIDLSKRRVSPEEAIKCEDK 100

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 84.9 bits (211), Expect = 2e-21
 Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 10/91 (10%)

Query: 49  WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDIL 103
           +N + +      I  G+       GA + L   DG+    G +  SE S D ++D   +L
Sbjct: 22  FNNWVALNKKGAIVTGKVTAVDAKGATVELA--DGV---EGYLRASEASRDRVEDATLVL 76

Query: 104 NEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
           + GDEV  K   +DR+   I+LS++  +E  
Sbjct: 77  SVGDEVEAKFTGVDRKNRAISLSVRAKDEAD 107

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 1/38 (2%), Positives = 10/38 (26%), Gaps = 2/38 (5%)

Query: 114 IKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVIS 151
           +         +  +           +     + G++++
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMFNNWVALN--KKGAIVT 36

>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 Length = 175

 Score = 86.4 bits (214), Expect = 4e-21
 Identities = 22/90 (24%), Positives = 48/90 (53%), Gaps = 8/90 (8%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
            ++DI +       + GA++ L   D +    G++ +SE+S   I+ I+ ++  G     
Sbjct: 14  EIDDIVMVNVQQIAEMGAYVKLLEYDNI---EGMILLSELSRRRIRSIQKLIRVGKNDVA 70

Query: 112 KVIKIDREKSRITLSIKQLEEDPLLETLEK 141
            V+++D+EK  I LS +++  + +++  EK
Sbjct: 71  VVLRVDKEKGYIDLSKRRVSSEDIIKCEEK 100

>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 Length = 175

 Score = 44.0 bits (104), Expect = 9e-06
 Identities = 13/123 (10%), Positives = 30/123 (24%), Gaps = 13/123 (10%)

Query: 12  KSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-DY 67
           +SI ++ +   G      V++ ++E   +  S++        K   +            Y
Sbjct: 56  RSIQKLIR--VGKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRY 113

Query: 68  GAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 126
            A       + LY                     +              I+     +   
Sbjct: 114 CAEKFQIPLEELYK------TIAWPLSRKFGHAYEAFKLSIIDETVWEGIEPPSKDVLDE 167

Query: 127 IKQ 129
           +K 
Sbjct: 168 LKN 170

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115

 Score = 79.2 bits (196), Expect = 5e-19
 Identities = 32/92 (34%), Positives = 46/92 (50%), Gaps = 11/92 (11%)

Query: 49  WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDI 102
           W   + R        GR     DYG F+ +   +G+    GLVHVSE+ W         +
Sbjct: 21  WVAIAKRYPEGTKLTGRVTNLTDYGCFVEIE--EGV---EGLVHVSEMDWTNKNIHPSKV 75

Query: 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
           +N GD V V V+ ID E+ RI+L +KQ + +P
Sbjct: 76  VNVGDVVEVMVLDIDEERRRISLGLKQCKANP 107

>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 Length = 308

 Score = 82.3 bits (203), Expect = 1e-18
 Identities = 25/90 (27%), Positives = 49/90 (54%), Gaps = 8/90 (8%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
            VED+ +       + GA++ L   + +    G++H+SE+S   I+ I  ++  G    V
Sbjct: 12  EVEDVVMVNVRSIQEMGAYVSLLEYNNI---EGMIHLSELSRRRIRSINKLIRIGRNECV 68

Query: 112 KVIKIDREKSRITLSIKQLEEDPLLETLEK 141
           KVI++D+EK  I LS +++  +  ++  +K
Sbjct: 69  KVIRVDKEKGYIDLSKRRVSPEEAIKCEDK 98

>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* Length = 266

 Score = 81.6 bits (201), Expect = 2e-18
 Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 8/90 (8%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
           +  +I +       DYG+++ L    GL      +  SEVS   +++IRD+L E  +V V
Sbjct: 10  SEGEILIATVKQVFDYGSYVSLDEYGGL---QAFLPWSEVSSKWVKNIRDVLKENRKVIV 66

Query: 112 KVIKIDREKSRITLSIKQLEEDPLLETLEK 141
           KVI++DR K  + +S+K++ +D   +   +
Sbjct: 67  KVIRVDRRKGTVDVSLKKVTDDERRKKNLQ 96

>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} Length = 119

 Score = 74.8 bits (184), Expect = 2e-17
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 6/71 (8%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID--REKSRI 123
           DYGAFI +          GLVH + +S   +    +I++ GD+V VK+I  +   ++ ++
Sbjct: 35  DYGAFIKI----PGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKV 90

Query: 124 TLSIKQLEEDP 134
           +LS+K + +  
Sbjct: 91  SLSMKVVNQGT 101

>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} Length = 103

 Score = 72.3 bits (178), Expect = 1e-16
 Identities = 20/92 (21%), Positives = 45/92 (48%), Gaps = 10/92 (10%)

Query: 49  WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDI 102
                    + DI+ G+      +G F+  +         GLVH+SE+  +  + ++ D+
Sbjct: 3   SGSSGEEPTIGDIYNGKVTSIMQFGCFV--QLEGLRKRWEGLVHISELRREGRVANVADV 60

Query: 103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
           +++G  V+VKV+       + +LS+K ++++ 
Sbjct: 61  VSKGQRVKVKVLSFTGT--KTSLSMKDVDQET 90

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 74.8 bits (185), Expect = 1e-15
 Identities = 27/86 (31%), Positives = 47/86 (54%), Gaps = 15/86 (17%)

Query: 56  VNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 108
             V  I+ G+     D+GAF++  F   DGL      VHVS++S + +    D+L EG  
Sbjct: 635 AEVGKIYDGKVVKVVDFGAFVNF-FGAKDGL------VHVSQISNERVAKPSDVLKEGQM 687

Query: 109 VRVKVIKIDREKSRITLSIKQLEEDP 134
           V+VK++  D  + +  LS+K ++++ 
Sbjct: 688 VKVKLLGFDD-RGKTKLSMKVVDQET 712

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 74.5 bits (184), Expect = 2e-15
 Identities = 28/86 (32%), Positives = 48/86 (55%), Gaps = 15/86 (17%)

Query: 56  VNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 108
           + V  ++ G+     D+GAF+ +     +GL      VH+S+++   ++ + D L  G E
Sbjct: 625 IEVGRVYTGKVTRIVDFGAFVAI-GGGKEGL------VHISQIADKRVEKVTDYLQMGQE 677

Query: 109 VRVKVIKIDREKSRITLSIKQLEEDP 134
           V VKV+++DR + RI LSIK+  E  
Sbjct: 678 VPVKVLEVDR-QGRIRLSIKEATEQS 702

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80

 Score = 68.1 bits (167), Expect = 2e-15
 Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 9/68 (13%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
            YGAFI+L        + GL+   ++    +++    LN GDE+ V+ I +  EK  I  
Sbjct: 18  KYGAFINL-----NEQVRGLLRPRDMISLRLEN----LNVGDEIIVQAIDVRPEKREIDF 68

Query: 126 SIKQLEED 133
               LE  
Sbjct: 69  KYIPLEHH 76

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Length = 275

 Score = 71.6 bits (175), Expect = 7e-15
 Identities = 27/90 (30%), Positives = 46/90 (51%), Gaps = 8/90 (8%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
              +  V       +YGAF+ L    G       +H+SEV+   +++IRD L EG +V  
Sbjct: 10  EEGEFVVATVKRIHNYGAFLELDEYPGK---EAFMHISEVASTWVRNIRDYLKEGQKVVA 66

Query: 112 KVIKIDREKSRITLSIKQLEEDPLLETLEK 141
           KVI++D  K  I LS++++ +      L++
Sbjct: 67  KVIRVDPRKGHIDLSLRRVTQQQRKAKLQE 96

>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 Length = 757

 Score = 66.5 bits (163), Expect = 9e-13
 Identities = 21/90 (23%), Positives = 44/90 (48%), Gaps = 19/90 (21%)

Query: 56  VNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDL----IQDIRDILN 104
             V +  +G       +GAF+ L  P  DGL      +H+S++        ++++ D+L 
Sbjct: 665 PEVGERILGSVVKTTTFGAFVSL-LPGKDGL------LHISQIRKLAGGKRVENVEDVLG 717

Query: 105 EGDEVRVKVIKIDREKSRITLSIKQLEEDP 134
            G +V+V++ +ID  + +++L      E+ 
Sbjct: 718 VGQKVQVEIAEIDS-RGKLSLIPVIEGEEA 746

>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 Length = 785

 Score = 63.8 bits (156), Expect = 8e-12
 Identities = 27/114 (23%), Positives = 55/114 (48%), Gaps = 5/114 (4%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 125
           ++GAF+ +    G+ H  GLVH+S +S   ++D  +++  GD V+VKV+++D  ++R+ L
Sbjct: 667 NFGAFVDI----GV-HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGL 721

Query: 126 SIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ 179
           S++  +        ++     GS        +    +       + A+F    Q
Sbjct: 722 SMRMSDTPGEKVEGQRGGRPTGSGQPRQERGAPRGQSAPPANNAMAALFANAKQ 775

>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 = 48.7 bits (116), Expect = 2e-07
 Identities = 26/124 (20%), Positives = 58/124 (46%), Gaps = 14/124 (11%)

Query: 20  GLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLR 74
           GL  +I++VK  +    +     +  +  ++  +    V+++  G      +YG F++L 
Sbjct: 43  GLVLAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQEVVEGEVLQVDNYGVFVNLG 102

Query: 75  FPDGLYHLTGL----VHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREK----SRITL 125
             DGL H++ +    +    V   +  +  + ++ +GD+VR +VI +         RI L
Sbjct: 103 PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTGRLPRIAL 162

Query: 126 SIKQ 129
           +++Q
Sbjct: 163 TMRQ 166

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Length = 1030

 Score = 50.3 bits (120), Expect = 3e-07
 Identities = 9/65 (13%), Positives = 18/65 (27%), Gaps = 6/65 (9%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-IRDILNEGDEVRVKVIKIDREKSRIT 124
                           +  +V+    +   ++    +I   G     KVI ID       
Sbjct: 918 HNDIICTTNS-----EVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAE 972

Query: 125 LSIKQ 129
           +S+  
Sbjct: 973 VSLLD 977

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Length = 1219

 Score = 49.9 bits (119), Expect = 4e-07
 Identities = 9/50 (18%), Positives = 18/50 (36%), Gaps = 1/50 (2%)

Query: 81  HLTGLVHVSEVSWDLIQD-IRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129
            +  +V+    +   ++    +I   G     KVI ID       +S+  
Sbjct: 925 EVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLD 974

>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 = 48.0 bits (114), Expect = 4e-07
 Identities = 30/154 (19%), Positives = 62/154 (40%), Gaps = 26/154 (16%)

Query: 2   SPSHSCKEPQKSIHEIAK-----------GLTGSIISVKVIQANEEMKKLVFSEKDAVWN 50
            P    K+ ++++ +I             G   SI+ VK I   + +     +    V+ 
Sbjct: 14  PPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFE 73

Query: 51  KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL----VHVSEVSWDLI-QDIR 100
                  + ++  G      ++G+F+ L   DGL H++ +    V        +I ++  
Sbjct: 74  TLVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETG 133

Query: 101 DILNEGDEVRVKVIKIDREKSR-----ITLSIKQ 129
            +L  GD VR +++ I  +  R     I L+++Q
Sbjct: 134 KVLEIGDYVRARIVAISLKAERKRGSKIALTMRQ 167

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Length = 285

 Score = 47.3 bits (112), Expect = 2e-06
 Identities = 19/124 (15%), Positives = 40/124 (32%), Gaps = 17/124 (13%)

Query: 25  IISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGL 79
            I ++V + +     L + E      + +        +       +  G F++L  P+  
Sbjct: 119 YIRLEVDKKDRIWGLLAYQEDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYL--PENN 176

Query: 80  YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETL 139
               G +H SE               G  +  +VI        + LS+K    + L    
Sbjct: 177 ML--GFIHPSE--------RYAEPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDA 226

Query: 140 EKVI 143
           + ++
Sbjct: 227 QMIL 230

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A Length = 179

 Score = 42.3 bits (99), Expect = 4e-05
 Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 15/91 (16%)

Query: 51  KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGL-----YHLTGLVHVSEVSWDLIQDIR 100
                +   D+ +GR     +  A I +    G          G++HVS V    +++I 
Sbjct: 50  SPIPEIVKGDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEIS 109

Query: 101 DILNEGDEVRVKVIKIDREKSRITLSIKQLE 131
           + +   D ++ +VI        + LS K+ E
Sbjct: 110 EAVGYLDILKARVI-----GDNLRLSTKEEE 135

>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 Length = 119

 Score = 40.4 bits (94), Expect = 7e-05
 Identities = 11/82 (13%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           D+G  + +    G+      + + +    +  ++    L  G  +   V K+      ++
Sbjct: 34  DHGYLVDI----GVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVS 89

Query: 125 LSIKQLEEDPLLETLEKVIPQD 146
           LS+   E    + T ++    +
Sbjct: 90  LSVGHSEVSTAIATEQQSWNLN 111

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

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 21/152 (13%), Positives = 43/152 (28%), Gaps = 24/152 (15%)

Query: 2   SPSHSCKEPQKSIHEIAK--------GLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYS 53
            PS+     Q  +             G  G II V      +  K  V   +     +  
Sbjct: 15  HPSYFGPRMQDYLKAKLLADVEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVK 74

Query: 54  SRVNVEDIFVG----------RDYGAFIHLRFPDGLYHLTGL----VHVSEVSWDLIQDI 99
            R  +   F G             G F ++   +       +          +       
Sbjct: 75  YRAVLWRPFRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGE 134

Query: 100 RDILNEGDEVRVKVI--KIDREKSRITLSIKQ 129
             ++ +G  VR+K++  + D  +     ++K+
Sbjct: 135 DQVIEKGSNVRLKIVGTRTDATEIFAIATMKE 166

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	259
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.92
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.84
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.74
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.7
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.69
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.67
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.62
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.61
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.61
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.61
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.59
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.59
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.55
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.55
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.47
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.42
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.37
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.35
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.31
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.27
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.26
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	99.23
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.17
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.16
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.13
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.12
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.1
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	99.08
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	99.03
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.03
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	99.03
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	99.02
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	99.01
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.0
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.0
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.96
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	98.96
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	98.94
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	98.93
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	98.9
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.87
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.87
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.74
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.73
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.71
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.69
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.65
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.64
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.48
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.28
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.27
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.25
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	98.25
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.16
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	98.09
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.06
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	98.05
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.04
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.01
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.94
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	97.9
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	97.86
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.84
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	97.81
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	97.68
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.65
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	97.63
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	97.63
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	97.58
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.56
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.39
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	97.37
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	97.16
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	97.14
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	97.07
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	96.76
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	96.44
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	95.7
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	95.57
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	95.43
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	95.23
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	95.21
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	95.05
2r7d_A	469	Ribonuclease II family protein; structural genomic	94.93
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	93.64
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	93.41
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	89.33
1jjg_A	102	M156R; beta barrel, S1 motif, OB fold, MYXV156R, N	88.56

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

Probab=99.92  E-value=1.1e-25  Score=201.54  Aligned_cols=174  Identities=13%  Similarity=0.079  Sum_probs=141.9

Q ss_pred             CCCCEEEEEEEEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE------eeeEEEEEccCCCCc-cEEEEEEceecCc
Q 024995           21 LTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR------DYGAFIHLRFPDGLY-HLTGLVHVSEVSW   93 (259)
Q Consensus        21 ~vG~~v~~~Vl~id~~~~~v~lS~k~~~~~~~~~~l~~G~iv~G~------~~G~fV~l~~~~g~~-gi~glv~isels~   93 (259)
                      .+||+|+|+|+ .|.+ +++++|.+.+       .+++|+++.|+      +|||||+++     . +.+||||+||++|
T Consensus        41 ~vGdevev~v~-~d~~-~r~iat~~~p-------~~~~G~~~~g~V~~v~~~~GaFVdiG-----~~~~d~lvp~sel~~  106 (285)
T 3go5_A           41 TVGDTVKGFAY-TDMK-QKLRLTTLEV-------TATQDQFGWGRVTEVRKDLGVFVDTG-----LPDKEIVVSLDILPE  106 (285)
T ss_dssp             CTTSEEEEEEE-ECTT-SCEEEECSCC-------CSCSSSCEEEEEEEEETTTEEEEECS-----CTTCCEEEEGGGSCS
T ss_pred             ccCCEEEEEEE-ECCC-CCEEEecccc-------cccCCCEEEEEEEEEccCceEEEEEC-----CCCcEEEEEHHHCCc
Confidence            59999999986 5754 6777887654       57899999998      399999997     4 5899999999998


Q ss_pred             ccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecc-ccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccc
Q 024995           94 DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL-EEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA  172 (259)
Q Consensus        94 ~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~-~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~  172 (259)
                      .+.    ..+++||.+.|+ +++|+ ++||.+|+|+. ..+||....++ ++        +|+.++|+|+++++||    
T Consensus       107 ~~~----~~~~~Gd~v~v~-l~iD~-~~Ri~ls~k~~~~~~~~~~~~~~-~~--------~G~~V~g~V~~i~~~G----  167 (285)
T 3go5_A          107 LKE----LWPKKGDQLYIR-LEVDK-KDRIWGLLAYQEDFQRLARPAYN-NM--------QNQNWPAIVYRLKLSG----  167 (285)
T ss_dssp             SGG----GSCCTTCEEEEE-EEECT-TSCEEEEECCHHHHHHHCCCCCS-CC--------TTCEEEEEEEEEETTE----
T ss_pred             ccc----cccCCCCEEEEE-EEECC-CCcEEEEehhhhhcchhhhhhhh-CC--------CCCEEEEEEEEEeCCc----
Confidence            653    346899999766 59998 79999999976 46788654333 34        3677999999999999    


Q ss_pred             eee-eecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhhh
Q 024995          173 IFE-ELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCNE  246 (259)
Q Consensus       173 ~fv-~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~~  246 (259)
                      +|+ .+  ++|+.||+ +|+++                     .    .+++||+|    ++|+.+.+||+||+|++...
T Consensus       168 ~fV~~i--~~g~~Glih~SEl~---------------------~----~l~~Gd~v~~~V~~id~~d~kI~LSlk~~~~~  220 (285)
T 3go5_A          168 TFVYLP--ENNMLGFIHPSERY---------------------A----EPRLGQVLDARVIGFREVDRTLNLSLKPRSFE  220 (285)
T ss_dssp             EEEEET--TTTEEEEECGGGCS---------------------S----CCCTTCEEEEEEEEEETTTTEEEEECSCCCCC
T ss_pred             EEEEEe--CCCeEEEEEHHHcc---------------------c----cCCCCCEEEEEEEEEECCCCeEEEEeChhhhh
Confidence            998 88  89999999 66654                     1    24899998    79999999999999999888


Q ss_pred             hhHHhhhh
Q 024995          247 YWNVFHET  254 (259)
Q Consensus       247 p~~~~~~~  254 (259)
                      +++..+++
T Consensus       221 ~~~~~a~~  228 (285)
T 3go5_A          221 MLENDAQM  228 (285)
T ss_dssp             CCCHHHHH
T ss_pred             ccchHHHH
Confidence            88876654

>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=99.84  E-value=1.3e-22  Score=170.39  Aligned_cols=117  Identities=23%  Similarity=0.332  Sum_probs=91.4

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecc
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~  130 (259)
                      +++|+++.|+     +||+||+|.+.   .|++||||+|+|+|.++.++++.|++||.|+|+|+++|.+++||.||+|++
T Consensus        13 p~~G~iv~G~V~~I~~fGaFV~L~e~---~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~~   89 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAEMGAYVSLLEY---NNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRV   89 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTT---TTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTTC
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccC---CCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence            4899999999     99999999311   279999999999999999999999999999999999999999999999999


Q ss_pred             ccCcchHhhhhhcCCCCccccCCCCccccceeeecc-CCCccceeeeecccCCeeEEE-Ecccc
Q 024995          131 EEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEP-LPGLGAIFEELLQEDGIDDVR-ITRQG  192 (259)
Q Consensus       131 ~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~-~G~~~~~fv~l~~~~gv~gl~-~s~~~  192 (259)
                      .++||....++ ++.        |+.++|+|.++++ ||      ++|  ++|++||+ .|+.+
T Consensus        90 ~~~p~~~~~~~-~~~--------g~~v~g~v~~i~~~~g------v~l--~~giegl~h~s~~~  136 (182)
T 1kl9_A           90 SPEEAIKCEDK-FTK--------SKTVYSILRHVAEVLE------YTK--DEQLESLFQRTAWV  136 (182)
T ss_dssp             CHHHHHHHHHH-HHH--------HHHHHHHHHHHHHHTT------CCS--HHHHHHHHHHTHHH
T ss_pred             CcChHHHHHHh-ccC--------CCEEEEEEEEchhhcC------Ccc--cCChhheEEeeecc
Confidence            99999876665 454        5559999999998 99      667  89999998 67655

>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=99.74  E-value=6.3e-19  Score=147.17  Aligned_cols=100  Identities=23%  Similarity=0.383  Sum_probs=81.4

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccc
Q 024995           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (259)
Q Consensus        57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~  131 (259)
                      ++|+++.|+     +||+||+|..+   .|++||||+|+|+|.++.++.+.|++||.|+|+|+++|+++++|.||+|++.
T Consensus        14 ~~G~iv~G~V~~i~~fGaFV~L~e~---~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~~~   90 (175)
T 2a19_A           14 EIDDIVMVNVQQIAEMGAYVKLLEY---DNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVS   90 (175)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTT---TTCEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTTCC
T ss_pred             CCCCEEEEEEEEEecceEEEEEcCC---CCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEecC
Confidence            489999999     89999999310   2799999999999999999999999999999999999999999999999999


Q ss_pred             cCcchHhhhhhcCCCCccccCCCCccccceeeec-cCC
Q 024995          132 EDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE-PLP  168 (259)
Q Consensus       132 ~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~-~~G  168 (259)
                      ++||....++ ++.        |+.+.|+|.+++ +||
T Consensus        91 ~~~~~~~~~~-~~~--------g~~v~g~V~~i~~~~G  119 (175)
T 2a19_A           91 SEDIIKCEEK-YQK--------SKTVHSILRYCAEKFQ  119 (175)
T ss_dssp             HHHHHHHHHH-HHH--------HHHHHHHHHHHHHHTT
T ss_pred             cChHHHHHHh-ccC--------CCcceEEEEEchhhcC
Confidence            9999877666 454        555999999999 788

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

Probab=99.70  E-value=1.2e-17  Score=130.26  Aligned_cols=87  Identities=36%  Similarity=0.620  Sum_probs=78.7

Q ss_pred             hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcc-cccChhhhcCCCCeEEEEEEEEeCCCC
Q 024995           48 VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKS  121 (259)
Q Consensus        48 ~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~-~~~~~~~~~~~Gd~V~vkVl~id~~~~  121 (259)
                      +|+.+...+++|+++.|+     +||+||+|+     .+++||||+|++++. +..++.+.|++||.|+|+|+++|.+++
T Consensus        20 p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~-----~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~   94 (115)
T 2khi_A           20 HWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIE-----EGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERR   94 (115)
T ss_dssp             -CCCSSCSSCSSCEEEEEEEEEETTEEEEECS-----TTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEETTTT
T ss_pred             CHHHHhhcCCCCCEEEEEEEEEECCEEEEEEC-----CCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEECCCC
Confidence            477777889999999999     899999998     489999999999984 778899999999999999999999899


Q ss_pred             eeEEEEeccccCcchHhh
Q 024995          122 RITLSIKQLEEDPLLETL  139 (259)
Q Consensus       122 ri~lS~K~~~~~p~~~~~  139 (259)
                      ||.||+|++.++||..+.
T Consensus        95 rI~lslk~~~~~p~~~~~  112 (115)
T 2khi_A           95 RISLGLKQCKANPWQQFA  112 (115)
T ss_dssp             EEEECCCCCCSSCCCCCC
T ss_pred             EEEEEEEecCcCHHHHHH
Confidence            999999999999997543

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

Probab=99.69  E-value=9.7e-17  Score=143.49  Aligned_cols=138  Identities=17%  Similarity=0.105  Sum_probs=110.7

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccc
Q 024995           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (259)
Q Consensus        57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~  131 (259)
                      .+|++++|+     +||+||+++      |.+||||.++++.          ++||+|+|.|. .|. .+|+.+|.    
T Consensus         5 ~~G~~v~g~V~~~~~~G~fv~~~------g~egllp~se~~~----------~vGdevev~v~-~d~-~~r~iat~----   62 (285)
T 3go5_A            5 NLASFIVGLIIDENDRFYFVQKD------GQTYALAKEEGQH----------TVGDTVKGFAY-TDM-KQKLRLTT----   62 (285)
T ss_dssp             TTTEEEEEEEEEECSSEEEEEET------TEEEEEEGGGCCC----------CTTSEEEEEEE-ECT-TSCEEEEC----
T ss_pred             cCCCEEEEEEEEEECCEEEEEcC------CeEEEEEHHHCcc----------ccCCEEEEEEE-ECC-CCCEEEec----
Confidence            579999998     899999996      7999999999942          78999999997 575 56777764    


Q ss_pred             cCcchHhhhhhcCCCCccccCCCCccccceeeec-cCCCccceeeeecccC-CeeEEE-Eccccccccccchhhhhhccc
Q 024995          132 EDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE-PLPGLGAIFEELLQED-GIDDVR-ITRQGFEKRVVSQDLQLWLSN  208 (259)
Q Consensus       132 ~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~-~~G~~~~~fv~l~~~~-gv~gl~-~s~~~~~~~~~~~~~~~~~~~  208 (259)
                      .+||       +++        |+.+.|+|++++ +||    +|+++  .. |++||+ .|+++            |...
T Consensus        63 ~~p~-------~~~--------G~~~~g~V~~v~~~~G----aFVdi--G~~~~d~lvp~sel~------------~~~~  109 (285)
T 3go5_A           63 LEVT-------ATQ--------DQFGWGRVTEVRKDLG----VFVDT--GLPDKEIVVSLDILP------------ELKE  109 (285)
T ss_dssp             SCCC-------SCS--------SSCEEEEEEEEETTTE----EEEEC--SCTTCCEEEEGGGSC------------SSGG
T ss_pred             cccc-------ccC--------CCEEEEEEEEEccCce----EEEEE--CCCCcEEEEEHHHCC------------cccc
Confidence            3565       233        666999999999 899    99988  54 799999 57766            3211


Q ss_pred             CCCCCcceeeeccCCCee---EEEecccchhhhhhchh-hhhhhHHhhhhcccCC
Q 024995          209 APPSGKKFTLLARAGRQV---QEIQLSHSLIRKASKRH-CNEYWNVFHETAIVNN  259 (259)
Q Consensus       209 ~~~~~~~~~~~~r~G~~V---~~v~~~~~~i~ls~k~~-~~~p~~~~~~~~~~~~  259 (259)
                           .    .+++||.|   +++|. ++||++|+|++ ..+||+.+.++|++|.
T Consensus       110 -----~----~~~~Gd~v~v~l~iD~-~~Ri~ls~k~~~~~~~~~~~~~~~~~G~  154 (285)
T 3go5_A          110 -----L----WPKKGDQLYIRLEVDK-KDRIWGLLAYQEDFQRLARPAYNNMQNQ  154 (285)
T ss_dssp             -----G----SCCTTCEEEEEEEECT-TSCEEEEECCHHHHHHHCCCCCSCCTTC
T ss_pred             -----c----ccCCCCEEEEEEEECC-CCcEEEEehhhhhcchhhhhhhhCCCCC
Confidence                 0    23789988   78888 68999999987 5699999999999884

>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=99.67  E-value=1.2e-17  Score=150.68  Aligned_cols=104  Identities=27%  Similarity=0.425  Sum_probs=92.1

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEecc
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~  130 (259)
                      +++|+++.|+     +||+||+|++++   +++||||+|+++|.++.++.+.|++||.|.|+|+++|+++++|.||+|++
T Consensus        11 ~~vG~iv~G~V~~I~~fGaFV~L~ey~---gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~   87 (308)
T 1q8k_A           11 PEVEDVVMVNVRSIQEMGAYVSLLEYN---NIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRV   87 (308)
T ss_dssp             CSSCCEEEEEEEEEETTEEEEESCTTT---SCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSSC
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEECCCC---CeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEec
Confidence            5699999999     899999996211   79999999999999999999999999999999999999999999999999


Q ss_pred             ccCcchHhhhhhcCCCCccccCCCCccccceeeecc-CCCccceee
Q 024995          131 EEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEP-LPGLGAIFE  175 (259)
Q Consensus       131 ~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~-~G~~~~~fv  175 (259)
                      .++||....+++ +.        |+.+.|+|.++.+ ||    +|+
T Consensus        88 ~~~p~~~~~~~~-~~--------G~~v~G~V~~v~~~~G----~fi  120 (308)
T 1q8k_A           88 SPEEAIKCEDKF-TK--------SKTVYSILRHVAEVLE----YTK  120 (308)
T ss_dssp             CHHHHHHHHHHH-HH--------HHHHHHHHHHHHHHTT----CCS
T ss_pred             ccChHHHHHHHc-cC--------CCeeEEEEEEcccccC----Ccc
Confidence            999998776654 43        5669999999999 79    763

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

Probab=99.62  E-value=1.4e-16  Score=141.64  Aligned_cols=102  Identities=26%  Similarity=0.420  Sum_probs=90.3

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      .+++|+++.|+     +||+||+|+.++   |++||||+|++++.++.++.+.|++||.|.|+|+++|+++++|.||+|+
T Consensus         8 ~p~~Gdiv~G~V~~I~~fGaFV~L~e~~---gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~   84 (275)
T 3aev_A            8 YPEEGEFVVATVKRIHNYGAFLELDEYP---GKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRR   84 (275)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTST---TCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCCCEEEEEEEEEECcEEEEEECCCC---CeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            34689999999     999999996211   7999999999999999999999999999999999999999999999999


Q ss_pred             cccCcchHhhhhhcCCCCccccCCCCccccceeeec-cCC
Q 024995          130 LEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE-PLP  168 (259)
Q Consensus       130 ~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~-~~G  168 (259)
                      +.++||....+++ +.        |+.+.|.|.++. +||
T Consensus        85 ~~~~~~~~~~~~~-~~--------g~~v~g~v~~v~~~~G  115 (275)
T 3aev_A           85 VTQQQRKAKLQEF-KR--------AQKAENLLRLAAEKLG  115 (275)
T ss_dssp             CCHHHHHHHHHHH-HH--------HHHHHHHHHHHHHHHT
T ss_pred             cCcchhHHHHHhc-cC--------CCeEEEEEEEchhhcC
Confidence            9999998766654 43        566999999999 888

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

Probab=99.61  E-value=8.8e-16  Score=114.21  Aligned_cols=76  Identities=33%  Similarity=0.453  Sum_probs=68.5

Q ss_pred             cCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEEce-ecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        54 ~~l~~G~iv~G~----~~G~fV~l~~~~g~~gi~glv~is-els~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      ...++|+++.|+    +||+||+|.++   .|++||||+| +++++++.++++.+ +||.|+|+|+++|.+++||.||+|
T Consensus         7 ~~~~vG~~~~G~V~v~~fG~FVel~~~---~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lslk   82 (88)
T 1luz_A            7 SLPNAGDVIKGRVYEKDYALYIYLFDY---PHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYK   82 (88)
T ss_dssp             CCCCTTCEEEEEEEEETTEEEEEETTC---TTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEE
T ss_pred             cCCCCCCEEEEEEEEEccEEEEEECCC---CCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEEe
Confidence            457899999998    99999999631   1699999999 99999999999999 999999999999999999999999


Q ss_pred             ccccC
Q 024995          129 QLEED  133 (259)
Q Consensus       129 ~~~~~  133 (259)
                      ++.++
T Consensus        83 ~~~~~   87 (88)
T 1luz_A           83 RMCRH   87 (88)
T ss_dssp             EECSC
T ss_pred             ecCCC
Confidence            98765

>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=99.61  E-value=3.5e-16  Score=122.72  Aligned_cols=87  Identities=28%  Similarity=0.389  Sum_probs=77.4

Q ss_pred             hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCC--
Q 024995           48 VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--  120 (259)
Q Consensus        48 ~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~--  120 (259)
                      .|+.+...+++|++|.|+     +||+||+|++    .+.+||||++++++.++.++.+.|++||.|+|+|+++|.++  
T Consensus        12 ~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g----~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~~   87 (119)
T 2cqo_A           12 RPETMENLPALYTIFQGEVAMVTDYGAFIKIPG----CRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDR   87 (119)
T ss_dssp             CCCCSCCSCCTTCEEEEEEEEEETTEEEEECTT----CSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECSSC
T ss_pred             chhhhhcccCCCCEEEEEEEEEeCceEEEEECC----CcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEeccccC
Confidence            366677789999999999     9999999962    24699999999999999999999999999999999999854  


Q ss_pred             CeeEEEEeccccCcchHh
Q 024995          121 SRITLSIKQLEEDPLLET  138 (259)
Q Consensus       121 ~ri~lS~K~~~~~p~~~~  138 (259)
                      ++|.||+|++.++||...
T Consensus        88 ~~i~LSlk~~~~~~~~~~  105 (119)
T 2cqo_A           88 IKVSLSMKVVNQGTGKDL  105 (119)
T ss_dssp             EEEEEESTTBCSSSCCBS
T ss_pred             ceEEEEEeecccCCcccc
Confidence            699999999999999653

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

Probab=99.61  E-value=1.3e-15  Score=121.15  Aligned_cols=78  Identities=41%  Similarity=0.747  Sum_probs=73.5

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      ..+++|+++.|+     +||+||+|+     .+++||||+|++++.++.++.+.|++||.|.|+|+++|.++++|.||+|
T Consensus         3 ~~~~vG~iv~G~V~~i~~~G~FV~l~-----~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk   77 (130)
T 2k4k_A            3 AKFEVGSVYTGKVTGLQAYGAFVALD-----EETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIR   77 (130)
T ss_dssp             CCCCTTCEEEEEEEEEETTEEEEEEE-----TTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESH
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEEC-----CCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence            478999999999     899999997     4899999999999999999999999999999999999998999999999


Q ss_pred             ccccCcch
Q 024995          129 QLEEDPLL  136 (259)
Q Consensus       129 ~~~~~p~~  136 (259)
                      ++.++||.
T Consensus        78 ~~~~~p~~   85 (130)
T 2k4k_A           78 ATQAAPEK   85 (130)
T ss_dssp             HHHHSCCC
T ss_pred             ecccCccc
Confidence            99999974

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

Probab=99.59  E-value=1.1e-15  Score=117.83  Aligned_cols=86  Identities=28%  Similarity=0.412  Sum_probs=74.8

Q ss_pred             EEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEE
Q 024995           42 FSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKV  113 (259)
Q Consensus        42 lS~k~~---~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkV  113 (259)
                      -|.|+.   +|+.+...+++|+++.|+     +||+||+|+     .+++||||++++++.++.++.+.|++||.|+|+|
T Consensus        12 ~~iKq~~~~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~-----~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V   86 (109)
T 2khj_A           12 SGLVPRGSHMFNNWVALNKKGAIVTGKVTAVDAKGATVELA-----DGVEGYLRASEASRDRVEDATLVLSVGDEVEAKF   86 (109)
T ss_dssp             ---------CHHHHTTTCCSSSEEEEEEEEECSSCEEEECS-----TTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEE
T ss_pred             cchhhcccCHHHHHhhcCCCCCEEEEEEEEEECCeEEEEEC-----CCCEEEEEHHHcCcccccChhhccCCCCEEEEEE
Confidence            355554   588889999999999999     899999998     4899999999999999999999999999999999


Q ss_pred             EEEeCCCCeeEEEEecccc
Q 024995          114 IKIDREKSRITLSIKQLEE  132 (259)
Q Consensus       114 l~id~~~~ri~lS~K~~~~  132 (259)
                      +++|.++++|.||+|++.+
T Consensus        87 ~~vd~~~~ki~LS~k~~~~  105 (109)
T 2khj_A           87 TGVDRKNRAISLSVRAKDE  105 (109)
T ss_dssp             EEEETTTTEEEEETTSSSS
T ss_pred             EEEECCCCEEEEEEeecCh
Confidence            9999988899999998754

>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=99.59  E-value=3.1e-15  Score=114.30  Aligned_cols=81  Identities=26%  Similarity=0.553  Sum_probs=71.4

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceec-CcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV-SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isel-s~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      ...+++|+++.|+     +||+||+|++.+  .+++||||+|++ ++.++.++.+.|++||.|+|+|+++|.  +||.||
T Consensus         7 ~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~--~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~--~~i~LS   82 (103)
T 2eqs_A            7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLR--KRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG--TKTSLS   82 (103)
T ss_dssp             CSSCCTTCEEEEEEEEECSSCEEEEECSSS--SCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET--TEEEEE
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEEcCCC--CCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC--CeeEEE
Confidence            4578999999999     899999997311  069999999999 667888999999999999999999996  699999


Q ss_pred             EeccccCcchH
Q 024995          127 IKQLEEDPLLE  137 (259)
Q Consensus       127 ~K~~~~~p~~~  137 (259)
                      +|++.++||..
T Consensus        83 lk~~~~~~~~~   93 (103)
T 2eqs_A           83 MKDVDQETGED   93 (103)
T ss_dssp             STTBCTTTCCB
T ss_pred             EeecccCCchh
Confidence            99999999964

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

Probab=99.55  E-value=6.9e-16  Score=120.21  Aligned_cols=100  Identities=16%  Similarity=0.246  Sum_probs=70.7

Q ss_pred             EEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccceeeeecccCCeeEEE-Eccccccccccchhhh
Q 024995          125 LSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQ  203 (259)
Q Consensus       125 lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~  203 (259)
                      -|+|++..+||...... +.        +|+++.|+|+++++||    +||+|  .+|++||+ +|+++.+.        
T Consensus        11 ~~~k~~~~~p~~~~~~~-~~--------~G~~~~G~V~~v~~~G----~FV~l--~~~~~Glvhisel~~~~--------   67 (115)
T 2khi_A           11 SSGLVPRGSHWVAIAKR-YP--------EGTKLTGRVTNLTDYG----CFVEI--EEGVEGLVHVSEMDWTN--------   67 (115)
T ss_dssp             ----------CCCSSCS-SC--------SSCEEEEEEEEEETTE----EEEEC--STTCEEEEETTSSSCSS--------
T ss_pred             cchhhcccCCHHHHhhc-CC--------CCCEEEEEEEEEECCE----EEEEE--CCCCEEEEEHHHCCccc--------
Confidence            47899999999753322 33        4777999999999999    99988  78999999 67776321        


Q ss_pred             hhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhhhhhHHhhhhc
Q 024995          204 LWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCNEYWNVFHETA  255 (259)
Q Consensus       204 ~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~~p~~~~~~~~  255 (259)
                          .......    .+++||.|    +++|.++++|+||+|++.++||+.+.++|
T Consensus        68 ----~~~~~~~----~~~vGd~V~vkV~~vd~~~~rI~lslk~~~~~p~~~~~~~~  115 (115)
T 2khi_A           68 ----KNIHPSK----VVNVGDVVEVMVLDIDEERRRISLGLKQCKANPWQQFAETH  115 (115)
T ss_dssp             ----TTCSSTT----TCCTTCEEEEEEEEEETTTTEEEECCCCCCSSCCCCCCCCC
T ss_pred             ----cccCccc----EECCCCEEEEEEEEEECCCCEEEEEEEecCcCHHHHHHhhC
Confidence                1222233    56999999    68899999999999999999999998876

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

Probab=99.55  E-value=1.9e-14  Score=104.89  Aligned_cols=69  Identities=32%  Similarity=0.496  Sum_probs=62.8

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      ++++|+++.|+     +||+||+++     .+++||||+|++++.++    +.|++||.|+|+|+++|.+++||.||+|+
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~-----~~~~Gllh~sel~~~~~----~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~   72 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLN-----EQVRGLLRPRDMISLRL----ENLNVGDEIIVQAIDVRPEKREIDFKYIP   72 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEE-----TTEEEEECGGGCSSCCG----GGCCTTCEEEEEEEEEETTTTEEEEEECS
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEEC-----CCCEEEEEHHHCCcccc----eeeCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            57899999999     899999998     48999999999998775    67999999999999999988999999998


Q ss_pred             ccc
Q 024995          130 LEE  132 (259)
Q Consensus       130 ~~~  132 (259)
                      +.+
T Consensus        73 ~~~   75 (80)
T 2k52_A           73 LEH   75 (80)
T ss_dssp             CC-
T ss_pred             ccc
Confidence            764

>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=99.47  E-value=5.9e-15  Score=130.75  Aligned_cols=103  Identities=26%  Similarity=0.388  Sum_probs=86.7

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      ..+++|+++.|+     +||+||+|++++   +++||||+|++++.++.++.+.|++||.|.|+|+++|.++++|.||+|
T Consensus         7 ~~~~vG~iv~G~V~~I~~~GaFV~l~e~~---~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk   83 (266)
T 3cw2_C            7 KLPSEGEILIATVKQVFDYGSYVSLDEYG---GLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLK   83 (266)
T ss_dssp             SSCCTTCEEEEEEEECCSSSBEEEETTTT---SEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEEST
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEEcCCC---CeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEE
Confidence            357899999999     999999995211   799999999999999999999999999999999999998999999999


Q ss_pred             ccccCcchHhhhhhcCCCCccccCCCCccccceeeec-cCC
Q 024995          129 QLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE-PLP  168 (259)
Q Consensus       129 ~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~-~~G  168 (259)
                      .+.++||....+++ +.        |+.+.|.|..+. .+|
T Consensus        84 ~~~~~~~~~~~~~~-~~--------~~~~~~iv~~lae~~~  115 (266)
T 3cw2_C           84 KVTDDERRKKNLQW-KK--------IQRLDKILELVSQKLK  115 (266)
T ss_dssp             TSCTTHHHHHHHHH-HH--------HHHHHHHHHHHHHHTT
T ss_pred             ecchhhHHHHHHhc-cc--------cCccceeeeehhhhCC
Confidence            99999998766654 32        334667777665 344

>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=99.42  E-value=8e-14  Score=116.85  Aligned_cols=85  Identities=14%  Similarity=0.163  Sum_probs=66.9

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      +|+++.|+|++|++||    +||+|...+|++||+ +|++++.          |+   .++.    .++++||.|    +
T Consensus        15 ~G~iv~G~V~~I~~fG----aFV~L~e~~g~eGLvhiSels~~----------~v---~~~~----~~~~vGd~V~VkVl   73 (182)
T 1kl9_A           15 VEDVVMVNVRSIAEMG----AYVSLLEYNNIEGMILLSELSRR----------RI---RSIN----KLIRIGRNECVVVI   73 (182)
T ss_dssp             TTCEEEEEEEEECSSE----EEEEETTTTTEEEEEEGGGC-----------------------------CTTCEEEEEEE
T ss_pred             CCCEEEEEEEEEeccE----EEEEEccCCCcEEEEEHHHCCCc----------cc---CCHH----HhcCCCCEEEEEEE
Confidence            4788999999999999    999995457999999 7888743          22   2223    367999999    7


Q ss_pred             EEecccchhhhhhchhhhhhhHHhhhhcccC
Q 024995          228 EIQLSHSLIRKASKRHCNEYWNVFHETAIVN  258 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~~~~~p~~~~~~~~~~~  258 (259)
                      +||.++++|+||+|++.++||+.+.++|++|
T Consensus        74 ~vD~~~~rI~LSlk~~~~~p~~~~~~~~~~g  104 (182)
T 1kl9_A           74 RVDKEKGYIDLSKRRVSPEEAIKCEDKFTKS  104 (182)
T ss_dssp             EEETTTTEEEEESTTCCHHHHHHHHHHHHHH
T ss_pred             EEECCCCEEEEEEeecCcChHHHHHHhccCC
Confidence            8999999999999999999999999999876

>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=99.37  E-value=3e-13  Score=112.67  Aligned_cols=85  Identities=16%  Similarity=0.195  Sum_probs=67.2

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      +|+++.|+|++|++||    +||+|...+|++||+ +|++++.          |+   .++..    .+++||.|    +
T Consensus        15 ~G~iv~G~V~~i~~fG----aFV~L~e~~gveGLvhiSels~~----------~v---~~~~~----~~~vGd~V~vkVl   73 (175)
T 2a19_A           15 IDDIVMVNVQQIAEMG----AYVKLLEYDNIEGMILLSELSRR----------RI---RSIQK----LIRVGKNDVAVVL   73 (175)
T ss_dssp             TTCEEEEEEEEEETTE----EEEEETTTTTCEEEEECC---------------------CCCC----CCCTTSEEEEEEE
T ss_pred             CCCEEEEEEEEEecce----EEEEEcCCCCcEEEEEHHHcCCc----------cc---CCHHH----cCCCCCEEEEEEE
Confidence            4777999999999999    999993337999999 7888743          22   22333    67999999    7


Q ss_pred             EEecccchhhhhhchhhhhhhHHhhhhcccC
Q 024995          228 EIQLSHSLIRKASKRHCNEYWNVFHETAIVN  258 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~~~~~p~~~~~~~~~~~  258 (259)
                      +||.++++|+||+|++.++||+.+.++|++|
T Consensus        74 ~vd~~~~~I~LSlk~~~~~~~~~~~~~~~~g  104 (175)
T 2a19_A           74 RVDKEKGYIDLSKRRVSSEDIIKCEEKYQKS  104 (175)
T ss_dssp             EEETTTTEEEEESTTCCHHHHHHHHHHHHHH
T ss_pred             EEECCCCeEEEEEEecCcChHHHHHHhccCC
Confidence            8999999999999999999999999999876

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

Probab=99.35  E-value=6.7e-14  Score=138.46  Aligned_cols=101  Identities=28%  Similarity=0.475  Sum_probs=2.4

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc
Q 024995           31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (259)
Q Consensus        31 l~id~~~~~v~lS~k~~--------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~   97 (259)
                      ++++. .+.+.++....        .++.+...+++|++|.|+     +||+||+|.     .|++||||+|+++|.++.
T Consensus       603 idi~d-dG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V~~I~~fGaFVel~-----~g~eGLvHiSels~~rv~  676 (726)
T 4aid_A          603 VDIND-DGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFF-----GAKDGLVHVSQISNERVA  676 (726)
T ss_dssp             ------------CCSCHHHHHHHHHC------------------------------------------------------
T ss_pred             eeEEC-CceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEEEEEEEEeccEEEEEEC-----CCcEEEEEHHHcCccccc
Confidence            56663 46666665421        255667889999999999     999999998     489999999999999999


Q ss_pred             ChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHh
Q 024995           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET  138 (259)
Q Consensus        98 ~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~  138 (259)
                      ++.+.|++||.|+|||+++|+ ++||.||+|++.++||.+.
T Consensus       677 ~~~d~~kvGD~V~VkVi~iD~-~grI~LS~K~~~~~~G~~~  716 (726)
T 4aid_A          677 KPSDVLKEGQMVKVKLLGFDD-RGKTKLSMKVVDQETGEDL  716 (726)
T ss_dssp             -----------------------------------------
T ss_pred             CccccCCCCCEEEEEEEEECC-CCcEEEEEeecccCcchhh
Confidence            999999999999999999997 8999999999999998654

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

Probab=99.31  E-value=1.8e-13  Score=135.71  Aligned_cols=101  Identities=30%  Similarity=0.541  Sum_probs=0.0

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc
Q 024995           31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (259)
Q Consensus        31 l~id~~~~~v~lS~k~~--------~~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~   97 (259)
                      ++++. .+.+.+|....        .++.+...+++|++|.|+     +||+||++.     .|++||||+|+++|.++.
T Consensus       593 IdI~~-dg~v~I~~~~~~~~~~a~~~i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~-----~g~eGLvHiSel~~~~v~  666 (723)
T 3cdi_A          593 IEIED-DGTVKIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIG-----GGKEGLVHISQIADKRVE  666 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEecC-CccEEEecCCHHHHHHHHHHHHHHhhhhhcCcEEEEEEEEEecceEEEEeC-----CCceEEEEHHHcCCcccc
Confidence            45554 46777765432        245567789999999999     999999997     489999999999999999


Q ss_pred             ChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHh
Q 024995           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET  138 (259)
Q Consensus        98 ~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~  138 (259)
                      ++.+.|++||.|+|+|+++|. ++||.||+|++.++||.+.
T Consensus       667 ~~~~~~~vGd~V~VkVi~vd~-~grI~LS~k~~~~~~g~~~  706 (723)
T 3cdi_A          667 KVTDYLQMGQEVPVKVLEVDR-QGRIRLSIKEATEQSQPAA  706 (723)
T ss_dssp             -----------------------------------------
T ss_pred             CcccccCCCCEEEEEEEEECC-CCcEEEEEEeccCCCCccc
Confidence            999999999999999999998 8999999999999999753

>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=99.27  E-value=7.2e-14  Score=139.09  Aligned_cols=101  Identities=22%  Similarity=0.412  Sum_probs=38.8

Q ss_pred             EEEeCCCCEEEEEechhh--------Hhhhc--cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceec----
Q 024995           31 IQANEEMKKLVFSEKDAV--------WNKYS--SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV----   91 (259)
Q Consensus        31 l~id~~~~~v~lS~k~~~--------~~~~~--~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isel----   91 (259)
                      ++++. .+.+.+|.....        ++.+.  ..+++|++|.|+     +||+||+|.     .|++||||+|++    
T Consensus       631 IdI~~-dG~v~Is~~~~~~~~~a~~~i~~i~~p~~~~vG~i~~G~V~~i~~fGaFV~l~-----~g~eGLvHiSel~~~~  704 (757)
T 1e3p_A          631 ITIED-DGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGAFVSLL-----PGKDGLLHISQIRKLA  704 (757)
T ss_dssp             C---------CCCBSSHHHHCC---------------------CBEEECC-CSCEECCC--------CCCCC--------
T ss_pred             EEecC-CceEEEecCCHHHHHHHHHHHHHhcchhhcccccEEEEEEEEccccEEEEEEc-----CCcEEEEEhHHhcccc
Confidence            56664 588888876531        23344  678999999999     999999997     489999999999    


Q ss_pred             CcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHh
Q 024995           92 SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET  138 (259)
Q Consensus        92 s~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~  138 (259)
                      +|.++.++++.|++||+|+|+|+++|. ++||.||+|++.++||...
T Consensus       705 s~~rv~~~~~~~~vGd~V~VkVi~vd~-~grI~LS~k~~~~~pw~~~  750 (757)
T 1e3p_A          705 GGKRVENVEDVLGVGQKVQVEIAEIDS-RGKLSLIPVIEGEEAASDE  750 (757)
T ss_dssp             -----------CCSSCBCCCCCCCCCS-SCC----------------
T ss_pred             CCCcccCcccccCCCCEEEEEEEEECC-CCCEEEEEecCCCCchhhh
Confidence            999999999999999999999999998 9999999999999999753

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

Probab=99.26  E-value=1.6e-12  Score=100.03  Aligned_cols=90  Identities=10%  Similarity=0.151  Sum_probs=61.9

Q ss_pred             EEEEeccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccceeeeecccCCeeEEE-Eccccccccccchhh
Q 024995          124 TLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDL  202 (259)
Q Consensus       124 ~lS~K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~  202 (259)
                      +-|+|++.++||...... +.        +|+++.|+|+++++||    +|++|  .+|++||+ +|+++...       
T Consensus        11 ~~~iKq~~~~p~~~~~~~-~~--------~G~iv~G~V~~v~~~G----~fV~l--~~~~~Gll~~sel~~~~-------   68 (109)
T 2khj_A           11 SSGLVPRGSHMFNNWVAL-NK--------KGAIVTGKVTAVDAKG----ATVEL--ADGVEGYLRASEASRDR-------   68 (109)
T ss_dssp             ----------CHHHHTTT-CC--------SSSEEEEEEEEECSSC----EEEEC--STTCBCCBCTTCCCSSS-------
T ss_pred             ccchhhcccCHHHHHhhc-CC--------CCCEEEEEEEEEECCe----EEEEE--CCCCEEEEEHHHcCccc-------
Confidence            458999999999866544 33        3777999999999999    99988  78999999 77776321       


Q ss_pred             hhhcccCCCCCcceeeeccCCCee----EEEecccchhhhhhchhhh
Q 024995          203 QLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHSLIRKASKRHCN  245 (259)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~~i~ls~k~~~~  245 (259)
                         .   ..+    ...+++||.|    +++|.++++|.||+|++.+
T Consensus        69 ---~---~~~----~~~~~vGd~V~v~V~~vd~~~~ki~LS~k~~~~  105 (109)
T 2khj_A           69 ---V---EDA----TLVLSVGDEVEAKFTGVDRKNRAISLSVRAKDE  105 (109)
T ss_dssp             ---S---SSG----GGSCCTTCEEEEEEEEEETTTTEEEEETTSSSS
T ss_pred             ---c---cCh----hhccCCCCEEEEEEEEEECCCCEEEEEEeecCh
Confidence               1   112    2256999999    6889988999999998754

>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=99.23  E-value=3.5e-12  Score=106.51  Aligned_cols=82  Identities=27%  Similarity=0.563  Sum_probs=66.9

Q ss_pred             HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc-----------cChhhhcCCCCeEEEE
Q 024995           49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVK  112 (259)
Q Consensus        49 ~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~-----------~~~~~~~~~Gd~V~vk  112 (259)
                      ++.+..++.+|++++|+     +||+||+++      +++||+|+|+++++++           ++..+.|++||.|++|
T Consensus        72 ~~~iv~~p~~Gev~~G~V~~v~~~G~fv~l~------~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~Vrvk  145 (180)
T 4ayb_E           72 FDMITYVPVVQEVVEGEVLQVDNYGVFVNLG------PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRAR  145 (180)
T ss_dssp             EEEEEECCCTTCEEEEEEEEEETTEEEEECS------SSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEE
T ss_pred             hheeeeeccCCCEEEEEEeeeccceEEEEEC------CccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEE
Confidence            34456689999999999     999999997      6899999999999876           4677789999999999


Q ss_pred             EEEEeCC----CCeeEEEEeccc--cCcch
Q 024995          113 VIKIDRE----KSRITLSIKQLE--EDPLL  136 (259)
Q Consensus       113 Vl~id~~----~~ri~lS~K~~~--~~p~~  136 (259)
                      |+++|.+    ..||.||+|+.-  +.+|-
T Consensus       146 V~~v~~~~~~~~~rI~ls~k~~gLG~~~W~  175 (180)
T 4ayb_E          146 VISVASTVTGRLPRIALTMRQPYLGKLEWI  175 (180)
T ss_dssp             EEEECC-------CEEEECCSTTCEEHHHH
T ss_pred             EEEEeCCCCcccCcEEEEcCCCCCCCChhH
Confidence            9999863    458999999843  34453

>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=99.17  E-value=2.4e-11  Score=94.85  Aligned_cols=76  Identities=13%  Similarity=0.187  Sum_probs=62.3

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceec-CcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV-SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isel-s~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      ..++++|+++.|+     +||+||+|+.    .+..||+|.+++ +|.++.++.+.|++||.|+|+|+++|.++++|.||
T Consensus        16 ~~~l~~G~i~~G~V~~v~~fG~fV~l~~----~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~Ls   91 (119)
T 1wi5_A           16 AEALKPGMLLTGTVSSLEDHGYLVDIGV----DGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS   91 (119)
T ss_dssp             TTTCCTTCEEEEEEEEECSSEEEEECCC----SSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEE
T ss_pred             HhcCCCCCEEEEEEEEEeCceEEEEECC----CCeEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCCCCEEEEE
Confidence            4679999999999     9999999971    156777666664 24445678899999999999999999988999999


Q ss_pred             Eecccc
Q 024995          127 IKQLEE  132 (259)
Q Consensus       127 ~K~~~~  132 (259)
                      +|+...
T Consensus        92 lk~~~l   97 (119)
T 1wi5_A           92 VGHSEV   97 (119)
T ss_dssp             CCCCCS
T ss_pred             Echhhc
Confidence            987544

>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=99.16  E-value=5.3e-11  Score=99.83  Aligned_cols=80  Identities=25%  Similarity=0.493  Sum_probs=68.1

Q ss_pred             hhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc-----------ChhhhcCCCCeEEEEEE
Q 024995           51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVI  114 (259)
Q Consensus        51 ~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~-----------~~~~~~~~Gd~V~vkVl  114 (259)
                      ......++|+++.|+     +||+||+++      +.+||+|+|++++.++.           ++.+.|++||.|+|+|+
T Consensus        74 ~i~~~~~~Gev~~G~V~~v~~~G~fV~l~------~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~  147 (187)
T 1go3_E           74 TLVYIPEMYELIEGEVVDVVEFGSFVRLG------PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIV  147 (187)
T ss_dssp             EEEECCCTTCEEEEEEEEEETTEEEEECS------SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEE
T ss_pred             EEEEccCCCCEEEEEEEEEeCcEEEEEEc------CccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEE
Confidence            345688999999999     899999997      59999999999988765           78889999999999999


Q ss_pred             EEeCCCC-----eeEEEEeccc--cCcch
Q 024995          115 KIDREKS-----RITLSIKQLE--EDPLL  136 (259)
Q Consensus       115 ~id~~~~-----ri~lS~K~~~--~~p~~  136 (259)
                      ++|.+++     +|.||+|+..  +.+|-
T Consensus       148 ~vd~~~~~p~~~~I~lS~k~~~LG~~~w~  176 (187)
T 1go3_E          148 AISLKAERKRGSKIALTMRQPYLGKLEWI  176 (187)
T ss_dssp             EEECCC-----CEEEEECCSTTCEEHHHH
T ss_pred             EEEcccCCCCccEEEEEEcCCCCCcHHHH
Confidence            9998655     9999999854  34553

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

Probab=99.13  E-value=4.6e-11  Score=123.86  Aligned_cols=74  Identities=15%  Similarity=0.104  Sum_probs=69.1

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc-ccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~-~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      ...+++|+++.|+     +||+||+|+     .|++||||+|+|++.+ +.+|.+.|++||.|+|+|+++|.+++||.||
T Consensus       897 ~~~l~~G~iv~G~V~~V~~fGaFV~L~-----~gveGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LS  971 (1219)
T 3psi_A          897 EKTFFKGSIIPVRVERFWHNDIICTTN-----SEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVS  971 (1219)
T ss_dssp             TTTSCTTCEEEEEEEEECSSCEEEECT-----TSCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEE
T ss_pred             HhhCCCCCEEEEEEEEEecceEEEEeC-----CCceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence            3789999999999     999999998     5899999999999998 8999999999999999999999999999999


Q ss_pred             Eeccc
Q 024995          127 IKQLE  131 (259)
Q Consensus       127 ~K~~~  131 (259)
                      +|...
T Consensus       972 lk~~d  976 (1219)
T 3psi_A          972 LLDHD  976 (1219)
T ss_dssp             CCHHH
T ss_pred             ecHHH
Confidence            98643

>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=99.12  E-value=2.6e-11  Score=109.16  Aligned_cols=85  Identities=15%  Similarity=0.176  Sum_probs=70.5

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      +|+++.|+|++|++||    +||+|...+|++||+ +|++++.          |   ...+..    .+++||.|    +
T Consensus        13 vG~iv~G~V~~I~~fG----aFV~L~ey~gveGLvhiSels~~----------~---i~~~~~----~~kvGd~V~VkVl   71 (308)
T 1q8k_A           13 VEDVVMVNVRSIQEMG----AYVSLLEYNNIEGMIHLSELSRR----------R---IRSINK----LIRIGRNECVKVI   71 (308)
T ss_dssp             SCCEEEEEEEEEETTE----EEEESCTTTSCCEEECGGGTSCS----------S---CSCCTT----TCSSSCEEEEEEE
T ss_pred             CCCEEEEEEEEEeCcE----EEEEECCCCCeEEEEEhHHcCcc----------c---ccCHHH----hcCCCCEEEEEEE
Confidence            5888999999999999    999992117999999 7888732          2   222333    56999999    6


Q ss_pred             EEecccchhhhhhchhhhhhhHHhhhhcccC
Q 024995          228 EIQLSHSLIRKASKRHCNEYWNVFHETAIVN  258 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~~~~~p~~~~~~~~~~~  258 (259)
                      ++|+++++|+||+|++.++||..+.++|++|
T Consensus        72 ~vD~~~~rI~LSlK~~~~~p~~~~~~~~~~G  102 (308)
T 1q8k_A           72 RVDKEKGYIDLSKRRVSPEEAIKCEDKFTKS  102 (308)
T ss_dssp             EEETTTTEEEEECSSCCHHHHHHHHHHHHHH
T ss_pred             EEeCCCCEEEEEEEecccChHHHHHHHccCC
Confidence            8999999999999999999999999999876

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

Probab=99.10  E-value=4e-11  Score=106.49  Aligned_cols=85  Identities=13%  Similarity=0.129  Sum_probs=69.8

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      +|+++.|+|++|++||    +||+|...+|++||+ +|+++..          |+   ..+.    ..+++||.|    +
T Consensus        11 ~Gdiv~G~V~~I~~fG----aFV~L~e~~gieGlIhiSels~~----------~v---~~~~----~~~kvGd~V~vkVi   69 (275)
T 3aev_A           11 EGEFVVATVKRIHNYG----AFLELDEYPGKEAFMHISEVAST----------WV---RNIR----DYLKEGQKVVAKVI   69 (275)
T ss_dssp             TTCEEEEEEEEEETTE----EEEEETTSTTCEEEEEGGGSCSS----------CC---SCGG----GTCCTTCEEEEEEE
T ss_pred             CCCEEEEEEEEEECcE----EEEEECCCCCeEEEEEHHHcCcc----------cc---cCHH----hccCCCCEEEEEEE
Confidence            4777999999999999    999993226999999 7887733          22   2222    356999999    6


Q ss_pred             EEecccchhhhhhchhhhhhhHHhhhhcccC
Q 024995          228 EIQLSHSLIRKASKRHCNEYWNVFHETAIVN  258 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~~~~~p~~~~~~~~~~~  258 (259)
                      ++|.++++|+||+|++.++||....++|++|
T Consensus        70 ~vD~~~~~I~LSlk~~~~~~~~~~~~~~~~g  100 (275)
T 3aev_A           70 RVDPRKGHIDLSLRRVTQQQRKAKLQEFKRA  100 (275)
T ss_dssp             EEETTTTEEEEESTTCCHHHHHHHHHHHHHH
T ss_pred             EEECCCCEEEEEEeecCcchhHHHHHhccCC
Confidence            8999999999999999999999999998875

>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=99.08  E-value=3.4e-11  Score=120.25  Aligned_cols=74  Identities=30%  Similarity=0.585  Sum_probs=68.4

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      +.++++|+++.|+     +||+||+|+     .+++||||+|+|++.++.++.+.|++||.|+|+|+++|.++++|.||+
T Consensus       649 ~~~l~vG~iv~G~V~~V~~fGaFV~l~-----~~~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~LSl  723 (785)
T 3bzc_A          649 LKDLKPGMVLEGVVTNVTNFGAFVDIG-----VHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSM  723 (785)
T ss_dssp             STTCCTTCBCCCEEEEEETTEEEEECS-----SSSEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEECC
T ss_pred             hhhcCCCCEEEEEEEEEecCCeEEEeC-----CCcEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEEE
Confidence            4568999999888     999999997     489999999999999999999999999999999999999999999999


Q ss_pred             eccc
Q 024995          128 KQLE  131 (259)
Q Consensus       128 K~~~  131 (259)
                      |...
T Consensus       724 k~~~  727 (785)
T 3bzc_A          724 RMSD  727 (785)
T ss_dssp             SSCC
T ss_pred             ecCC
Confidence            9644

>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=99.03  E-value=2.3e-10  Score=94.74  Aligned_cols=114  Identities=14%  Similarity=0.160  Sum_probs=71.1

Q ss_pred             CCCCCCCC-CchhHhhhcccCCCCEEE---EE--EEEEe--C-CCCEEEEEech----hhHhhhccCCCCCCEEEEE---
Q 024995            2 SPSHSCKE-PQKSIHEIAKGLTGSIIS---VK--VIQAN--E-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR---   65 (259)
Q Consensus         2 ~~~~~~~~-p~~~~~~~~~~~vG~~v~---~~--Vl~id--~-~~~~v~lS~k~----~~~~~~~~~l~~G~iv~G~---   65 (259)
                      .|++|+.+ |+....+....++|+.+.   ..  +++++  . ..+++.-+-..    ..+........+|++++|+   
T Consensus        14 pp~~l~~~~p~~i~~~i~~~~i~~vig~~G~~I~~~di~~~di~~g~i~~~d~~~~~~~~~~~~~~~~~~Gev~~G~V~~   93 (171)
T 1y14_B           14 HPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVS   93 (171)
T ss_dssp             CTTSCSTTHHHHHHHHHHHHHTTEEETTTEEEEEECCGGGCBCC------------CEEEEEEEEECCCTTCEEEEEEEE
T ss_pred             CHHHhCChHHHHHHHHHHHHHcCcCcCCceEEEEEEEecccccCccEEeCCCCCEEEEEEEEEEEccCCCCCEEEEEEEE
Confidence            46777544 444444445556666553   12  23333  2 13444422111    1123345578999999999   


Q ss_pred             --eeeEEEEEccCCCCccEEEEEEceecCcccccCh----------hhhcCCCCeEEEEEEEEeCCCC
Q 024995           66 --DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI----------RDILNEGDEVRVKVIKIDREKS  121 (259)
Q Consensus        66 --~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~----------~~~~~~Gd~V~vkVl~id~~~~  121 (259)
                        +||+||+++     + .+||+|+|+|++.+.-++          ++.+++||.|+|+|+++|.+.+
T Consensus        94 v~~fG~FV~l~-----~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  155 (171)
T 1y14_B           94 CSQHGFEVQVG-----P-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVS  155 (171)
T ss_dssp             EETTEEEEEET-----T-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETT
T ss_pred             EecCEEEEEec-----C-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEEcCCC
Confidence              999999998     5 999999999986533222          2669999999999999998664

>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=99.03  E-value=8e-12  Score=124.42  Aligned_cols=122  Identities=16%  Similarity=0.112  Sum_probs=45.1

Q ss_pred             eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhhhhhcCC
Q 024995           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ  145 (259)
Q Consensus        66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~~~~~~~  145 (259)
                      ++|+||+++       -+|.+|++..++.......+                    ++.    .. .+|+      .+. 
T Consensus       626 ~~G~~IdI~-------~dG~v~Is~~~~~~~~~a~~--------------------~i~----~i-~~p~------~~~-  666 (757)
T 1e3p_A          626 DTGAEITIE-------DDGTIYIGAADGPAAEAARA--------------------TIN----GI-ANPT------SPE-  666 (757)
T ss_dssp             CCCSCC---------------CCCBSSHHHHCC-----------------------------------------------
T ss_pred             hhCCEEEec-------CCceEEEecCCHHHHHHHHH--------------------HHH----Hh-cchh------hcc-
Confidence            899999996       38999999988754322111                    010    01 1231      123 


Q ss_pred             CCccccCCCCccccceeeeccCCCccceeeeecccCCeeEEE-Eccc----cccccccchhhhhhcccCCCCCcceeeec
Q 024995          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQ----GFEKRVVSQDLQLWLSNAPPSGKKFTLLA  220 (259)
Q Consensus       146 g~~~~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  220 (259)
                             +|++++|+|+++++||    +||+|  .+|++||+ +|++    +++          |+   ..+.    .++
T Consensus       667 -------vG~i~~G~V~~i~~fG----aFV~l--~~g~eGLvHiSel~~~~s~~----------rv---~~~~----~~~  716 (757)
T 1e3p_A          667 -------VGERILGSVVKTTTFG----AFVSL--LPGKDGLLHISQIRKLAGGK----------RV---ENVE----DVL  716 (757)
T ss_dssp             -------------CBEEECC-CS----CEECC--C---CCCCC------------------------------------C
T ss_pred             -------cccEEEEEEEEccccE----EEEEE--cCCcEEEEEhHHhccccCCC----------cc---cCcc----ccc
Confidence                   3667999999999999    99988  89999998 8888    532          22   2222    367


Q ss_pred             cCCCee----EEEecccchhhhhhchhhhhhhHHhhhhccc
Q 024995          221 RAGRQV----QEIQLSHSLIRKASKRHCNEYWNVFHETAIV  257 (259)
Q Consensus       221 r~G~~V----~~v~~~~~~i~ls~k~~~~~p~~~~~~~~~~  257 (259)
                      ++||.|    ++||. ++||+||+|++.++||+....+|+.
T Consensus       717 ~vGd~V~VkVi~vd~-~grI~LS~k~~~~~pw~~~~~~~~~  756 (757)
T 1e3p_A          717 GVGQKVQVEIAEIDS-RGKLSLIPVIEGEEAASDEKKDDAE  756 (757)
T ss_dssp             CSSCBCCCCCCCCCS-SCC----------------------
T ss_pred             CCCCEEEEEEEEECC-CCCEEEEEecCCCCchhhhhhcccC
Confidence            999999    68888 8899999999999999999998864

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

Probab=99.03  E-value=2.6e-11  Score=123.99  Aligned_cols=74  Identities=15%  Similarity=0.104  Sum_probs=0.0

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc-ccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~-~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      ...+++|+++.|+     +||+||+|+     .|++||||+|+|++.+ +.+|.+.|++||.|+|+|+++|.+++||.||
T Consensus       900 ~~~l~~G~iv~G~V~~V~~fGaFV~L~-----~gveGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LS  974 (1030)
T 3psf_A          900 EKTFFKGSIIPVRVERFWHNDIICTTN-----SEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVS  974 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHhcCCCEEEEEEEEEccCeEEEEeC-----CCcEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence            3689999999999     999999998     5899999999999998 8999999999999999999999999999999


Q ss_pred             Eeccc
Q 024995          127 IKQLE  131 (259)
Q Consensus       127 ~K~~~  131 (259)
                      +|...
T Consensus       975 lk~~d  979 (1030)
T 3psf_A          975 LLDHD  979 (1030)
T ss_dssp             -----
T ss_pred             echHH
Confidence            98644

>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=99.02  E-value=1.5e-10  Score=99.24  Aligned_cols=128  Identities=15%  Similarity=0.122  Sum_probs=86.0

Q ss_pred             CCCCCCCC-CchhHhhhcccCCCCEEE---EEEEEEeCC-----CCEEEEEech----hhHhhhccCCCCCCEEEEE---
Q 024995            2 SPSHSCKE-PQKSIHEIAKGLTGSIIS---VKVIQANEE-----MKKLVFSEKD----AVWNKYSSRVNVEDIFVGR---   65 (259)
Q Consensus         2 ~~~~~~~~-p~~~~~~~~~~~vG~~v~---~~Vl~id~~-----~~~v~lS~k~----~~~~~~~~~l~~G~iv~G~---   65 (259)
                      .|++|.++ |+....+....++|+.+.   ..|..+|-+     .+.+.-.--.    ..+.......++|++++|+   
T Consensus        14 pp~~~~~~~p~~i~~~I~~~~ig~vIg~~G~vI~~~dI~~~di~dG~I~~gdg~~~~~v~~~~i~~~p~vGev~~G~V~~   93 (215)
T 2b8k_G           14 HPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVS   93 (215)
T ss_dssp             CGGGCSSSHHHHHHHHHHHSSTTCEETTTEEEEEECCSTTCBCCCEEECSSSCCEEEEEECCEEEECCCTTEEEEEEEEE
T ss_pred             CHHHHChhHhHHHHhcCCHHHCCeEcCCCCEEEEEEEeeecccccceEeCCCHHHHHHHHhhhheeccCCCCEEEEEEEE
Confidence            35666543 444445556678888774   333334444     3444421000    1123344578999999999   


Q ss_pred             --eeeEEEEEccCCCCccEEEEEEceecCcccccChh----------hhcCCCCeEEEEEEEEeCCCC---eeEEEEecc
Q 024995           66 --DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR----------DILNEGDEVRVKVIKIDREKS---RITLSIKQL  130 (259)
Q Consensus        66 --~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~----------~~~~~Gd~V~vkVl~id~~~~---ri~lS~K~~  130 (259)
                        +||+||+|+     + .+||||+|+|++.+..++.          +.+++||.|+|+|+++|.+.+   +|. |+|+.
T Consensus        94 vt~fG~FVelg-----~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~~i~~Ig-Smk~~  166 (215)
T 2b8k_G           94 CSQHGFEVQVG-----P-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIG-SIKED  166 (215)
T ss_dssp             EETTEEEEECT-----T-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETTEEEEEE-ECCST
T ss_pred             EecceEEEEec-----C-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcCCCccEEEE-EcCCC
Confidence              999999997     5 9999999999865443332          569999999999999998764   677 88876


Q ss_pred             ccCcch
Q 024995          131 EEDPLL  136 (259)
Q Consensus       131 ~~~p~~  136 (259)
                      ..-||.
T Consensus       167 ~LG~~~  172 (215)
T 2b8k_G          167 YLGAIS  172 (215)
T ss_dssp             TCEEC-
T ss_pred             CCCCcc
Confidence            666664

>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=99.01  E-value=5.5e-11  Score=108.37  Aligned_cols=98  Identities=17%  Similarity=0.150  Sum_probs=74.5

Q ss_pred             cccCCCCEEEEEEEEEeCCCCEEEEEechhh--------HhhhccCCC--CCCEEEEE-----eeeEEEEEccCCCCccE
Q 024995           18 AKGLTGSIISVKVIQANEEMKKLVFSEKDAV--------WNKYSSRVN--VEDIFVGR-----DYGAFIHLRFPDGLYHL   82 (259)
Q Consensus        18 ~~~~vG~~v~~~Vl~id~~~~~v~lS~k~~~--------~~~~~~~l~--~G~iv~G~-----~~G~fV~l~~~~g~~gi   82 (259)
                      .+..+|+++++.|...|.. +....+.|+..        ++.++..++  .|++++|+     ++|+||+++      +.
T Consensus        85 ~~~~vGd~ie~~I~~~dfg-R~aa~~aKqvi~qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~v~VDlG------k~  157 (344)
T 1hh2_P           85 PLAEVGSIVKKELNVKNFG-RIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIG------KL  157 (344)
T ss_dssp             TTCCTTCEEEEECCCCCSS-SCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEET------TE
T ss_pred             ccccCCCEEEEEEccccCc-cHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCcEEEEeC------Ce
Confidence            4467999999998777643 33444445432        223455565  89999999     789999997      79


Q ss_pred             EEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCC--eeEEEEe
Q 024995           83 TGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIK  128 (259)
Q Consensus        83 ~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~--ri~lS~K  128 (259)
                      +|++|.+|++      |.+.|++||.|+|.|++++.+++  +|.||.+
T Consensus       158 EgiLp~sE~i------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt  199 (344)
T 1hh2_P          158 ETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRR  199 (344)
T ss_dssp             EEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESS
T ss_pred             EEEEeHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEee
Confidence            9999999986      56789999999999999997655  5666654

>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=99.00  E-value=5.2e-10  Score=95.59  Aligned_cols=77  Identities=19%  Similarity=0.205  Sum_probs=65.9

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCC---CccEEEEEEceecCccccc--ChhhhcCCCCeEEEEEEEEeCCCCee
Q 024995           54 SRVNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRI  123 (259)
Q Consensus        54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g---~~gi~glv~isels~~~~~--~~~~~~~~Gd~V~vkVl~id~~~~ri  123 (259)
                      ..+++|+++.|+     ++|+||+|.++++   ..+.+|+||++|+++.+..  ++.+.|++||.|+|+|++++..++++
T Consensus        77 y~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i  156 (209)
T 2nn6_I           77 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNY  156 (209)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEE
T ss_pred             CCCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeE
Confidence            367999999999     8999999963211   0257999999999998887  89999999999999999999866789


Q ss_pred             EEEEecc
Q 024995          124 TLSIKQL  130 (259)
Q Consensus       124 ~lS~K~~  130 (259)
                      .||+|+.
T Consensus       157 ~LS~k~~  163 (209)
T 2nn6_I          157 LLTTAEN  163 (209)
T ss_dssp             EEECCSS
T ss_pred             EEEEecC
Confidence            9999864

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

Probab=99.00  E-value=2e-10  Score=91.06  Aligned_cols=75  Identities=9%  Similarity=0.122  Sum_probs=61.6

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      .+|+++.|+|++|++||    +||+|  .+|++||+ +|++++.          |+   ..    ....+++||.|    
T Consensus         6 ~vG~iv~G~V~~i~~~G----~FV~l--~~~~~Glihisel~~~----------~~---~~----~~~~~~vGd~V~vkV   62 (130)
T 2k4k_A            6 EVGSVYTGKVTGLQAYG----AFVAL--DEETQGLVHISEVTHG----------FV---KD----INEHLSVGDEVQVKV   62 (130)
T ss_dssp             CTTCEEEEEEEEEETTE----EEEEE--ETTEEEEEEGGGTSSS----------CC---SC----GGGTCCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEeCCe----EEEEE--CCCcEEEEEHHHCCcc----------cc---cC----ccccCCCCCEEEEEE
Confidence            35788999999999999    99999  78999999 7777633          11   11    22356999999    


Q ss_pred             EEEecccchhhhhhchhhhhhhH
Q 024995          227 QEIQLSHSLIRKASKRHCNEYWN  249 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~~~~p~~  249 (259)
                      ++||.++++|+||+|++.++||.
T Consensus        63 ~~vd~~~~kI~LSlk~~~~~p~~   85 (130)
T 2k4k_A           63 LAVDEEKGKISLSIRATQAAPEK   85 (130)
T ss_dssp             EEEETTTTEEEEESHHHHHSCCC
T ss_pred             EEEeCCCCEEEEEEeecccCccc
Confidence            68898899999999999999986

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

Probab=98.96  E-value=1.2e-09  Score=91.09  Aligned_cols=70  Identities=27%  Similarity=0.393  Sum_probs=60.3

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCC-----CccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeE
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDG-----LYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT  124 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g-----~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~  124 (259)
                      ..+ |++|.|+     ++|+||+|..+++     ..+.+|+||+|++++.++.++.+.|++||.|+|+|++     +++.
T Consensus        55 ~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~-----~~i~  128 (179)
T 3m7n_A           55 IVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG-----DNLR  128 (179)
T ss_dssp             CCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE-----TTTE
T ss_pred             cCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC-----CeEE
Confidence            467 9999999     8999999982100     0179999999999999999999999999999999997     8899


Q ss_pred             EEEecc
Q 024995          125 LSIKQL  130 (259)
Q Consensus       125 lS~K~~  130 (259)
                      ||+|+.
T Consensus       129 LS~k~~  134 (179)
T 3m7n_A          129 LSTKEE  134 (179)
T ss_dssp             EECCST
T ss_pred             EEEecC
Confidence            998864

>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=98.96  E-value=2.2e-10  Score=87.26  Aligned_cols=78  Identities=12%  Similarity=0.046  Sum_probs=59.3

Q ss_pred             CCCccccceeeeccCCCccceeeeeccc-CCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~-~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      .|+++.|+|++|++||    +|++|... +|++||+ +|++....         |   ..    +....+++||.|    
T Consensus        12 vG~i~~G~V~~v~~fG----~FV~l~~~~~~~~Glvhisel~~~~---------~---~~----~~~~~~~~Gd~V~VkV   71 (103)
T 2eqs_A           12 IGDIYNGKVTSIMQFG----CFVQLEGLRKRWEGLVHISELRREG---------R---VA----NVADVVSKGQRVKVKV   71 (103)
T ss_dssp             TTCEEEEEEEEECSSC----EEEEECSSSSCCEEEECGGGTSSSS---------C---CC----CHHHHCCTTCEEEEEE
T ss_pred             CCCEEEEEEEEEeccE----EEEEEcCCCCCeEEEEEHHHCCCCc---------c---cC----CcccEeCCCCEEEEEE
Confidence            5788999999999999    99999321 3999999 77773221         1   12    123356999999    


Q ss_pred             EEEecccchhhhhhchhhhhhhHHhh
Q 024995          227 QEIQLSHSLIRKASKRHCNEYWNVFH  252 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~~~~p~~~~~  252 (259)
                      +++|.  ++|+||+|++.++||+.+.
T Consensus        72 ~~vd~--~~i~LSlk~~~~~~~~~~~   95 (103)
T 2eqs_A           72 LSFTG--TKTSLSMKDVDQETGEDLN   95 (103)
T ss_dssp             EEEET--TEEEEESTTBCTTTCCBCC
T ss_pred             EEEEC--CeeEEEEeecccCCchhcC
Confidence            46665  6999999999999998764

>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=98.94  E-value=9.4e-11  Score=91.62  Aligned_cols=91  Identities=7%  Similarity=-0.011  Sum_probs=66.7

Q ss_pred             cccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccceeeeecccC-CeeEEE-Eccccccccccchhhhhhcc
Q 024995          130 LEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR-ITRQGFEKRVVSQDLQLWLS  207 (259)
Q Consensus       130 ~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~-gv~gl~-~s~~~~~~~~~~~~~~~~~~  207 (259)
                      +.+++|.... ..+.        +|+++.|+|++|++||    +||+|  .+ +++||+ +|++++..          + 
T Consensus         8 ~~~~~~~~~~-~~~~--------vG~iv~G~V~~I~~fG----aFV~l--~g~~~~Glvhisel~~~~----------~-   61 (119)
T 2cqo_A            8 MNSGRPETME-NLPA--------LYTIFQGEVAMVTDYG----AFIKI--PGCRKQGLVHRTHMSSCR----------V-   61 (119)
T ss_dssp             SCCCCCCCSC-CSCC--------TTCEEEEEEEEEETTE----EEEEC--TTCSSCEEEEHHHHCSSC----------C-
T ss_pred             ccccchhhhh-cccC--------CCCEEEEEEEEEeCce----EEEEE--CCCcEEEEEEHHHCCccc----------c-
Confidence            4567775432 2223        4777999999999999    99999  44 479999 67776321          1 


Q ss_pred             cCCCCCcceeeeccCCCee----EEEeccc--chhhhhhchhhhhhhHHhh
Q 024995          208 NAPPSGKKFTLLARAGRQV----QEIQLSH--SLIRKASKRHCNEYWNVFH  252 (259)
Q Consensus       208 ~~~~~~~~~~~~~r~G~~V----~~v~~~~--~~i~ls~k~~~~~p~~~~~  252 (259)
                        .    +....+++||.|    +++|.++  ++|+||||++.++||+.+.
T Consensus        62 --~----~~~~~~~~Gd~V~VkV~~vd~~~~~~~i~LSlk~~~~~~~~~~~  106 (119)
T 2cqo_A           62 --D----KPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVNQGTGKDLD  106 (119)
T ss_dssp             --S----CHHHHCCTTCEEEEEEEEEEECSSCEEEEEESTTBCSSSCCBSC
T ss_pred             --c----ChhhcCCCCCEEEEEEEEEeccccCceEEEEEeecccCCccccC
Confidence              1    233357999998    5778764  6899999999999998764

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

Probab=98.93  E-value=2e-10  Score=85.08  Aligned_cols=72  Identities=10%  Similarity=0.211  Sum_probs=56.3

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-Ec-cccccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-IT-RQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---  226 (259)
                      .+|+++.|+|+ +++||    +|++|...+|++||+ +| +++++          |+..       .+..+ +||.|   
T Consensus        10 ~vG~~~~G~V~-v~~fG----~FVel~~~~~~eGLvhis~el~~~----------~~~~-------~~~~~-~Gd~V~Vk   66 (88)
T 1luz_A           10 NAGDVIKGRVY-EKDYA----LYIYLFDYPHFEAILAESVKMHMD----------RYVE-------YRDKL-VGKTVKVK   66 (88)
T ss_dssp             CTTCEEEEEEE-EETTE----EEEEETTCTTSEEEEGGGSSCCHH----------HHHH-------HHHHH-TTCEEEEE
T ss_pred             CCCCEEEEEEE-EEccE----EEEEECCCCCeEEEEEeeHHhCcc----------cccC-------HhHEe-CCCEEEEE
Confidence            35888999999 99999    999994335899999 78 87733          2221       12245 99998   


Q ss_pred             -EEEecccchhhhhhchhhhh
Q 024995          227 -QEIQLSHSLIRKASKRHCNE  246 (259)
Q Consensus       227 -~~v~~~~~~i~ls~k~~~~~  246 (259)
                       +++|.++++|+||+|++.++
T Consensus        67 V~~vd~~~~kI~lslk~~~~~   87 (88)
T 1luz_A           67 VIRVDYTKGYIDVNYKRMCRH   87 (88)
T ss_dssp             EEEEETTTTEEEEEEEEECSC
T ss_pred             EEEEECCCCEEEEEEeecCCC
Confidence             78999999999999998654

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

Probab=98.90  E-value=8.6e-10  Score=79.98  Aligned_cols=67  Identities=10%  Similarity=0.048  Sum_probs=55.3

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|+++++||    +|++|  .+|++||+ +|+++...          .           ..+++||.|    
T Consensus         4 ~~G~iv~G~V~~v~~~G----~fV~l--~~~~~Gllh~sel~~~~----------~-----------~~~~~Gd~V~v~V   56 (80)
T 2k52_A            4 EPGKFYKGVVTRIEKYG----AFINL--NEQVRGLLRPRDMISLR----------L-----------ENLNVGDEIIVQA   56 (80)
T ss_dssp             CTTCEEEEEEEEEETTE----EEEEE--ETTEEEEECGGGCSSCC----------G-----------GGCCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEeCCE----EEEEE--CCCCEEEEEHHHCCccc----------c-----------eeeCCCCEEEEEE
Confidence            46888999999999999    99998  78999999 77765221          1           245999999    


Q ss_pred             EEEecccchhhhhhchhhh
Q 024995          227 QEIQLSHSLIRKASKRHCN  245 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~~~  245 (259)
                      +++|.++++|+||+|++.+
T Consensus        57 ~~vd~~~~~i~lsl~~~~~   75 (80)
T 2k52_A           57 IDVRPEKREIDFKYIPLEH   75 (80)
T ss_dssp             EEEETTTTEEEEEECSCC-
T ss_pred             EEEECCCCEEEEEEeeccc
Confidence            6889999999999999875

>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=98.87  E-value=2.8e-10  Score=100.68  Aligned_cols=86  Identities=7%  Similarity=0.072  Sum_probs=69.0

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      .+|+++.|+|++|++||    +||+|...+|++||+ +|+++++          |+   .    +....+++||.|    
T Consensus        10 ~vG~iv~G~V~~I~~~G----aFV~l~e~~~~~GlihiSels~~----------~v---~----~~~~~~~vGd~V~VkV   68 (266)
T 3cw2_C           10 SEGEILIATVKQVFDYG----SYVSLDEYGGLQAFLPWSEVSSK----------WV---K----NIRDVLKENRKVIVKV   68 (266)
T ss_dssp             CTTCEEEEEEEECCSSS----BEEEETTTTSEECBBCGGGSSCS----------SC---C----CHHHHSCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEeccE----EEEEEcCCCCeEEEEEhHHcCcc----------cc---c----CHHHhCcCCCEEEEEE
Confidence            35888999999999999    999992127999999 7887633          22   2    133367999999    


Q ss_pred             EEEecccchhhhhhchhhhhhhHHhhhhcccC
Q 024995          227 QEIQLSHSLIRKASKRHCNEYWNVFHETAIVN  258 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~~~~p~~~~~~~~~~~  258 (259)
                      +.+|.++++|+||+|++.++||..+.++|+.|
T Consensus        69 i~vd~~~g~I~LSlk~~~~~~~~~~~~~~~~~  100 (266)
T 3cw2_C           69 IRVDRRKGTVDVSLKKVTDDERRKKNLQWKKI  100 (266)
T ss_dssp             CCCCSSSCCCBEESTTSCTTHHHHHHHHHHHH
T ss_pred             EEEeCCCCEEEEEEEecchhhHHHHHHhcccc
Confidence            46777789999999999999999999888765

>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=98.87  E-value=3.1e-09  Score=87.93  Aligned_cols=70  Identities=16%  Similarity=0.269  Sum_probs=55.9

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccCh------------hhhcCCCCeEEEEEEE
Q 024995           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI------------RDILNEGDEVRVKVIK  115 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~------------~~~~~~Gd~V~vkVl~  115 (259)
                      ....++|++++|+     +||+||+++      ..+||||+|+|++.+..++            .+.|++||.|+|+|++
T Consensus        76 ~~~~~~Gev~~G~V~~v~~fG~fV~l~------~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~  149 (172)
T 2c35_B           76 VFRPFKGEVVDAVVTQVNKVGLFTEIG------PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVG  149 (172)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEET------TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEE
T ss_pred             EeeCCCCCEEEEEEEEEeCCEEEEEEC------CEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEE
Confidence            4567899999999     999999997      5779999999986533222            4579999999999999


Q ss_pred             EeCCCC---eeEEEEec
Q 024995          116 IDREKS---RITLSIKQ  129 (259)
Q Consensus       116 id~~~~---ri~lS~K~  129 (259)
                      +|.+.+   ++. |+|+
T Consensus       150 vd~~~~~~~~ig-sm~~  165 (172)
T 2c35_B          150 TRVDKNDIFAIG-SLMD  165 (172)
T ss_dssp             EEEETTEEEEEE-ECCS
T ss_pred             EEcCCCCcEEEE-EecC
Confidence            998655   444 6654

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

Probab=98.74  E-value=4e-09  Score=87.41  Aligned_cols=68  Identities=18%  Similarity=0.258  Sum_probs=56.3

Q ss_pred             HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccCh----------hhhcCCCCeEEEEE
Q 024995           49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI----------RDILNEGDEVRVKV  113 (259)
Q Consensus        49 ~~~~~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~----------~~~~~~Gd~V~vkV  113 (259)
                      +..+.-+...|++++|+     +||+||+++      .++||+|+|+|++.+.-++          .+.+++||.|+|||
T Consensus        75 f~~ivf~p~~Gev~~G~V~~v~~fG~FV~l~------~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV  148 (172)
T 3h0g_G           75 YRAVLWRPFRGEVVDAIVTTVNKMGFFANIG------PLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKI  148 (172)
T ss_dssp             EEEEEECCCTTCEEECCCCEEETTEEECCBT------TBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEE
T ss_pred             EEEeeeccCCCCEEEEEEEEEEcceEEEEeC------CeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEE
Confidence            33455688999999999     999999997      5789999999986644333          46899999999999


Q ss_pred             EEEeCCCCe
Q 024995          114 IKIDREKSR  122 (259)
Q Consensus       114 l~id~~~~r  122 (259)
                      +++|.+.++
T Consensus       149 ~~vd~~~~~  157 (172)
T 3h0g_G          149 VGTRTDATE  157 (172)
T ss_dssp             EEEEESSSC
T ss_pred             EEEECCCCC
Confidence            999987754

>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=98.73  E-value=9.7e-09  Score=90.02  Aligned_cols=71  Identities=25%  Similarity=0.359  Sum_probs=63.4

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc---cChhhhcCCCCeEEEEEEEEeCCCCeeEE
Q 024995           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI---QDIRDILNEGDEVRVKVIKIDREKSRITL  125 (259)
Q Consensus        54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~---~~~~~~~~~Gd~V~vkVl~id~~~~ri~l  125 (259)
                      ..+++|++|.|+     ++|+||+|+     .+.+|+||++++++.+.   .++.+.|++||.|.|+|++++. .+++.|
T Consensus        70 y~p~~GDiV~G~V~~v~~~ga~VdI~-----~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~-~~~i~L  143 (251)
T 2je6_I           70 YYPKINDIVIGLVEDVEIYGWVVDIK-----APYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVL  143 (251)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECS-----SSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEE
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEcC-----CCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECC-CCcEEE
Confidence            357999999999     899999998     47999999999998777   7888999999999999999996 579999


Q ss_pred             EEecc
Q 024995          126 SIKQL  130 (259)
Q Consensus       126 S~K~~  130 (259)
                      |+|+.
T Consensus       144 S~r~~  148 (251)
T 2je6_I          144 SVKGK  148 (251)
T ss_dssp             ECCST
T ss_pred             EEccc
Confidence            98753

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

Probab=98.71  E-value=1.4e-09  Score=107.85  Aligned_cols=77  Identities=14%  Similarity=0.149  Sum_probs=0.0

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      +|++++|+|+++++||    +||+|  .+|++||+ +|+++++          |+   ..    ...++++||.|    +
T Consensus       627 vG~i~~G~V~~i~~fG----aFVel--~~g~eGLvHiSel~~~----------~v---~~----~~~~~~vGd~V~VkVi  683 (723)
T 3cdi_A          627 VGRVYTGKVTRIVDFG----AFVAI--GGGKEGLVHISQIADK----------RV---EK----VTDYLQMGQEVPVKVL  683 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCcEEEEEEEEEecce----EEEEe--CCCceEEEEHHHcCCc----------cc---cC----cccccCCCCEEEEEEE
Confidence            3677999999999999    99988  78999998 7888743          12   22    23367999999    5


Q ss_pred             EEecccchhhhhhchhhhhhhHHhhh
Q 024995          228 EIQLSHSLIRKASKRHCNEYWNVFHE  253 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~~~~~p~~~~~~  253 (259)
                      +||. +++|+||+|++.++||....-
T Consensus       684 ~vd~-~grI~LS~k~~~~~~g~~~~p  708 (723)
T 3cdi_A          684 EVDR-QGRIRLSIKEATEQSQPAAAP  708 (723)
T ss_dssp             --------------------------
T ss_pred             EECC-CCcEEEEEEeccCCCCcccCc
Confidence            7777 889999999999999987643

>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=98.69  E-value=1.1e-08  Score=88.76  Aligned_cols=70  Identities=17%  Similarity=0.343  Sum_probs=61.4

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcc----cccChhhhcCCCCeEEEEEEEEeCCCCeeE
Q 024995           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQDIRDILNEGDEVRVKVIKIDREKSRIT  124 (259)
Q Consensus        54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~----~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~  124 (259)
                      ..+++|+++.|+     ++|+||+|+     .+.+|++|+++++..    +..++.+.|++||.|.|+|++++. .+++.
T Consensus        62 y~p~~GDiV~G~V~~v~~~~~~V~I~-----~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~-~~~i~  135 (235)
T 2z0s_A           62 YVPQAGDVVIGLIQSVGIMNWFVDIN-----SPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPL  135 (235)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECS-----SSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEE
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeC-----CCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECC-CCcEE
Confidence            367999999999     899999998     479999999999863    456788899999999999999996 56999


Q ss_pred             EEEec
Q 024995          125 LSIKQ  129 (259)
Q Consensus       125 lS~K~  129 (259)
                      ||+|+
T Consensus       136 LS~k~  140 (235)
T 2z0s_A          136 LTVQG  140 (235)
T ss_dssp             EECCS
T ss_pred             EEEec
Confidence            99874

>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=98.65  E-value=4.5e-08  Score=84.63  Aligned_cols=70  Identities=26%  Similarity=0.356  Sum_probs=62.7

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcc-cccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~-~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      .+++|++|.|+     ++|+||+|+     .+.+|++|+++++.. +..++.+.|++||.|.|+|++++. .+++.||+|
T Consensus        54 ~p~~GDiV~G~V~~v~~~~a~V~I~-----~~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~-~~~i~LS~r  127 (229)
T 2ba0_A           54 TPSVGDVVIGIIREVAANGWAVDIY-----SPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMK  127 (229)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS-----SSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECC
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC-----CCeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECC-CCcEEEEEc
Confidence            57999999999     899999998     478999999999974 677889999999999999999996 589999987


Q ss_pred             cc
Q 024995          129 QL  130 (259)
Q Consensus       129 ~~  130 (259)
                      +.
T Consensus       128 ~~  129 (229)
T 2ba0_A          128 DR  129 (229)
T ss_dssp             SS
T ss_pred             cc
Confidence            53

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

Probab=98.64  E-value=3.4e-09  Score=105.01  Aligned_cols=82  Identities=9%  Similarity=0.043  Sum_probs=0.0

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      .+|+++.|+|++|++||    +||+|  .+|++||+ +|+++++          |+   ..    .+.++++||.|    
T Consensus       636 ~vG~v~~G~V~~I~~fG----aFVel--~~g~eGLvHiSels~~----------rv---~~----~~d~~kvGD~V~VkV  692 (726)
T 4aid_A          636 EVGKIYDGKVVKVVDFG----AFVNF--FGAKDGLVHVSQISNE----------RV---AK----PSDVLKEGQMVKVKL  692 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCCcEEEEEEEEEeccE----EEEEE--CCCcEEEEEHHHcCcc----------cc---cC----ccccCCCCCEEEEEE
Confidence            46888999999999999    99999  78999999 7898743          12   22    23367999999    


Q ss_pred             EEEecccchhhhhhchhhhhhhHHhhhhccc
Q 024995          227 QEIQLSHSLIRKASKRHCNEYWNVFHETAIV  257 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~~~~p~~~~~~~~~~  257 (259)
                      ++||. ++||+||+|++.++|++.+.+|.++
T Consensus       693 i~iD~-~grI~LS~K~~~~~~G~~~~~k~~~  722 (726)
T 4aid_A          693 LGFDD-RGKTKLSMKVVDQETGEDLSKKEAA  722 (726)
T ss_dssp             -------------------------------
T ss_pred             EEECC-CCcEEEEEeecccCcchhhhhhhhh
Confidence            68887 6899999999999999999777553

>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=98.48  E-value=3.9e-08  Score=76.47  Aligned_cols=72  Identities=7%  Similarity=0.135  Sum_probs=54.1

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      ++|+++.|+|++|++||    +|++|. .+++.||+++++..          .|..... +..    .+++||.|    +
T Consensus        20 ~~G~i~~G~V~~v~~fG----~fV~l~-~~~~~~l~~~~~~~----------~~~~~~~-~~~----~~~~Gd~V~vkV~   79 (119)
T 1wi5_A           20 KPGMLLTGTVSSLEDHG----YLVDIG-VDGTRAFLPLLKAQ----------EYIRQKN-KGA----KLKVGQYLNCIVE   79 (119)
T ss_dssp             CTTCEEEEEEEEECSSE----EEEECC-CSSCEEEEEHHHHH----------HHHHHHS-SSC----CCCTTCEEEEEEE
T ss_pred             CCCCEEEEEEEEEeCce----EEEEEC-CCCeEEEEEEeccc----------ccccccC-ccC----EeCCCCEEEEEEE
Confidence            35788999999999999    999993 25888888877541          1433211 223    56999999    6


Q ss_pred             EEecccchhhhhhchh
Q 024995          228 EIQLSHSLIRKASKRH  243 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~~  243 (259)
                      +||.++++|+||+|+.
T Consensus        80 ~vd~~~~~i~Lslk~~   95 (119)
T 1wi5_A           80 KVKGNGGVVSLSVGHS   95 (119)
T ss_dssp             ECCTTSCEEEEECCCC
T ss_pred             EEeCCCCEEEEEEchh
Confidence            7888889999999973

>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=98.28  E-value=5e-07  Score=75.41  Aligned_cols=89  Identities=11%  Similarity=0.100  Sum_probs=60.8

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      .|+++.|+|+++++||    +|++|  .+ ++||+ +|+++.+.-...++-..|+..  .+.    ..+++||.|    +
T Consensus        81 ~Gev~~G~V~~v~~~G----~fV~l--~~-~eglvhis~l~~~~~~~d~~~~~~~~~--~~~----~~~~~Gd~V~vkV~  147 (187)
T 1go3_E           81 MYELIEGEVVDVVEFG----SFVRL--GP-LDGLIHVSQIMDDYVSYDPKREAIIGK--ETG----KVLEIGDYVRARIV  147 (187)
T ss_dssp             TTCEEEEEEEEEETTE----EEEEC--SS-SEEEEEGGGSCSSCEEECCC--CEEET--TTC----CEECTTCEEEEEEE
T ss_pred             CCCEEEEEEEEEeCcE----EEEEE--cC-ccEEEEhHHhCCCcceECCccceEEec--CCC----eEEcCCCEEEEEEE
Confidence            4778999999999999    99999  44 99999 677764432222222233321  122    356999999    6


Q ss_pred             EEecccc-----hhhhhhch--hhhhhhHHhhhh
Q 024995          228 EIQLSHS-----LIRKASKR--HCNEYWNVFHET  254 (259)
Q Consensus       228 ~v~~~~~-----~i~ls~k~--~~~~p~~~~~~~  254 (259)
                      +++.+.+     +|+||+|+  |-..+|-.-.++
T Consensus       148 ~vd~~~~~p~~~~I~lS~k~~~LG~~~w~~~~~~  181 (187)
T 1go3_E          148 AISLKAERKRGSKIALTMRQPYLGKLEWIEEEKA  181 (187)
T ss_dssp             EEECCC-----CEEEEECCSTTCEEHHHHHHHHH
T ss_pred             EEEcccCCCCccEEEEEEcCCCCCcHHHHhhhhh
Confidence            8888766     89999999  556777554444

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

Probab=98.27  E-value=9.1e-07  Score=66.86  Aligned_cols=78  Identities=19%  Similarity=0.200  Sum_probs=55.3

Q ss_pred             CCCCCEEEEE--------eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           56 VNVEDIFVGR--------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        56 l~~G~iv~G~--------~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      .+.++..+|+        .|| |+.-+.    .+.++|+|+|++++...                               
T Consensus        11 ~~~~~~~~G~Vk~fn~~kGfG-FI~~~~----gg~dvfvH~s~l~~~~~-------------------------------   54 (101)
T 2bh8_A           11 RLQSGKMTGIVKWFNADKGFG-FITPDD----GSKDVFVHFSAGSSGAA-------------------------------   54 (101)
T ss_dssp             -----CEEEEEEEEEGGGTEE-EEEESS----SSCEEEEECCCSCSSSC-------------------------------
T ss_pred             ccccccceeEEEEEECCCCCE-EEEeCC----CCcEEEEEEEEEecCCc-------------------------------
Confidence            3456667777        588 887652    26899999999987642                               


Q ss_pred             eccccCcchHhhhhhcCCCCccccCCCCccccceeeeccCCCccceeeeecccCCeeEEE-Ecccccc
Q 024995          128 KQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFE  194 (259)
Q Consensus       128 K~~~~~p~~~~~~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~  194 (259)
                        .         .+.+.        +|+.++++|.++++||    +|++|  .++++||+ +|++++.
T Consensus        55 --~---------~~~l~--------~Ge~V~g~V~~i~~fG----~fv~l--~~~~eGlvhis~i~~~   97 (101)
T 2bh8_A           55 --V---------RGNPQ--------QGDRVEGKIKSITDFG----IFIGL--DGGIDGLVHLSDISWA   97 (101)
T ss_dssp             --C---------CCCCC--------TTCEEEEEEEECCSEE----EEECT--TSCEEEEEEEEEEEEC
T ss_pred             --c---------ccCCC--------CCCEEEEEEEEeCCcE----EEEEc--CCCceEEEEHHHCccC
Confidence              0         01122        3667999999999999    99888  78999999 8888743

>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=98.25  E-value=1.3e-06  Score=86.03  Aligned_cols=70  Identities=11%  Similarity=0.071  Sum_probs=57.6

Q ss_pred             CCCCCC--EEEEE-----eeeEEEEEccCCCCccEEEEEEceecCc--ccc----------cChhhhcCCCCeEEEEEEE
Q 024995           55 RVNVED--IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI----------QDIRDILNEGDEVRVKVIK  115 (259)
Q Consensus        55 ~l~~G~--iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~--~~~----------~~~~~~~~~Gd~V~vkVl~  115 (259)
                      .-++|+  +++|+     +||+||+|..    .|++||||+|+|++  +++          .+....|++||.|+|+|.+
T Consensus       555 ~~~vGe~~~f~g~V~~V~~~G~fV~L~~----~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~  630 (644)
T 2id0_A          555 KDKAGTDTRFAAEIVDISRGGMRVRLVD----NGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAE  630 (644)
T ss_dssp             GGGTTSCCCEEEEEEEEETTEEEEEETT----TCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEE
T ss_pred             hhccCCCceEEEEEEEEeCCceEEEEcC----CcEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEEEE
Confidence            447888  88888     8999999953    58999999999973  321          1345679999999999999


Q ss_pred             EeCCCCeeEEEEe
Q 024995          116 IDREKSRITLSIK  128 (259)
Q Consensus       116 id~~~~ri~lS~K  128 (259)
                      +|.++++|.+++-
T Consensus       631 vd~~~~~I~~~l~  643 (644)
T 2id0_A          631 VRMETRSIIARPV  643 (644)
T ss_dssp             EETTTTEEEEEEC
T ss_pred             EeCCCCEEEEEEc
Confidence            9999999999873

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

Probab=98.25  E-value=6.5e-07  Score=93.11  Aligned_cols=71  Identities=11%  Similarity=0.026  Sum_probs=58.1

Q ss_pred             ccCCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee--
Q 024995          150 ISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV--  226 (259)
Q Consensus       150 ~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V--  226 (259)
                      +.++|+++.|+|++|++||    +||+|  .+|++||+ +|++++.          +.  +.++..    ++++||.|  
T Consensus       899 ~l~~G~iv~G~V~~V~~fG----aFV~L--~~gveGLVHiSelsd~----------~~--v~~p~~----v~kvGd~V~v  956 (1219)
T 3psi_A          899 TFFKGSIIPVRVERFWHND----IICTT--NSEVECVVNAQRHAGA----------QL--RRPANE----IYEIGKTYPA  956 (1219)
T ss_dssp             TSCTTCEEEEEEEEECSSC----EEEEC--TTSCEEEECTTSSSST----------TS--CSCSTT----TSCTTCEEEE
T ss_pred             hCCCCCEEEEEEEEEecce----EEEEe--CCCceEEEEHHHcCCC----------cc--cCCHHH----cCCCCCEEEE
Confidence            3467999999999999999    99998  78999999 7888743          10  222333    66999999  


Q ss_pred             --EEEecccchhhhhhch
Q 024995          227 --QEIQLSHSLIRKASKR  242 (259)
Q Consensus       227 --~~v~~~~~~i~ls~k~  242 (259)
                        ++||.++++|+||||.
T Consensus       957 kVl~VD~~~~rI~LSlk~  974 (1219)
T 3psi_A          957 KVIYIDYANITAEVSLLD  974 (1219)
T ss_dssp             EEEEEEGGGTEEEEECCH
T ss_pred             EEEEEECCCCEEEEEecH
Confidence              7999999999999996

>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=98.16  E-value=8.6e-07  Score=73.57  Aligned_cols=87  Identities=10%  Similarity=0.113  Sum_probs=57.6

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      .|++++|+|+++++||    +|+++   ++++||+ +|++..+.-..-++-..|...  ..+    ..++.||.|    +
T Consensus        81 ~Gev~~G~V~~v~~~G----~fv~l---~~~~glvh~s~l~~d~~~~d~~~~~~~g~--~~~----~~~~~Gd~VrvkV~  147 (180)
T 4ayb_E           81 VQEVVEGEVLQVDNYG----VFVNL---GPMDGLVHISQITDDTLKYDNVRGIIFGE--KSK----KVIQKGDKVRARVI  147 (180)
T ss_dssp             TTCEEEEEEEEEETTE----EEEEC---SSSEEEEEGGGSCSSCEEECSSSCCEEET--TTC----CCCCTTCEEEEEEE
T ss_pred             CCCEEEEEEeeeccce----EEEEE---CCccceEEeeecCCCccccchhcceEEEe--ccC----eEECCCCEEEEEEE
Confidence            3778999999999999    99988   4699998 677765422111111122211  122    256999999    5


Q ss_pred             EEeccc----chhhhhhch--hhhhhhHHhh
Q 024995          228 EIQLSH----SLIRKASKR--HCNEYWNVFH  252 (259)
Q Consensus       228 ~v~~~~----~~i~ls~k~--~~~~p~~~~~  252 (259)
                      .|+.+.    .+|+||||+  |-..+|-..+
T Consensus       148 ~v~~~~~~~~~rI~ls~k~~gLG~~~W~~~~  178 (180)
T 4ayb_E          148 SVASTVTGRLPRIALTMRQPYLGKLEWITQA  178 (180)
T ss_dssp             EECC-------CEEEECCSTTCEEHHHHTTC
T ss_pred             EEeCCCCcccCcEEEEcCCCCCCCChhHhhh
Confidence            777653    379999999  6677776544

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

Probab=98.09  E-value=4.1e-07  Score=93.25  Aligned_cols=70  Identities=11%  Similarity=0.029  Sum_probs=0.0

Q ss_pred             cCCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995          151 SDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---  226 (259)
Q Consensus       151 ~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---  226 (259)
                      .++|+++.|+|++|++||    +||+|  .+|++||+ +|++++.          +.  +.++..    ++++||.|   
T Consensus       903 l~~G~iv~G~V~~V~~fG----aFV~L--~~gveGLVHiSelsd~----------~~--v~~~~~----v~kvGd~V~vk  960 (1030)
T 3psf_A          903 FFKGSIIPVRVERFWHND----IICTT--NSEVECVVNAQRHAGA----------QL--RRPANE----IYEIGKTYPAK  960 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hcCCCEEEEEEEEEccCe----EEEEe--CCCcEEEEEHHHcCCC----------cc--cCCHHH----cCCCCCEEEEE
Confidence            467999999999999999    99988  78999999 7888733          10  122333    67999999   


Q ss_pred             -EEEecccchhhhhhch
Q 024995          227 -QEIQLSHSLIRKASKR  242 (259)
Q Consensus       227 -~~v~~~~~~i~ls~k~  242 (259)
                       ++||.++++|+||||+
T Consensus       961 Vl~VD~~~~rI~LSlk~  977 (1030)
T 3psf_A          961 VIYIDYANITAEVSLLD  977 (1030)
T ss_dssp             -----------------
T ss_pred             EEEEECCCCEEEEEech
Confidence             7899999999999997

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

Probab=98.06  E-value=5e-06  Score=70.44  Aligned_cols=62  Identities=11%  Similarity=0.212  Sum_probs=52.1

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc-------------------cChhhhcCCCCe
Q 024995           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDE  108 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~-------------------~~~~~~~~~Gd~  108 (259)
                      .-+..+|+++.|+     +||+||+|+      .++|++|++++.+++.                   .+....|++||.
T Consensus        76 ~f~p~~GEv~~G~Vs~vt~~GifV~lg------~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~  149 (203)
T 3ayh_B           76 IFRPFRGEVMLGKIKSCSEEGIRVTIS------FFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEE  149 (203)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECS------SCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCE
T ss_pred             EEccCCCCEEEEEEEEEeccEEEEEEe------CceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCE
Confidence            3467999999999     899999996      6899999999977653                   344567999999


Q ss_pred             EEEEEEEEeCCC
Q 024995          109 VRVKVIKIDREK  120 (259)
Q Consensus       109 V~vkVl~id~~~  120 (259)
                      |++||.++|...
T Consensus       150 VrvrV~~v~~~~  161 (203)
T 3ayh_B          150 IRFQIESEDFVD  161 (203)
T ss_dssp             EEEEEEEEEECC
T ss_pred             EEEEEEEEEccc
Confidence            999999999743

>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=98.05  E-value=4.9e-06  Score=76.12  Aligned_cols=79  Identities=10%  Similarity=0.170  Sum_probs=56.0

Q ss_pred             hhccCCC--CCCEEEEE--e-------eeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCC
Q 024995           51 KYSSRVN--VEDIFVGR--D-------YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDRE  119 (259)
Q Consensus        51 ~~~~~l~--~G~iv~G~--~-------~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~  119 (259)
                      ..+..++  +|++++|+  .       +++||+|+...  .+.+|+||.+|+.      |.+.|++||.|+|.|++++.+
T Consensus       121 ~i~~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~--~k~EgiLP~~Eqi------P~E~~~~GDrVkvyV~~V~~~  192 (366)
T 1k0r_A          121 RTYGEFSTREGEIVAGVIQRDSRANARGLVVVRIGTET--KASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRG  192 (366)
T ss_dssp             ------CCCTTCEEEEEEECCHHHHHTTCEEEEECCSS--SCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECC
T ss_pred             HHHHHHHhcCCCEEEEEEEEccccccCCeEEEEeCCCc--cceEEEEcHHHcC------CCccCCCCCEEEEEEEEEecC
Confidence            3455565  99999999  3       58999997100  1499999999986      457899999999999999987


Q ss_pred             CCeeEEEEeccccCcchH
Q 024995          120 KSRITLSIKQLEEDPLLE  137 (259)
Q Consensus       120 ~~ri~lS~K~~~~~p~~~  137 (259)
                      ++...+.+..+.++....
T Consensus       193 ~kgpqI~LSRT~p~lv~~  210 (366)
T 1k0r_A          193 AREPLITLSRTHPNLVRK  210 (366)
T ss_dssp             SSSCEEEEESSCHHHHHH
T ss_pred             CCccEEEEEeCChHHHHH
Confidence            666666665555554433

>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=98.04  E-value=4.9e-06  Score=79.55  Aligned_cols=73  Identities=23%  Similarity=0.407  Sum_probs=60.1

Q ss_pred             ccCCCCCCEEEEE-----ee--eEEEEEccCCCCccEEEEEEceecCcccc---------cChhhhcCCCCeEEEEEEEE
Q 024995           53 SSRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSWDLI---------QDIRDILNEGDEVRVKVIKI  116 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~--G~fV~l~~~~g~~gi~glv~isels~~~~---------~~~~~~~~~Gd~V~vkVl~i  116 (259)
                      .....+|++|.|+     ++  ||||+++     .|..||+|++++++.++         .++.+.+++||.|.|+|++.
T Consensus        40 ~~~~~vGnIY~GkV~rv~p~~~aAFVdiG-----~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke  114 (517)
T 2bx2_L           40 GHEQKKANIYKGKITRIEPSLEAAFVDYG-----AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE  114 (517)
T ss_dssp             SSCCCTTCEEEEEEEEEETTTTEEEEESS-----SSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEEC
T ss_pred             CCcCCCCCEEEEEEEEeccCCceEEEEeC-----CCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEee
Confidence            3467899999999     77  9999998     58999999999988763         34667899999999999998


Q ss_pred             eCCCCeeEEEEecc
Q 024995          117 DREKSRITLSIKQL  130 (259)
Q Consensus       117 d~~~~ri~lS~K~~  130 (259)
                      ...++.-.||..-.
T Consensus       115 ~~g~KGa~lTt~is  128 (517)
T 2bx2_L          115 ERGNKGAALTTFIS  128 (517)
T ss_dssp             CCTTCCCEEESSCC
T ss_pred             ccccCCceEEeeEE
Confidence            87767666665443

>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=98.01  E-value=1.8e-06  Score=86.32  Aligned_cols=69  Identities=10%  Similarity=0.134  Sum_probs=56.4

Q ss_pred             cCCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995          151 SDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---  226 (259)
Q Consensus       151 ~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---  226 (259)
                      ..+|+++.|+|++|++||    +||+|  ..+++||+ +|++++.          |   +.++.    .++++||.|   
T Consensus       652 l~vG~iv~G~V~~V~~fG----aFV~l--~~~~eGLVhiS~Lsd~----------~---v~d~~----~~~~vGd~V~Vk  708 (785)
T 3bzc_A          652 LKPGMVLEGVVTNVTNFG----AFVDI--GVHQDGLVHISALSEK----------F---VKDPY----EVVKAGDIVKVK  708 (785)
T ss_dssp             CCTTCBCCCEEEEEETTE----EEEEC--SSSSEEEEETTTSCSS----------C---CSCHH----HHCCTTCCCCCB
T ss_pred             cCCCCEEEEEEEEEecCC----eEEEe--CCCcEEEEEHHHcCcc----------c---cCChh----heeCCCCEEEEE
Confidence            457999999999999999    99988  78999999 7887632          1   22222    366999998   


Q ss_pred             -EEEecccchhhhhhch
Q 024995          227 -QEIQLSHSLIRKASKR  242 (259)
Q Consensus       227 -~~v~~~~~~i~ls~k~  242 (259)
                       ++||.++++|+||||.
T Consensus       709 Vi~VD~~~~rI~LSlk~  725 (785)
T 3bzc_A          709 VMEVDIPRNRVGLSMRM  725 (785)
T ss_dssp             EEEEETTTTEEEECCSS
T ss_pred             EEEEECCCCEEEEEEec
Confidence             7999999999999995

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

Probab=97.94  E-value=1.2e-05  Score=60.67  Aligned_cols=70  Identities=23%  Similarity=0.299  Sum_probs=48.6

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEe-----------chhhHhhh-ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEE
Q 024995           22 TGSIISVKVIQANEEMKKLVFSE-----------KDAVWNKY-SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTG   84 (259)
Q Consensus        22 vG~~v~~~Vl~id~~~~~v~lS~-----------k~~~~~~~-~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~g   84 (259)
                      .++.+..+|..+|..++-=.++.           ....+..+ ...+++|+++.+.     +||+||+|.     .+++|
T Consensus        13 ~~~~~~G~Vk~fn~~kGfGFI~~~~gg~dvfvH~s~l~~~~~~~~~l~~Ge~V~g~V~~i~~fG~fv~l~-----~~~eG   87 (101)
T 2bh8_A           13 QSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITDFGIFIGLD-----GGIDG   87 (101)
T ss_dssp             ---CEEEEEEEEEGGGTEEEEEESSSSCEEEEECCCSCSSSCCCCCCCTTCEEEEEEEECCSEEEEECTT-----SCEEE
T ss_pred             ccccceeEEEEEECCCCCEEEEeCCCCcEEEEEEEEEecCCccccCCCCCCEEEEEEEEeCCcEEEEEcC-----CCceE
Confidence            57778888888876554323332           22222211 2689999999999     799999997     38999


Q ss_pred             EEEceecCcccc
Q 024995           85 LVHVSEVSWDLI   96 (259)
Q Consensus        85 lv~isels~~~~   96 (259)
                      |||+|+|+|.++
T Consensus        88 lvhis~i~~~~~   99 (101)
T 2bh8_A           88 LVHLSDISWAQA   99 (101)
T ss_dssp             EEEEEEEEECCC
T ss_pred             EEEHHHCccCcC
Confidence            999999999764

>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=97.90  E-value=9e-06  Score=81.38  Aligned_cols=65  Identities=17%  Similarity=0.199  Sum_probs=46.9

Q ss_pred             CEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC--cccc-----------cC----hhhhcCCCCeEEEEEEEEe
Q 024995           60 DIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS--WDLI-----------QD----IRDILNEGDEVRVKVIKID  117 (259)
Q Consensus        60 ~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels--~~~~-----------~~----~~~~~~~Gd~V~vkVl~id  117 (259)
                      +++.|+     +||+||.|..    +|++||||+++|+  .+++           .+    ....|++||.|+|+|+.+|
T Consensus       671 ~~~~g~V~~V~~~G~fV~l~~----~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV~~vd  746 (760)
T 2vnu_D          671 STETGYVIKVFNNGIVVLVPK----FGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVM  746 (760)
T ss_dssp             SEEEEEEEEEETTEEEEEETT----TTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC---
T ss_pred             eEEEEEEEEEECCeEEEEEeC----CCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCCEEEEEEEEEE
Confidence            688887     8999999973    4899999999996  4331           12    2578999999999999999


Q ss_pred             CC---CCeeEEEEe
Q 024995          118 RE---KSRITLSIK  128 (259)
Q Consensus       118 ~~---~~ri~lS~K  128 (259)
                      .+   ++||.||+|
T Consensus       747 ~~~~~~~kI~lslk  760 (760)
T 2vnu_D          747 DPITSKRKAELLLK  760 (760)
T ss_dssp             -----CCEEEC---
T ss_pred             CccccCCcEEEEeC
Confidence            87   699999986

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

Probab=97.86  E-value=9.7e-06  Score=83.05  Aligned_cols=66  Identities=18%  Similarity=0.214  Sum_probs=54.5

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecC--cccc-----------cC----hhhhcCCCCeEEEEEEEE
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS--WDLI-----------QD----IRDILNEGDEVRVKVIKI  116 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels--~~~~-----------~~----~~~~~~~Gd~V~vkVl~i  116 (259)
                      |+++.|+     +||+||.|..    +|++|+||+++|+  .+++           .+    ....|++||.|+|+|..+
T Consensus       887 ge~~~g~V~~V~~~G~fV~L~~----~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~VkV~~v  962 (977)
T 2wp8_J          887 ESTETGYVIKVFNNGIVVLVPK----FGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSV  962 (977)
T ss_dssp             TCEEEEEEEEECSSEEEEECTT----TCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEEECCC
T ss_pred             ceEEEEEEEEEcCCeEEEEEcC----CCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCCEEEEEEEEE
Confidence            8899998     8999999973    4899999999997  4331           12    347899999999999999


Q ss_pred             eCC---CCeeEEEEe
Q 024995          117 DRE---KSRITLSIK  128 (259)
Q Consensus       117 d~~---~~ri~lS~K  128 (259)
                      |.+   ++||.||+|
T Consensus       963 d~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          963 MDPITSKRKAELLLK  977 (977)
T ss_dssp             CCSSSCCCCCCEEEC
T ss_pred             cCcccCCCceEEEeC
Confidence            863   389999987

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

Probab=97.84  E-value=1.5e-05  Score=68.24  Aligned_cols=115  Identities=10%  Similarity=0.139  Sum_probs=72.1

Q ss_pred             CCCCCCCCCchhHhhhcc-cCCCCEEE-----EEEEEEeC-CCCEEEEEech----hhHhhhccCCCCCCEEEEE-----
Q 024995            2 SPSHSCKEPQKSIHEIAK-GLTGSIIS-----VKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR-----   65 (259)
Q Consensus         2 ~~~~~~~~p~~~~~~~~~-~~vG~~v~-----~~Vl~id~-~~~~v~lS~k~----~~~~~~~~~l~~G~iv~G~-----   65 (259)
                      .|++|.++....+.+.++ .+.|+.+.     +.|.++.. ..++|.-..-.    .......-+..+|++++|+     
T Consensus        14 ~P~~f~~~l~~~i~~~L~~kyegkv~~~~Gl~I~v~di~~i~eG~I~~GdG~~~~~V~fk~~~f~p~vGEv~~G~Is~Vt   93 (218)
T 2ckz_B           14 PPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVVFKPFLGEIVTGWISKCT   93 (218)
T ss_dssp             CGGGTTSCHHHHHHHHHHHHHTTEEETTTEEEEEEEEEEEECCCEECSSSSCEEEEEEEEEEEECCCTTCEEEEEEEEEE
T ss_pred             CHHHcCchHHHHHHHHHHHHhcCcCcCCccEEEEEEEeeeccCcEEeCCCCCEEEEEEEEEEEecCCCCCEEEEEEEEEc
Confidence            577776655555554444 34565443     33333332 22333211000    0112234478899999999     


Q ss_pred             eeeEEEEEccCCCCccEEEEEEceecCcccc--------------cChhhhcCCCCeEEEEEEEEeCCCC
Q 024995           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI--------------QDIRDILNEGDEVRVKVIKIDREKS  121 (259)
Q Consensus        66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~--------------~~~~~~~~~Gd~V~vkVl~id~~~~  121 (259)
                      +||+||+|.+     .++|++|++++..+++              .+....|++||.|++||.++|...+
T Consensus        94 ~fGifVeL~g-----~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~~~~  158 (218)
T 2ckz_B           94 AEGIKVSLLG-----IFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVDV  158 (218)
T ss_dssp             TTEEEEECTT-----SCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEECCC
T ss_pred             cCcEEEEccC-----ccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEcccC
Confidence            9999999952     5899999999976543              2335569999999999999998654

>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=97.81  E-value=1.1e-05  Score=68.71  Aligned_cols=73  Identities=10%  Similarity=0.023  Sum_probs=53.9

Q ss_pred             CCCCccccceeeeccCCCccceeeeec------ccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCC
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELL------QEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~------~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~  224 (259)
                      .+|+++.|+|++++++|    +|++|.      +..+++|++ +|+++...             .+.  -+....+++||
T Consensus        80 ~vGDvV~G~V~~v~~~~----a~V~I~~v~~~~L~~~~~GlIhisei~~~~-------------~~~--~~~~~~l~~GD  140 (209)
T 2nn6_I           80 DVGAIVTCKVSSINSRF----AKVHILYVGSMPLKNSFRGTIRKEDVRATE-------------KDK--VEIYKSFRPGD  140 (209)
T ss_dssp             CTTCEEEEEEEEECSSE----EEEEEEESSSSCCCCSSCSCEEEEGGGTCS-------------SCC--CCGGGTCCSSS
T ss_pred             CCCCEEEEEEEEEECce----EEEEECccccccccCCceeEEEHHHccccc-------------ccc--cchhhhcCCCC
Confidence            45888999999999999    999984      236889998 77776321             110  12444779999


Q ss_pred             ee----EEEecccchhhhhhchh
Q 024995          225 QV----QEIQLSHSLIRKASKRH  243 (259)
Q Consensus       225 ~V----~~v~~~~~~i~ls~k~~  243 (259)
                      .|    +.++.+.++++||+|+.
T Consensus       141 ~V~akVisi~~~~~~i~LS~k~~  163 (209)
T 2nn6_I          141 IVLAKVISLGDAQSNYLLTTAEN  163 (209)
T ss_dssp             EEEEEEEEEETTTTEEEEECCSS
T ss_pred             EEEEEEEEEeCCCCeEEEEEecC
Confidence            99    57776667899999973

>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=97.68  E-value=2e-05  Score=67.35  Aligned_cols=87  Identities=3%  Similarity=-0.149  Sum_probs=53.8

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      +|++++|+|+++++||    +||+|  .+ ++||+ +|++... -..-+.-..|.-...  +    .+++.||.|    +
T Consensus        83 vGev~~G~V~~vt~fG----~FVel--g~-~dGlVhiS~l~d~-~~~d~~~~~w~~~~~--~----~~~~~Gd~VrVkV~  148 (215)
T 2b8k_G           83 KGEVVDGTVVSCSQHG----FEVQV--GP-MKVFVTKHLMPQD-LTFNAGSNPPSYQSS--E----DVITIKSRIRVKIE  148 (215)
T ss_dssp             TTEEEEEEEEEEETTE----EEEEC--TT-SEEEEEGGGSCSS-CCCBSSCSSCEEECS--S----CEEETTCEEEEEEE
T ss_pred             CCCEEEEEEEEEecce----EEEEe--cC-cEEEEEHHHCCcc-ceeccccccceeecc--c----cEECCCCEEEEEEE
Confidence            4888999999999999    99999  66 99999 6776421 000001011111111  1    257999999    6


Q ss_pred             EEecccc---hhhhhhchhhhhhhHHhhhh
Q 024995          228 EIQLSHS---LIRKASKRHCNEYWNVFHET  254 (259)
Q Consensus       228 ~v~~~~~---~i~ls~k~~~~~p~~~~~~~  254 (259)
                      ++|.+.+   +|. |||+----||+....+
T Consensus       149 ~vd~~~~~i~~Ig-Smk~~~LG~~~~~~~~  177 (215)
T 2b8k_G          149 GCISQVSSIHAIG-SIKEDYLGAISHEKRR  177 (215)
T ss_dssp             EEEEETTEEEEEE-ECCSTTCEEC------
T ss_pred             EEEcCCCccEEEE-EcCCCCCCCcchhhHH
Confidence            8888764   687 8988555566544333

>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=97.65  E-value=2.5e-05  Score=70.17  Aligned_cols=69  Identities=22%  Similarity=0.282  Sum_probs=56.3

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcc----cc------cChhhhcCCCCeEEEEEEEEeCC
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LI------QDIRDILNEGDEVRVKVIKIDRE  119 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~----~~------~~~~~~~~~Gd~V~vkVl~id~~  119 (259)
                      .+++|++|.|+     ++|+||+|+     ....+++|+|+++..    +.      .+..+.|++||.|.|+|++++. 
T Consensus        92 ~P~vGDvViG~Vt~V~~~~a~VdI~-----s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~-  165 (308)
T 2nn6_H           92 IGEVGDIVVGRITEVQQKRWKVETN-----SRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-  165 (308)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECS-----SSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEEC-----CCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCC-
Confidence            67999999998     899999997     357899999998752    22      2456789999999999999995 


Q ss_pred             CCeeEEEEec
Q 024995          120 KSRITLSIKQ  129 (259)
Q Consensus       120 ~~ri~lS~K~  129 (259)
                      .+++.||+|+
T Consensus       166 ~~~i~LStr~  175 (308)
T 2nn6_H          166 DGAVSLHTRS  175 (308)
T ss_dssp             TTEEEEECCS
T ss_pred             CCCEEEEecC
Confidence            7899999875

>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=97.63  E-value=4e-05  Score=63.00  Aligned_cols=73  Identities=5%  Similarity=-0.047  Sum_probs=47.5

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-Eccccccccccchhhh--hhcccCCCCCcceeeeccCCCee---
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQ--LWLSNAPPSGKKFTLLARAGRQV---  226 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~r~G~~V---  226 (259)
                      .|++++|+|+++++||    +|++|  .+ ++||+ +|++...- ..-+.-+  .|..  .  +.    +++.||.|   
T Consensus        83 ~Gev~~G~V~~v~~fG----~FV~l--~~-~dglvhis~l~~~~-~~d~~~~~~~~~~--~--~~----~~~~Gd~V~vk  146 (171)
T 1y14_B           83 KGEVVDGTVVSCSQHG----FEVQV--GP-MKVFVTKHLMPQDL-TFNAGSNPPSYQS--S--ED----VITIKSRIRVK  146 (171)
T ss_dssp             TTCEEEEEEEEEETTE----EEEEE--TT-EEEEEEGGGSCTTC-EECC-----CEEC--S--SC----EECTTCEEEEE
T ss_pred             CCCEEEEEEEEEecCE----EEEEe--cC-eEEEEEHHHCCCCc-eECcccCceEEec--c--ce----EECCCCEEEEE
Confidence            3778999999999999    99999  67 99999 67664210 0000111  1221  1  12    57999999   


Q ss_pred             -EEEecccc---hhhhhhch
Q 024995          227 -QEIQLSHS---LIRKASKR  242 (259)
Q Consensus       227 -~~v~~~~~---~i~ls~k~  242 (259)
                       +++|.+.+   +|. |||+
T Consensus       147 V~~vd~~~~~~~~ig-sm~~  165 (171)
T 1y14_B          147 IEGCISQVSSIHAIG-SIKE  165 (171)
T ss_dssp             EEEEEEETTEEEEEE-ECCS
T ss_pred             EEEEEcCCCCcEEEE-EcCC
Confidence             67887764   455 6654

>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=97.63  E-value=7.6e-06  Score=74.49  Aligned_cols=107  Identities=11%  Similarity=0.016  Sum_probs=68.3

Q ss_pred             hhcCCCCeEEEEEEEEeCCCCeeEEEEeccccCcchHhh-hhhcCCCCccccCCCCccccceeeeccCCCccceeeeecc
Q 024995          101 DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETL-EKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (259)
Q Consensus       101 ~~~~~Gd~V~vkVl~id~~~~ri~lS~K~~~~~p~~~~~-~~~~~~g~~~~~~~g~~v~G~V~~i~~~G~~~~~fv~l~~  179 (259)
                      ..+.+||.+.+.|...|. .+....+.|+....-+.+.. +..+.   ......|++++|+|.++.++|    +|+.|  
T Consensus        85 ~~~~vGd~ie~~I~~~df-gR~aa~~aKqvi~qkireaere~i~~---e~~~~~GeIV~G~V~ri~~~~----v~VDl--  154 (344)
T 1hh2_P           85 PLAEVGSIVKKELNVKNF-GRIAAQTAKQVLIQRIRELEKEKQFE---KYSELKGTVTTAEVIRVMGEW----ADIRI--  154 (344)
T ss_dssp             TTCCTTCEEEEECCCCCS-SSCSGGGHHHHHHHHHHHHTTCCSSC---CTTCCTTCEEEEEEEEECSSE----EEEEE--
T ss_pred             ccccCCCEEEEEEccccC-ccHHHHHHHHHHHHHHHHHHHHHHHH---HHhhcCCCEEEEEEEEEecCc----EEEEe--
Confidence            347899999999988876 33333444554322222110 11111   111236889999999999998    99888  


Q ss_pred             cCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEecccc--hhhhhhc
Q 024995          180 EDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSHS--LIRKASK  241 (259)
Q Consensus       180 ~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~~--~i~ls~k  241 (259)
                       ++++|+++ +++.                   +..    .+++||.|    ++|+.+++  .|.||.+
T Consensus       155 -Gk~EgiLp~sE~i-------------------p~E----~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt  199 (344)
T 1hh2_P          155 -GKLETRLPKKEWI-------------------PGE----EIKAGDLVKVYIIDVVKTTKGPKILVSRR  199 (344)
T ss_dssp             -TTEEEEEEGGGSC-------------------TTC----CCCTTCEEEEEEEEEEEETTEEEEEEESS
T ss_pred             -CCeEEEEeHHHcC-------------------CCc----CCCCCCEEEEEEEEEEcCCCCcEEEEEee
Confidence             49999994 5543                   222    34899999    67887665  4666655

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

Probab=97.58  E-value=4.8e-05  Score=63.08  Aligned_cols=64  Identities=5%  Similarity=-0.067  Sum_probs=48.8

Q ss_pred             CCccccceeeeccCCCccceeeeecccC----------CeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccC
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQED----------GIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARA  222 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~----------gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~  222 (259)
                      |+++.|+|++|.++|    +|++|  .+          +++|++ +|+++.+.             ..    +....+++
T Consensus        58 GdiV~G~V~~V~~~g----a~V~I--~~v~~~~~~~~~~~~Gll~isei~~~~-------------~~----~~~~~~~~  114 (179)
T 3m7n_A           58 GDVVLGRVVDLRNSI----ALIEV--SSKKGENRGPSNRGIGILHVSNVDEGY-------------VK----EISEAVGY  114 (179)
T ss_dssp             TCEEEEEEEEECSSE----EEEEE--EEETTCCSCCTTCEEEEEEGGGTTSSC-------------CS----SGGGTCCT
T ss_pred             CCEEEEEEEEEeCCc----EEEEE--ccccCcccccccCeeEEEEHHHcCcch-------------hh----CHhhcCCC
Confidence            666999999999999    99999  44          899999 67766321             11    24447799


Q ss_pred             CCeeE-EEecccchhhhhhch
Q 024995          223 GRQVQ-EIQLSHSLIRKASKR  242 (259)
Q Consensus       223 G~~V~-~v~~~~~~i~ls~k~  242 (259)
                      ||.|. +|..  ++++||+|.
T Consensus       115 GD~V~akVi~--~~i~LS~k~  133 (179)
T 3m7n_A          115 LDILKARVIG--DNLRLSTKE  133 (179)
T ss_dssp             TCEEEEEEEE--TTTEEECCS
T ss_pred             CCEEEEEEEC--CeEEEEEec
Confidence            99993 4433  889999997

>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=97.56  E-value=0.00011  Score=60.85  Aligned_cols=66  Identities=15%  Similarity=0.166  Sum_probs=56.1

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCc-cEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLY-HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~-gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      ..++||+|.|.     .++++|+|+     . ...|++|++++. ....+....|++||.|.|+|..++. ...+.||.
T Consensus         4 ~P~~gDvViG~V~~v~~~~~~VdI~-----~~~~~a~L~~s~~~-g~~k~~r~~l~~GDlV~ArV~~~~~-~~~~~Ltc   75 (175)
T 2ja9_A            4 IPSVNDFVIGVIIGTFSDSYKVSLQ-----NFSSSVSLSYMAFP-NASKKNRPTLQVGDLVYARVCTAEK-ELEAEIEC   75 (175)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESS-----TTSCCEEEETTSST-TCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEES
T ss_pred             cCCCcCEEEEEEEEEECcEEEEEEC-----CCCccEEEEHHHCC-chhhhhhccCCCCCEEEEEEEEecC-CCceEEEe
Confidence            56899999999     789999998     4 589999999986 3346677889999999999999986 57888884

>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=97.39  E-value=0.0005  Score=59.71  Aligned_cols=66  Identities=18%  Similarity=0.229  Sum_probs=52.4

Q ss_pred             CCCCCEEEEE--e-------eeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCC--CeeE
Q 024995           56 VNVEDIFVGR--D-------YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRIT  124 (259)
Q Consensus        56 l~~G~iv~G~--~-------~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~--~ri~  124 (259)
                      -++|++++|+  .       ..+||+++..+  .+.+|+||.+|+.      |.+.|++||.|+|.|++++...  .+|.
T Consensus         5 ~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~--~k~EgiLP~~Eqi------p~E~~~~GDrIkayV~~V~~~~~gpqIi   76 (251)
T 2asb_A            5 TREGEIVAGVIQRDSRANARGLVVVRIGTET--KASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLIT   76 (251)
T ss_dssp             CCTTCEEEEEEECCHHHHHTTCEEEEECSSS--SCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEE
T ss_pred             hcCCCEEEEEEEEccccccCCeEEEEeCCCC--cceEEEEcHHHcC------CCccCCCCCEEEEEEEEEEcCCCCCEEE
Confidence            4689999998  2       26999997100  0499999999985      4678999999999999999754  6899


Q ss_pred             EEEec
Q 024995          125 LSIKQ  129 (259)
Q Consensus       125 lS~K~  129 (259)
                      ||...
T Consensus        77 LSRt~   81 (251)
T 2asb_A           77 LSRTH   81 (251)
T ss_dssp             EESSC
T ss_pred             EEecc
Confidence            99754

>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=97.37  E-value=0.00013  Score=59.94  Aligned_cols=76  Identities=5%  Similarity=0.072  Sum_probs=48.7

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-Ecccccccc-ccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKR-VVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      .|++++|+|+++++||    +|++|   +.++||+ +|++...-+ ........|...  ...    ..++.||.|    
T Consensus        81 ~Gev~~G~V~~v~~fG----~fV~l---~~~~glvhis~l~~~~~~d~~~~~~~~~~~--~~~----~~~~~Gd~V~vkV  147 (172)
T 2c35_B           81 KGEVVDAVVTQVNKVG----LFTEI---GPMSCFISRHSIPSEMEFDPNSNPPCYKTM--DED----IVIQQDDEIRLKI  147 (172)
T ss_dssp             TTCEEEEEEEEEETTE----EEEEE---TTEEEEEEGGGSCTTEEEESSSSSCEEEET--TSC----SEEETTCEEEEEE
T ss_pred             CCCEEEEEEEEEeCCE----EEEEE---CCEEEEEEHHHCCCCcEECCCCCccEEEeC--CCC----EEECCCCEEEEEE
Confidence            3777999999999999    99999   4678999 666642100 000111123321  112    256999999    


Q ss_pred             EEEecccc---hhhhhhch
Q 024995          227 QEIQLSHS---LIRKASKR  242 (259)
Q Consensus       227 ~~v~~~~~---~i~ls~k~  242 (259)
                      .++|.+++   +|. |||+
T Consensus       148 ~~vd~~~~~~~~ig-sm~~  165 (172)
T 2c35_B          148 VGTRVDKNDIFAIG-SLMD  165 (172)
T ss_dssp             EEEEEETTEEEEEE-ECCS
T ss_pred             EEEEcCCCCcEEEE-EecC
Confidence            68888765   566 7775

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

Probab=97.16  E-value=0.00019  Score=59.08  Aligned_cols=72  Identities=8%  Similarity=0.093  Sum_probs=47.6

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-Eccccccccccch--hhhhhcccCCCCCcceeeeccCCCee----
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQ--DLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      |++++|+|+++++||    +|++|   +.++||+ +|++.. ....-+  +...|    ...+.    .++.||.|    
T Consensus        85 Gev~~G~V~~v~~fG----~FV~l---~~~~glVh~s~l~~-~~~~d~~~~~~~~----~~~~~----~~~~Gd~VrvkV  148 (172)
T 3h0g_G           85 GEVVDAIVTTVNKMG----FFANI---GPLNVFVSSHLVPP-DMKFDPTANPPNY----SGEDQ----VIEKGSNVRLKI  148 (172)
T ss_dssp             TCEEECCCCEEETTE----EECCB---TTBCCEEEGGGSCT-TCCCBSSSSSCBE----ESSSC----EECSSCCEEEEE
T ss_pred             CCEEEEEEEEEEcce----EEEEe---CCeEEEEEHHHCCC-ccccCcccccceE----ecCCc----EECCCCEEEEEE
Confidence            777999999999999    99998   4588999 666642 111111  01112    11222    56999999    


Q ss_pred             EEEecccc---hhhhhhch
Q 024995          227 QEIQLSHS---LIRKASKR  242 (259)
Q Consensus       227 ~~v~~~~~---~i~ls~k~  242 (259)
                      .+++.+++   +|. |||+
T Consensus       149 ~~vd~~~~~~~~Ig-tm~~  166 (172)
T 3h0g_G          149 VGTRTDATEIFAIA-TMKE  166 (172)
T ss_dssp             EEEEESSSCEEEEE-ECCS
T ss_pred             EEEECCCCCceEEE-EcCC
Confidence            68888874   466 6664

>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=97.14  E-value=0.00025  Score=61.90  Aligned_cols=70  Identities=7%  Similarity=-0.078  Sum_probs=50.7

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      .+|+++.|+|+++.++|    +||+|  ..+.+|++ +|+++..          |   .+.. .+....+++||.|    
T Consensus        73 ~~GDiV~G~V~~v~~~g----a~VdI--~~~~~GlL~isei~~~----------~---~~~~-~~~~~~l~vGD~V~arV  132 (251)
T 2je6_I           73 KINDIVIGLVEDVEIYG----WVVDI--KAPYKAYLPASNLLGR----------S---INVG-EDLRRYLDVGDYVIARI  132 (251)
T ss_dssp             CTTCEEEEEEEEECSSE----EEEEC--SSSSCEEEEHHHHHTS----------C---CCTT-CCCSSSCCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEeCce----EEEEc--CCCeEEEEEHHHhcCC----------c---cccc-cchhhcCCCCCEEEEEE
Confidence            35888999999999999    99988  67899999 6776521          1   1111 2344578999999    


Q ss_pred             EEEecccchhhhhhch
Q 024995          227 QEIQLSHSLIRKASKR  242 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~  242 (259)
                      +.++.+ .++.||+|+
T Consensus       133 i~v~~~-~~i~LS~r~  147 (251)
T 2je6_I          133 ENFDRS-IDPVLSVKG  147 (251)
T ss_dssp             EEEETT-EEEEEECCS
T ss_pred             EEECCC-CcEEEEEcc
Confidence            566644 478888875

>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=97.07  E-value=0.00031  Score=60.63  Aligned_cols=71  Identities=7%  Similarity=0.020  Sum_probs=49.9

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|+++.++|    +|++|  ..+.+|++ +|+++.. +            .+.........+++||.|    
T Consensus        65 ~~GDiV~G~V~~v~~~~----~~V~I--~~~~~g~l~isei~~~-~------------~~~~~~~~~~~l~~GD~V~a~V  125 (235)
T 2z0s_A           65 QAGDVVIGLIQSVGIMN----WFVDI--NSPYVAVLSVQDFLGR-P------------FNPAVDDMQSLLKVGDYIKAKV  125 (235)
T ss_dssp             CTTCCEEEEEEEECSSE----EEEEC--SSSSCEEEEHHHHHTS-C------------CCTTTTCCTTSSCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEeCCe----EEEEe--CCCeEEEEEHHHhCCC-c------------cccchhhHhhcCCCCCEEEEEE
Confidence            45888999999999999    99988  67899999 6776521 1            111112234467999999    


Q ss_pred             EEEecccchhhhhhch
Q 024995          227 QEIQLSHSLIRKASKR  242 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~  242 (259)
                      +.++.+ .++.||+|+
T Consensus       126 i~v~~~-~~i~LS~k~  140 (235)
T 2z0s_A          126 VAFDKT-RSPLLTVQG  140 (235)
T ss_dssp             EEECTT-SCEEEECCS
T ss_pred             EEECCC-CcEEEEEec
Confidence            455543 368888875

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

Probab=96.76  E-value=0.001  Score=57.21  Aligned_cols=68  Identities=9%  Similarity=-0.040  Sum_probs=48.5

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      .+|+++.|+|+.+.++|    +|++|  ....+|++ +|+++...         |.       .+....+++||.|    
T Consensus        56 ~~GDiV~G~V~~v~~~~----a~V~I--~~~~~g~l~isev~~~~---------~~-------~~~~~~l~~GD~V~arV  113 (229)
T 2ba0_A           56 SVGDVVIGIIREVAANG----WAVDI--YSPYQAFLPVSENPEMK---------PN-------KKPNEVLDIGDAIIAKV  113 (229)
T ss_dssp             CTTCEEEEEEEEECSSE----EEEEC--SSSSCEEEEGGGCTTCC---------TT-------SCGGGTCCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEeCCe----EEEEe--CCCeEEEEEHHHccccc---------cc-------cchhcccCCCCEEEEEE
Confidence            35888999999999999    99988  66799999 66665211         11       1233467999999    


Q ss_pred             EEEecccchhhhhhch
Q 024995          227 QEIQLSHSLIRKASKR  242 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~  242 (259)
                      +.++.+ .++.||+|+
T Consensus       114 i~v~~~-~~i~LS~r~  128 (229)
T 2ba0_A          114 LNIDPK-MKVTLTMKD  128 (229)
T ss_dssp             EEECTT-CCEEEECCS
T ss_pred             EEECCC-CcEEEEEcc
Confidence            455543 467777765

>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=96.44  E-value=0.0022  Score=62.93  Aligned_cols=74  Identities=9%  Similarity=0.035  Sum_probs=51.4

Q ss_pred             CCC--ccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcce----eeeccCCCe
Q 024995          153 SSS--MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKF----TLLARAGRQ  225 (259)
Q Consensus       153 ~g~--~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~r~G~~  225 (259)
                      +|+  .++|+|++|++||    +||+|. +.|++||+ +|++...+     +   |..... ....+    ...++.||.
T Consensus       558 vGe~~~f~g~V~~V~~~G----~fV~L~-~~gieGlVhis~l~~~~-----d---~~~~d~-~~~~l~~~~~~~~~lGD~  623 (644)
T 2id0_A          558 AGTDTRFAAEIVDISRGG----MRVRLV-DNGAIAFIPAPFLHAVR-----D---ELVCSQ-ENGTVQIKGETVYKVTDV  623 (644)
T ss_dssp             TTSCCCEEEEEEEEETTE----EEEEET-TTCCEEEEEGGGTCSCG-----G---GEEEET-TTTEEEETTEEEEETTCE
T ss_pred             cCCCceEEEEEEEEeCCc----eEEEEc-CCcEEEEEEchhccCcC-----c---eeEEcc-cccEEEecCCCEeCCCCE
Confidence            466  7999999999999    999983 36999999 67765210     1   321110 00101    225799999


Q ss_pred             e----EEEecccchhhhhh
Q 024995          226 V----QEIQLSHSLIRKAS  240 (259)
Q Consensus       226 V----~~v~~~~~~i~ls~  240 (259)
                      |    .+||.++++|.+++
T Consensus       624 V~VkV~~vd~~~~~I~~~l  642 (644)
T 2id0_A          624 IDVTIAEVRMETRSIIARP  642 (644)
T ss_dssp             EEEEEEEEETTTTEEEEEE
T ss_pred             EEEEEEEEeCCCCEEEEEE
Confidence            9    68999999998876

>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=95.70  E-value=0.0041  Score=62.17  Aligned_cols=74  Identities=8%  Similarity=-0.049  Sum_probs=42.6

Q ss_pred             CccccceeeeccCCCccceeeeecccC-CeeEEE-Ecccc--ccccccchhhhhhccc-----CCCCCcceeeeccCCCe
Q 024995          155 SMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR-ITRQG--FEKRVVSQDLQLWLSN-----APPSGKKFTLLARAGRQ  225 (259)
Q Consensus       155 ~~v~G~V~~i~~~G~~~~~fv~l~~~~-gv~gl~-~s~~~--~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~r~G~~  225 (259)
                      +.+.|+|.+|++||    +||+|  .+ |++||+ +|++.  .+.      + .|...     .....+.....++.||.
T Consensus       671 ~~~~g~V~~V~~~G----~fV~l--~~~giEGlVhis~L~~~~d~------~-~fd~~~~~l~g~~~~~~~~~~~~lGD~  737 (760)
T 2vnu_D          671 STETGYVIKVFNNG----IVVLV--PKFGVEGLIRLDNLTEDPNS------A-AFDEVEYKLTFVPTNSDKPRDVYVFDK  737 (760)
T ss_dssp             SEEEEEEEEEETTE----EEEEE--TTTTEEEEEEHHHHCSCGGG------C-EEETTTTEEEECCTTCSSCEEEETTCE
T ss_pred             eEEEEEEEEEECCe----EEEEE--eCCCcEEEEEeccccCCCce------e-EEcccccEEEEecCCCccCcEEecCCE
Confidence            56999999999999    99999  66 999999 67764  110      0 01100     00110001235699999


Q ss_pred             e----EEEecc---cchhhhhhc
Q 024995          226 V----QEIQLS---HSLIRKASK  241 (259)
Q Consensus       226 V----~~v~~~---~~~i~ls~k  241 (259)
                      |    ..+|.+   ++||+|+||
T Consensus       738 V~VkV~~vd~~~~~~~kI~lslk  760 (760)
T 2vnu_D          738 VEVQVRSVMDPITSKRKAELLLK  760 (760)
T ss_dssp             EEEEEC--------CCEEEC---
T ss_pred             EEEEEEEEECccccCCcEEEEeC
Confidence            9    467777   588999987

>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=95.57  E-value=0.01  Score=52.60  Aligned_cols=67  Identities=7%  Similarity=-0.043  Sum_probs=55.2

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEe
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K  128 (259)
                      ..++||+|.|+     ...+.|+|.     ....|++|.+++. ....+....|++||.|.|+|++++. .+.+.||..
T Consensus       124 iP~vGDiVIG~Vt~v~~~~~~VdI~-----s~~~a~L~~~~f~-Gatk~~r~~f~~GDlV~ArV~s~~~-~~~~eLsc~  195 (289)
T 2nn6_G          124 VPVKGDHVIGIVTAKSGDIFKVDVG-----GSEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVCI  195 (289)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECS-----SSSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCT-TSCCEEECS
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEEC-----CCceeEEehhhcC-cchhhhhhhcCCCCEEEEEEEEcCC-CCceEEEec
Confidence            57999999999     456899998     3678999999876 2345677889999999999999985 567888873

>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=95.43  E-value=0.017  Score=52.76  Aligned_cols=71  Identities=7%  Similarity=0.033  Sum_probs=52.1

Q ss_pred             CCCCccccceee----eccCCCccceeeeecccC---CeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCC
Q 024995          152 DSSSMSSSNSNT----IEPLPGLGAIFEELLQED---GIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAG  223 (259)
Q Consensus       152 ~~g~~v~G~V~~----i~~~G~~~~~fv~l~~~~---gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G  223 (259)
                      ..|++++|+|.+    +.+.+    +|+.|  ..   +++|++ .+++.                   |...|    ++|
T Consensus       129 r~GeIVtG~V~r~~~~v~~~~----v~VdL--G~~~~k~EgiLP~~Eqi-------------------P~E~~----~~G  179 (366)
T 1k0r_A          129 REGEIVAGVIQRDSRANARGL----VVVRI--GTETKASEGVIPAAEQV-------------------PGESY----EHG  179 (366)
T ss_dssp             CTTCEEEEEEECCHHHHHTTC----EEEEE--CCSSSCEEEEECGGGSC-------------------TTCCC----CTT
T ss_pred             cCCCEEEEEEEEccccccCCe----EEEEe--CCCccceEEEEcHHHcC-------------------CCccC----CCC
Confidence            468999999999    99888    99888  43   599999 55543                   22334    999


Q ss_pred             Cee----EEEecccchhhhhhchhhhhhhHHh
Q 024995          224 RQV----QEIQLSHSLIRKASKRHCNEYWNVF  251 (259)
Q Consensus       224 ~~V----~~v~~~~~~i~ls~k~~~~~p~~~~  251 (259)
                      |.|    ++|+.+.+...+.+.+..++....+
T Consensus       180 DrVkvyV~~V~~~~kgpqI~LSRT~p~lv~~L  211 (366)
T 1k0r_A          180 NRLRCYVVGVTRGAREPLITLSRTHPNLVRKL  211 (366)
T ss_dssp             CEEEEEEEEEECCSSSCEEEEESSCHHHHHHH
T ss_pred             CEEEEEEEEEecCCCccEEEEEeCChHHHHHH
Confidence            999    6888887776666666666655544

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

Probab=95.23  E-value=0.0076  Score=61.80  Aligned_cols=75  Identities=8%  Similarity=-0.048  Sum_probs=47.6

Q ss_pred             CCccccceeeeccCCCccceeeeecccC-CeeEEE-Ecccc--ccccccchhhhhhccc-----CCCCCcceeeeccCCC
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR-ITRQG--FEKRVVSQDLQLWLSN-----APPSGKKFTLLARAGR  224 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~-gv~gl~-~s~~~--~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~r~G~  224 (259)
                      |+.++|.|.+|++||    +||+|  .+ |++|++ +|++.  .+.      + .|...     .....+.....++.||
T Consensus       887 ge~~~g~V~~V~~~G----~fV~L--~~~giEGlVhis~L~~~~d~------y-~fde~~~~L~g~~~~g~~~~~~~lGD  953 (977)
T 2wp8_J          887 ESTETGYVIKVFNNG----IVVLV--PKFGVEGLIRLDNLTEDPNS------A-AFDEVEYKLTFVPTNSDKPRDVYVFD  953 (977)
T ss_dssp             TCEEEEEEEEECSSE----EEEEC--TTTCCEEEEEGGGTCSCGGG------C-EEETTTTEEEECCTTCCSCEEEETTC
T ss_pred             ceEEEEEEEEEcCCe----EEEEE--cCCCeEEEEEeccccCCCce------e-EEcccccEEEeecCCCccCcEEccCC
Confidence            667999999999999    99998  66 999999 67764  110      0 01100     0000000113569999


Q ss_pred             ee----EEEecc---cchhhhhhc
Q 024995          225 QV----QEIQLS---HSLIRKASK  241 (259)
Q Consensus       225 ~V----~~v~~~---~~~i~ls~k  241 (259)
                      .|    ..++.+   ++||+|+||
T Consensus       954 ~V~VkV~~vd~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          954 KVEVQVRSVMDPITSKRKAELLLK  977 (977)
T ss_dssp             EEEEEECCCCCSSSCCCCCCEEEC
T ss_pred             EEEEEEEEEcCcccCCCceEEEeC
Confidence            99    244543   268999987

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

Probab=95.21  E-value=0.026  Score=47.39  Aligned_cols=72  Identities=11%  Similarity=0.103  Sum_probs=44.4

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCC--CcceeeeccCCCee----
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPS--GKKFTLLARAGRQV----  226 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~r~G~~V----  226 (259)
                      |++++|+|+++++||    +|++|   +.++|++ ++++..+.-..-++-..|+-.-+.+  +.+-...++.||.|    
T Consensus        82 GEv~~G~Vs~vt~~G----ifV~l---g~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV  154 (203)
T 3ayh_B           82 GEVMLGKIKSCSEEG----IRVTI---SFFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQI  154 (203)
T ss_dssp             TCEEEEEEEEEETTE----EEEEC---SSCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEE
T ss_pred             CCEEEEEEEEEeccE----EEEEE---eCceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEE
Confidence            777999999999999    99998   4789998 6666543222222222333211000  01224467999999    


Q ss_pred             EEEecc
Q 024995          227 QEIQLS  232 (259)
Q Consensus       227 ~~v~~~  232 (259)
                      ..++..
T Consensus       155 ~~v~~~  160 (203)
T 3ayh_B          155 ESEDFV  160 (203)
T ss_dssp             EEEEEC
T ss_pred             EEEEcc
Confidence            455553

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

Probab=95.05  E-value=0.02  Score=48.74  Aligned_cols=72  Identities=11%  Similarity=0.057  Sum_probs=45.2

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |++++|+|+++++||    +|++|  ++.++|++ ++++..+.-..-++-..|+-..+ ++  -...++.||.|    ..
T Consensus        82 GEv~~G~Is~Vt~fG----ifVeL--~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~-e~--t~~~~~~Gd~VrvrV~~  152 (218)
T 2ckz_B           82 GEIVTGWISKCTAEG----IKVSL--LGIFDDIFIPQNMLFEGCYYTPEESAWIWPMD-EE--TKLYFDVNEKIRFRIER  152 (218)
T ss_dssp             TCEEEEEEEEEETTE----EEEEC--TTSCCCEEEETTTSCTTCEEETTTTEEEEECC-----CEEEECTTCEEEEEEEE
T ss_pred             CCEEEEEEEEEccCc----EEEEc--cCccceEEEcHHHCCCCcEEcCcCceEEeecc-cc--CCcEEcCCCEEEEEEEE
Confidence            778999999999999    99999  45689998 66665332111112122332110 11  13367999999    46


Q ss_pred             Eecccc
Q 024995          229 IQLSHS  234 (259)
Q Consensus       229 v~~~~~  234 (259)
                      ++...+
T Consensus       153 v~~~~~  158 (218)
T 2ckz_B          153 EVFVDV  158 (218)
T ss_dssp             EEECCC
T ss_pred             EEcccC
Confidence            666554

>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure initiative, northeast structural genomics consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5 b.40.4.16 PDB: 2r7f_A

Probab=94.93  E-value=0.036  Score=52.33  Aligned_cols=60  Identities=13%  Similarity=0.298  Sum_probs=48.4

Q ss_pred             CCCCCEEEEEeeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           56 VNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        56 l~~G~iv~G~~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      -..|+.+.    |+||++.      +.+|+||++++....  .....|++||.|+|+|.++|..+++|.+..
T Consensus       401 ~~~g~~f~----g~vv~l~------~~~glV~v~~l~~d~--~~~~~~~lGd~V~V~v~~vd~~~~~i~f~~  460 (469)
T 2r7d_A          401 AQPERVWD----AVVVDRR------GAQATLLIPDLAFDV--QVNTPAAPGTALQVQFADIDLPQMRVRARS  460 (469)
T ss_dssp             TCTTCCEE----EEEEEEE------TTEEEEEEGGGTEEE--EEECCCCTTCEEEEEEEEEETTTTEEEEEE
T ss_pred             hCCCCEEE----EEEEEEe------CcEEEEEECCCCeEE--ecCCcCCCCCEEEEEEEEEccCCCEEEEEE
Confidence            36788886    4688885      468999999998652  223569999999999999999999998865

>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=93.64  E-value=0.043  Score=52.40  Aligned_cols=58  Identities=14%  Similarity=0.174  Sum_probs=39.9

Q ss_pred             CCCccccceeeeccC--CCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCC--CCCcceeeeccCCCee
Q 024995          153 SSSMSSSNSNTIEPL--PGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAP--PSGKKFTLLARAGRQV  226 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~--G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~r~G~~V  226 (259)
                      +|.++.|+|++|.|+  |    +||++  .+|-.||+ .|+++.+.          .....  ....++..++++||.|
T Consensus        45 vGnIY~GkV~rv~p~~~a----AFVdi--G~gk~gfLhisei~~~~----------~~~~~~~~~~~~i~d~lk~Gq~V  107 (517)
T 2bx2_L           45 KANIYKGKITRIEPSLEA----AFVDY--GAERHGFLPLKEIAREY----------FPANYSAHGRPNIKDVLREGQEV  107 (517)
T ss_dssp             TTCEEEEEEEEEETTTTE----EEEES--SSSSCEEEEGGGSCGGG----------CC-------CCCGGGTCCTTCEE
T ss_pred             CCCEEEEEEEEeccCCce----EEEEe--CCCcEEEEEHHHcChhh----------hccccccccccchhhhccCCCEE
Confidence            477799999999998  7    99998  88999999 67765321          10000  0011345578999999

>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=93.41  E-value=0.032  Score=49.86  Aligned_cols=75  Identities=7%  Similarity=0.056  Sum_probs=46.4

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCC--CCcceeeeccCCCee--
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPP--SGKKFTLLARAGRQV--  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~r~G~~V--  226 (259)
                      .+|++|.|+|+++.+++    +|++|  .....|++ +|+++++.         .+.+...  +..+....|++||.|  
T Consensus        94 ~vGDvViG~Vt~V~~~~----a~VdI--~s~~~~~l~iS~v~f~g---------g~iR~~~~~D~~~m~~~l~vGDlV~A  158 (308)
T 2nn6_H           94 EVGDIVVGRITEVQQKR----WKVET--NSRLDSVLLLSSMNLPG---------GELRRRSAEDELAMRGFLQEGDLISA  158 (308)
T ss_dssp             CSSBCCCEEEEEEETTE----EEEEC--SSSSCEEEESSCCC----------------------CHHHHHHSCSSCEECC
T ss_pred             CCCCEEEEEEEEEeCce----EEEEE--CCCcCCceechhhcccc---------ceeecccchhhhhhhccCCCCCEEEE
Confidence            35888999999999999    99988  44567776 67765431         1111110  011233467999999  


Q ss_pred             --EEEecccchhhhhhch
Q 024995          227 --QEIQLSHSLIRKASKR  242 (259)
Q Consensus       227 --~~v~~~~~~i~ls~k~  242 (259)
                        +.++. ...+.||+|+
T Consensus       159 rVisv~~-~~~i~LStr~  175 (308)
T 2nn6_H          159 EVQAVFS-DGAVSLHTRS  175 (308)
T ss_dssp             EEEEEET-TTEEEEECCS
T ss_pred             EEEEcCC-CCCEEEEecC
Confidence              55552 3457777774

>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=89.33  E-value=0.37  Score=41.65  Aligned_cols=62  Identities=10%  Similarity=0.131  Sum_probs=43.2

Q ss_pred             CCCCccccceee----eccCCCccceeeeecccC---CeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCC
Q 024995          152 DSSSMSSSNSNT----IEPLPGLGAIFEELLQED---GIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAG  223 (259)
Q Consensus       152 ~~g~~v~G~V~~----i~~~G~~~~~fv~l~~~~---gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G  223 (259)
                      ..|++++|+|.+    +.+-.    +|+.|  ..   +++|++ .+++.                   +...|    ++|
T Consensus         6 r~GeIVtG~V~r~~~~v~~~~----ViVdl--G~~~~k~EgiLP~~Eqi-------------------p~E~~----~~G   56 (251)
T 2asb_A            6 REGEIVAGVIQRDSRANARGL----VVVRI--GTETKASEGVIPAAEQV-------------------PGESY----EHG   56 (251)
T ss_dssp             CTTCEEEEEEECCHHHHHTTC----EEEEE--CSSSSCEEEEECGGGSC-------------------TTCCC----CTT
T ss_pred             cCCCEEEEEEEEccccccCCe----EEEEe--CCCCcceEEEEcHHHcC-------------------CCccC----CCC
Confidence            358889999999    67655    89888  43   599999 44432                   22334    999


Q ss_pred             Cee----EEEecccc--hhhhhhch
Q 024995          224 RQV----QEIQLSHS--LIRKASKR  242 (259)
Q Consensus       224 ~~V----~~v~~~~~--~i~ls~k~  242 (259)
                      |.|    ++|+.+.+  +|-||...
T Consensus        57 DrIkayV~~V~~~~~gpqIiLSRt~   81 (251)
T 2asb_A           57 NRLRCYVVGVTRGAREPLITLSRTH   81 (251)
T ss_dssp             CEEEEEEEEEECCSSSCEEEEESSC
T ss_pred             CEEEEEEEEEEcCCCCCEEEEEecc
Confidence            999    57776653  46666543

>1jjg_A M156R; beta barrel, S1 motif, OB fold, MYXV156R, NESG project, structural genomics, EIF-2A homolog, PSI, protein structure initiative; NMR {Myxoma virus} SCOP: b.40.4.5

Probab=88.56  E-value=1  Score=32.84  Aligned_cols=62  Identities=13%  Similarity=0.136  Sum_probs=45.2

Q ss_pred             ccCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEEce-ecCcccccChhhhcCCCCeEEEEEEEEeC
Q 024995           53 SSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDR  118 (259)
Q Consensus        53 ~~~l~~G~iv~G~----~~G~fV~l~~~~g~~gi~glv~is-els~~~~~~~~~~~~~Gd~V~vkVl~id~  118 (259)
                      ..++-+|++.+|.    ++-++|.|.+++   |.+|++--. ++-.++..+..+.+ +|..|+++|+++|.
T Consensus        27 ~~~~~~g~VtkGiVy~kd~~fyV~L~dY~---glEaii~dYvnv~~dr~~klkkkL-VGKtIkVqVIRvD~   93 (102)
T 1jjg_A           27 AMDLSPGSVHEGIVYFKDGIFKVRLLGYE---GHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADG   93 (102)
T ss_dssp             CCCCCSSCEEEEEEEEETTEEEEECTTTS---SCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECS
T ss_pred             ccccCCCceEeeEEEEeCCEEEEEecCCC---CceeeeehhhhhhHHHHHHHHHHh-cCceEEEEEEEecc
Confidence            3478999999999    556789998744   688886421 22223455666666 79999999999986

---

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	259
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	4e-13
d1kl9a2	86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	1e-11
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	3e-11
d1e3pa2	62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	3e-11
d2ahob2	84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	1e-10
d1wi5a_	119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	8e-09
d1y14b1	91	b.40.4.5 (B:81-171) C-terminal domain of RNA polym	1e-08
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	3e-08
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	4e-08
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	6e-08
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	1e-07
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	2e-07
d2c35b1	94	b.40.4.5 (B:78-171) C-terminal domain of RNA polym	8e-06
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	8e-04
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	0.001
d2ix0a3	87	b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Esche	0.001
d2nn6i1	125	b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {H	0.002

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Length = 76

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]

 Score = 60.9 bits (148), Expect = 4e-13
 Identities = 27/81 (33%), Positives = 47/81 (58%), Gaps = 11/81 (13%)

Query: 54  SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 108
           + + V  ++ G+     D+GAF+ +          GLVH+S+++   ++ + D L  G E
Sbjct: 1   AEIEVGRVYTGKVTRIVDFGAFVAIG-----GGKEGLVHISQIADKRVEKVTDYLQMGQE 55

Query: 109 VRVKVIKIDREKSRITLSIKQ 129
           V VKV+++DR+  RI LSIK+
Sbjct: 56  VPVKVLEVDRQG-RIRLSIKE 75

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86

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]

 Score = 57.3 bits (138), Expect = 1e-11
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 8/78 (10%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
            VED+ +       + GA++ L   + +    G++ +SE+S   I+ I  ++  G    V
Sbjct: 12  EVEDVVMVNVRSIAEMGAYVSLLEYNNI---EGMILLSELSRRRIRSINKLIRIGRNECV 68

Query: 112 KVIKIDREKSRITLSIKQ 129
            VI++D+EK  I LS ++
Sbjct: 69  VVIRVDKEKGYIDLSKRR 86

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94

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]

 Score = 56.4 bits (136), Expect = 3e-11
 Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 10/84 (11%)

Query: 54  SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 108
             +    +  G      ++GAF+ +       H  GLVH+S +S   ++D  +++  GD 
Sbjct: 14  KDLKPGMVLEGVVTNVTNFGAFVDI-----GVHQDGLVHISALSEKFVKDPYEVVKAGDI 68

Query: 109 VRVKVIKIDREKSRITLSIKQLEE 132
           V+VKV+++D  ++R+ LS++  + 
Sbjct: 69  VKVKVMEVDIPRNRVGLSMRMSDT 92

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} Length = 62

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]

 Score = 55.1 bits (133), Expect = 3e-11
 Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 9/59 (15%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL----IQDIRDILNEGDEVRVKVIKIDREK 120
            +GAF+ L     L    GL+H+S++        ++++ D+L  G +V+V++ +ID   
Sbjct: 8   TFGAFVSL-----LPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRG 61

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

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]

 Score = 54.6 bits (131), Expect = 1e-10
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 8/78 (10%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
           +  +I +       DYG+++ L    GL      +  SEVS   +++IRD+L E  +V V
Sbjct: 10  SEGEILIATVKQVFDYGSYVSLDEYGGL---QAFLPWSEVSSKWVKNIRDVLKENRKVIV 66

Query: 112 KVIKIDREKSRITLSIKQ 129
           KVI++DR K  + +S+K+
Sbjct: 67  KVIRVDRRKGTVDVSLKK 84

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Length = 119

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]

 Score = 50.5 bits (120), Expect = 8e-09
 Identities = 11/82 (13%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRIT 124
           D+G  + +    G+      + + +    +  ++    L  G  +   V K+      ++
Sbjct: 34  DHGYLVDI----GVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVS 89

Query: 125 LSIKQLEEDPLLETLEKVIPQD 146
           LS+   E    + T ++    +
Sbjct: 90  LSVGHSEVSTAIATEQQSWNLN 111

>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 = 49.1 bits (117), Expect = 1e-08
 Identities = 14/80 (17%), Positives = 25/80 (31%), Gaps = 17/80 (21%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----------DIRDILNEGDEVRVKVIK 115
            +G  + +            V    +  DL               D++     +RVK+  
Sbjct: 16  QHGFEVQVGPMKVF------VTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEG 69

Query: 116 IDREKSRITLSIKQLEEDPL 135
              + S I   I  ++ED L
Sbjct: 70  CISQVSSIHA-IGSIKEDYL 88

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 83

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]

 Score = 47.7 bits (113), Expect = 3e-08
 Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 12/85 (14%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVR 110
           +V D+ +G        G  +     D        + VSE       +   ++L+ GD + 
Sbjct: 4   SVGDVVIGIIREVAANGWAV-----DIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAII 58

Query: 111 VKVIKIDREKSRITLSIKQLEEDPL 135
            KV+ ID +  ++TL++K     P+
Sbjct: 59  AKVLNIDPKM-KVTLTMKDRICRPI 82

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 88

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]

 Score = 47.6 bits (113), Expect = 4e-08
 Identities = 12/82 (14%), Positives = 30/82 (36%), Gaps = 15/82 (18%)

Query: 58  VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDE 108
             D+ +G          F+ +           ++ V +           D++ +L  GD 
Sbjct: 7   AGDVVIGLIQSVGIMNWFVDIN-----SPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDY 61

Query: 109 VRVKVIKIDREKSRITLSIKQL 130
           ++ KV+  D+ +    L+++  
Sbjct: 62  IKAKVVAFDKTR-SPLLTVQGE 82

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 106

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]

 Score = 47.7 bits (113), Expect = 6e-08
 Identities = 20/99 (20%), Positives = 45/99 (45%), Gaps = 15/99 (15%)

Query: 58  VEDIFVGR-----DYGAFIHLRFPDGLYHLTGL-----VHVSEVSWDLIQDIRDILNEGD 107
           + ++  G      ++G+F+ L   DGL H++ +      +  +    + ++   +L  GD
Sbjct: 3   MYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGD 62

Query: 108 EVRVKVIKIDREK-----SRITLSIKQLEEDPLLETLEK 141
            VR +++ I  +      S+I L+++Q     L    E+
Sbjct: 63  YVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIEEE 101

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 87

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]

 Score = 46.5 bits (110), Expect = 1e-07
 Identities = 17/82 (20%), Positives = 28/82 (34%), Gaps = 14/82 (17%)

Query: 57  NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDE 108
            + DI +G       YG  + ++           +  S +    I      R  L+ GD 
Sbjct: 6   KINDIVIGLVEDVEIYGWVVDIK-----APYKAYLPASNLLGRSINVGEDLRRYLDVGDY 60

Query: 109 VRVKVIKIDREKSRITLSIKQL 130
           V  ++   DR      LS+K  
Sbjct: 61  VIARIENFDRSI-DPVLSVKGK 81

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

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]

 Score = 45.7 bits (108), Expect = 2e-07
 Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 21/89 (23%)

Query: 58  VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----------LIQDIRDI 102
           V DI VGR          +          L  ++ +S ++                +R  
Sbjct: 8   VGDIVVGRITEVQQKRWKVET-----NSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGF 62

Query: 103 LNEGDEVRVKVIKIDREKSRITLSIKQLE 131
           L EGD +  +V  +  +   ++L  + L+
Sbjct: 63  LQEGDLISAEVQAVFSDG-AVSLHTRSLK 90

>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 = 41.4 bits (97), Expect = 8e-06
 Identities = 13/89 (14%), Positives = 28/89 (31%), Gaps = 12/89 (13%)

Query: 58  VEDIFVGR-----DYGAFIHLRFPDGLYHLTGL-----VHVSEVSWDLI-QDIRDILNEG 106
             ++           G F  +           +        +         D   ++ + 
Sbjct: 4   KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQD 63

Query: 107 DEVRVKVIKIDREKSRITLSIKQLEEDPL 135
           DE+R+K++    +K+ I   I  L +D L
Sbjct: 64  DEIRLKIVGTRVDKNDIFA-IGSLMDDYL 91

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]} Length = 90

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]

 Score = 35.6 bits (82), Expect = 8e-04
 Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 11/77 (14%)

Query: 57  NVEDIFVGRDYGAFIHLRFPDGLY-----HLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
           +V D  +G      I   F D          + +        +  +  R  L  GD V  
Sbjct: 6   SVNDFVIGV-----IIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYA 60

Query: 112 KVIKIDREKSRITLSIK 128
           +V   ++E     +   
Sbjct: 61  RVCTAEKE-LEAEIECF 76

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]} Length = 88

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]

 Score = 34.8 bits (80), Expect = 0.001
 Identities = 6/77 (7%), Positives = 19/77 (24%), Gaps = 12/77 (15%)

Query: 57  NVEDIFVGRDYGAFIHLRFPDGLY-----HLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 111
              D  +G      +  +  D             +          +  R  +  GD +  
Sbjct: 5   VKGDHVIGI-----VTAKSGDIFKVDVGGSEPASLSYLSFEGA-TKRNRPNVQVGDLIYG 58

Query: 112 KVIKIDREKSRITLSIK 128
           + +  +++     +   
Sbjct: 59  QFVVANKDM-EPEMVCI 74

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Length = 87

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]

 Score = 34.8 bits (80), Expect = 0.001
 Identities = 6/72 (8%), Positives = 15/72 (20%), Gaps = 16/72 (22%)

Query: 66  DYGAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKV 113
             G  + L            +    +               +      +    D + V +
Sbjct: 16  RGGMRVRLVD----NGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTI 71

Query: 114 IKIDREKSRITL 125
            ++  E   I  
Sbjct: 72  AEVRMETRSIIA 83

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Length = 125

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]

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 2/51 (3%)

Query: 81  HLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 129
              G +   +V        +I      GD V  KVI +   +S   L+  +
Sbjct: 38  SFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAE 88

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	259
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.69
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.66
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.65
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.63
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.56
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.51
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.42
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.4
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.38
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.18
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.15
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.11
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.09
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	99.07
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.06
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.04
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.01
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.9
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	98.86
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.76
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	98.68
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	98.66
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	98.64
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	98.59
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.57
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.3
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	97.93
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	97.87
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	97.84
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.81
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	97.44
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.34
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	97.23
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	96.22
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	95.52
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	95.37
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	94.61
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	94.56
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	92.82
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	92.53
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	89.7
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	86.79
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	83.6
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	83.34
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	82.12

>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=99.69  E-value=6.5e-18  Score=120.66  Aligned_cols=70  Identities=39%  Similarity=0.715  Sum_probs=66.0

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      ++++|+++.|+     +||+||+|+     .+++||||+++++|.++.+|++.|++||+|+|+|+++|+ ++||.||+|+
T Consensus         2 d~kvG~iv~G~V~~v~~~G~fV~l~-----~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~-~~ri~LS~k~   75 (76)
T d1sroa_           2 EIEVGRVYTGKVTRIVDFGAFVAIG-----GGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIKE   75 (76)
T ss_dssp             CCCTTSEEEEEEEEEETTEEEEECS-----SSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCT-TCCCEEEECC
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEeC-----CCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECC-CCCEEEEEEc
Confidence            68999999999     999999998     489999999999999999999999999999999999996 6899999997


Q ss_pred             c
Q 024995          130 L  130 (259)
Q Consensus       130 ~  130 (259)
                      +
T Consensus        76 a   76 (76)
T d1sroa_          76 A   76 (76)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.66  E-value=1.2e-16  Score=116.51  Aligned_cols=70  Identities=31%  Similarity=0.507  Sum_probs=53.5

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      ++|+++.|+     +||+||+|...   .|++||||+++++|.+..++.+.|++||.|+|+|+++|++++||.||+|+
T Consensus        12 ~~G~iv~G~V~~i~~~G~fV~l~~~---~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~ki~LS~Kq   86 (86)
T d1kl9a2          12 EVEDVVMVNVRSIAEMGAYVSLLEY---NNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTT---TTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCEEEEEEEEEeCCeEEEEEecC---CCEEEEEEeeeccccccccceEEeecccEEEEEEEEEECCCCEEEEEeeC
Confidence            689999999     99999999631   27999999999999999999999999999999999999999999999985

>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=99.65  E-value=1.1e-16  Score=118.73  Aligned_cols=76  Identities=30%  Similarity=0.603  Sum_probs=71.7

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEE
Q 024995           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~  127 (259)
                      ++++++|+++.|+     ++|+||+|+     .+++||||.++++|.+..++++.|++||.|+|+|+++|+++++|.||+
T Consensus        13 ~~~~k~G~iv~g~V~~v~~~G~~V~l~-----~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~~i~LS~   87 (94)
T d3bzka4          13 LKDLKPGMVLEGVVTNVTNFGAFVDIG-----VHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSM   87 (94)
T ss_dssp             GGGCCTTCEEEEEEEEEETTEEEEECS-----SSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEES
T ss_pred             HhcCCCCCEEEEEEEEEECcEEEEEeC-----CCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEE
Confidence            5789999999999     899999998     489999999999999999999999999999999999999999999999


Q ss_pred             eccccCc
Q 024995          128 KQLEEDP  134 (259)
Q Consensus       128 K~~~~~p  134 (259)
                      |+. ++|
T Consensus        88 K~~-e~P   93 (94)
T d3bzka4          88 RMS-DTP   93 (94)
T ss_dssp             CTT-CCC
T ss_pred             ecc-CCC
Confidence            975 666

>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=99.63  E-value=1.6e-16  Score=115.31  Aligned_cols=72  Identities=35%  Similarity=0.575  Sum_probs=61.2

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      ..++|+++.|+     +||+||+|+.++   |++||||.++++|.+..++.+.|++||.|+|+|+++|+++++|.||+|+
T Consensus         8 ~p~~G~iv~G~V~~v~~~G~fV~l~~~~---gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2           8 LPSEGEILIATVKQVFDYGSYVSLDEYG---GLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             SCCTTCCCEEEEEEEETTEEEEEETTTT---TEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCcC---CEEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEEcC
Confidence            35689999999     999999996311   7999999999999999999999999999999999999999999999985

>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=99.56  E-value=2.8e-15  Score=113.35  Aligned_cols=80  Identities=29%  Similarity=0.512  Sum_probs=68.9

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc-----------cChhhhcCCCCeEEEEEEEEeCC
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDRE  119 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~-----------~~~~~~~~~Gd~V~vkVl~id~~  119 (259)
                      .+.|++++|+     +||+||+|+      +++||||+++|+++++           .++.+.|++||.|+|+|+++|.+
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~------~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~   74 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLG------PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLK   74 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS------SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECC
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEee------CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchh
Confidence            3689999999     999999996      7999999999999876           37778999999999999999988


Q ss_pred             CCe-----eEEEEeccccCcchHhhhh
Q 024995          120 KSR-----ITLSIKQLEEDPLLETLEK  141 (259)
Q Consensus       120 ~~r-----i~lS~K~~~~~p~~~~~~~  141 (259)
                      +++     +.||+|+...+||....++
T Consensus        75 ~~~~~~~~i~ls~K~~~~~~~e~~~~~  101 (106)
T d1go3e1          75 AERKRGSKIALTMRQPYLGKLEWIEEE  101 (106)
T ss_dssp             C-----CEEEEECCSTTCEEHHHHHHH
T ss_pred             hccccCceeecccccCCCCcchhhhhH
Confidence            776     7899999999999765443

>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=99.51  E-value=1.3e-14  Score=104.73  Aligned_cols=73  Identities=26%  Similarity=0.351  Sum_probs=65.7

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc-ccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~-~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      .++|+++.|+     ++|+||+++     .+++||||+++++|.. ..++.+.|++||.|.|+|+++|+ +++|.||+|+
T Consensus         3 Pk~Gd~V~G~V~~v~~~g~~V~i~-----~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~LS~k~   76 (83)
T d2ba0a1           3 PSVGDVVIGIIREVAANGWAVDIY-----SPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMKD   76 (83)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECS-----SSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECCS
T ss_pred             CCCCCEEEEEEEEEECCEEEEecC-----CCeeEEEecccccccccccChhhhcccccEEEEEEEEECC-CCCEEEEecC
Confidence            5889999999     899999998     4899999999999875 67899999999999999999996 6899999998


Q ss_pred             cccCc
Q 024995          130 LEEDP  134 (259)
Q Consensus       130 ~~~~p  134 (259)
                      ....|
T Consensus        77 ~~~~k   81 (83)
T d2ba0a1          77 RICRP   81 (83)
T ss_dssp             SSCEE
T ss_pred             CCCCC
Confidence            76544

>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=99.42  E-value=6.8e-14  Score=107.73  Aligned_cols=78  Identities=13%  Similarity=0.175  Sum_probs=69.4

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccc-ccChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        53 ~~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~-~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      ...+++|+++.|+     ++|+||+|+.    .+++||||++++++.+ ..+|.+.|++||.|+|+|+++|++++++.||
T Consensus        16 ~~~l~~G~iv~G~V~~i~~~G~~V~lg~----~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS   91 (119)
T d1wi5a_          16 AEALKPGMLLTGTVSSLEDHGYLVDIGV----DGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS   91 (119)
T ss_dssp             TTTCCTTCEEEEEEEEECSSEEEEECCC----SSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEE
T ss_pred             HhhcCCCCEEEEEEEEEeccEEEEEEec----cccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEE
Confidence            4579999999999     9999999951    3799999999999874 7789899999999999999999999999999


Q ss_pred             EeccccCc
Q 024995          127 IKQLEEDP  134 (259)
Q Consensus       127 ~K~~~~~p  134 (259)
                      +|+.....
T Consensus        92 ~k~~~~~~   99 (119)
T d1wi5a_          92 VGHSEVST   99 (119)
T ss_dssp             CCCCCSCC
T ss_pred             ecHHHhhh
Confidence            99876543

>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=99.40  E-value=1.1e-13  Score=100.66  Aligned_cols=70  Identities=26%  Similarity=0.373  Sum_probs=62.6

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc---cChhhhcCCCCeEEEEEEEEeCCCCeeEEE
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI---QDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~---~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS  126 (259)
                      ..++|+++.|+     +||+||+++     .+++||||+++++|.++   .++.+.|++||.|.|+|+++|+ .+++.||
T Consensus         4 ~Pk~Gdiv~G~V~~i~~~g~fV~i~-----~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~-~~~i~LS   77 (87)
T d2je6i1           4 YPKINDIVIGLVEDVEIYGWVVDIK-----APYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVLS   77 (87)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS-----SSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEEE
T ss_pred             cCCCCCEEEEEEEEEECCEEEEEeC-----CCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECC-CCCEEEE
Confidence            46889999999     999999998     48999999999999865   4677899999999999999996 6899999


Q ss_pred             Eecc
Q 024995          127 IKQL  130 (259)
Q Consensus       127 ~K~~  130 (259)
                      +|+.
T Consensus        78 ~k~~   81 (87)
T d2je6i1          78 VKGK   81 (87)
T ss_dssp             CCST
T ss_pred             EecC
Confidence            9864

>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=99.38  E-value=1.5e-13  Score=100.08  Aligned_cols=70  Identities=17%  Similarity=0.323  Sum_probs=62.6

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc----ChhhhcCCCCeEEEEEEEEeCCCCeeEE
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----DIRDILNEGDEVRVKVIKIDREKSRITL  125 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~----~~~~~~~~Gd~V~vkVl~id~~~~ri~l  125 (259)
                      ..++|+++.|+     ++|+||+|+     .+.+||||.+++++.+..    ++++.|++||.|.|+|+++|+ .+++.|
T Consensus         4 ~Pk~GdvV~G~V~~v~~~g~fV~i~-----~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~L   77 (88)
T d2z0sa1           4 VPQAGDVVIGLIQSVGIMNWFVDIN-----SPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPLL   77 (88)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECS-----SSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEEE
T ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC-----CCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECC-CCCEEE
Confidence            46899999999     899999998     489999999999998754    677889999999999999996 689999


Q ss_pred             EEecc
Q 024995          126 SIKQL  130 (259)
Q Consensus       126 S~K~~  130 (259)
                      |+|+.
T Consensus        78 s~k~~   82 (88)
T d2z0sa1          78 TVQGE   82 (88)
T ss_dssp             ECCSS
T ss_pred             EEecC
Confidence            99864

>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=99.18  E-value=2.2e-13  Score=92.98  Aligned_cols=50  Identities=30%  Similarity=0.588  Sum_probs=29.2

Q ss_pred             eeeEEEEEccCCCCccEEEEEEceecCcc----cccChhhhcCCCCeEEEEEEEEeCCC
Q 024995           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQDIRDILNEGDEVRVKVIKIDREK  120 (259)
Q Consensus        66 ~~G~fV~l~~~~g~~gi~glv~isels~~----~~~~~~~~~~~Gd~V~vkVl~id~~~  120 (259)
                      +|||||+|.     .|++||||+|+||+.    ++.+|++.|++||+|+|+|+++|+++
T Consensus         8 ~fG~FV~l~-----~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           8 TFGAFVSLL-----PGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             -CSCEECCC--------CCCCC-------------------CCSSCBCCCCCCCCCSSC
T ss_pred             eceEEEEec-----CCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCCC
Confidence            999999998     489999999999864    67899999999999999999999743

>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=99.15  E-value=1e-11  Score=89.77  Aligned_cols=69  Identities=17%  Similarity=0.283  Sum_probs=51.5

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      +|+++.|+|+++++||    +|++|...+|++||+ .|+++++.             ..++..    .+++||.|    +
T Consensus        13 ~G~iv~G~V~~i~~~G----~fV~l~~~~~i~G~i~~sels~~~-------------~~~~~~----~~~~Gd~v~~kV~   71 (86)
T d1kl9a2          13 VEDVVMVNVRSIAEMG----AYVSLLEYNNIEGMILLSELSRRR-------------IRSINK----LIRIGRNECVVVI   71 (86)
T ss_dssp             TTCEEEEEEEEECSSE----EEEEETTTTTEEEEEEGGGC-----------------------------CTTCEEEEEEE
T ss_pred             CCCEEEEEEEEEeCCe----EEEEEecCCCEEEEEEeeeccccc-------------cccceE----EeecccEEEEEEE
Confidence            4777999999999999    999995557999999 67776331             222333    56999999    7


Q ss_pred             EEecccchhhhhhch
Q 024995          228 EIQLSHSLIRKASKR  242 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~  242 (259)
                      ++|+++++|+||+||
T Consensus        72 ~vd~~~~ki~LS~Kq   86 (86)
T d1kl9a2          72 RVDKEKGYIDLSKRR   86 (86)
T ss_dssp             EEETTTTEEEEESTT
T ss_pred             EEECCCCEEEEEeeC
Confidence            999999999999997

>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=99.11  E-value=1.5e-11  Score=90.72  Aligned_cols=70  Identities=23%  Similarity=0.287  Sum_probs=59.1

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcc----------cccChhhhcCCCCeEEEEEEEEeCC
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----------LIQDIRDILNEGDEVRVKVIKIDRE  119 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~----------~~~~~~~~~~~Gd~V~vkVl~id~~  119 (259)
                      ..++|+++.|+     ++|+||+|+     .+.+|+||+|+++|.          +..++++.|++||.|.|+|+++|. 
T Consensus         5 ~P~vGdiV~G~V~~v~~~g~~V~I~-----~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~-   78 (95)
T d2nn6h1           5 IGEVGDIVVGRITEVQQKRWKVETN-----SRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-   78 (95)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECS-----SSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-
T ss_pred             cCCCCCEEEEEEEEEecCcEEEEeC-----CCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECC-
Confidence            35789999998     899999998     478999999999763          344678889999999999999997 


Q ss_pred             CCeeEEEEecc
Q 024995          120 KSRITLSIKQL  130 (259)
Q Consensus       120 ~~ri~lS~K~~  130 (259)
                      .+++.||+|..
T Consensus        79 dg~i~Ls~r~~   89 (95)
T d2nn6h1          79 DGAVSLHTRSL   89 (95)
T ss_dssp             TTEEEEECCSS
T ss_pred             CCCEEEEeccc
Confidence            69999998864

>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=99.09  E-value=1.7e-11  Score=88.20  Aligned_cols=69  Identities=7%  Similarity=0.060  Sum_probs=54.4

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      +|++++|+|+++++||    +|++|...+|++||+ .|+++++.             ..++    ...+++||.|    +
T Consensus        11 ~G~iv~G~V~~v~~~G----~fV~l~~~~gi~Gli~~sels~~~-------------~~~~----~~~~~~G~~v~~kV~   69 (84)
T d2ahob2          11 EGEILIATVKQVFDYG----SYVSLDEYGGLQAFLPWSEVSSKW-------------VKNI----RDVLKENRKVIVKVI   69 (84)
T ss_dssp             TTCCCEEEEEEEETTE----EEEEETTTTTEEEEECGGGCC------------------CH----HHHTCSSCEEECEEE
T ss_pred             CCCEEEEEEEEEECCE----EEEEECCcCCEEEEEEcccccccc-------------cccc----ceEeecccEEEEEEE
Confidence            5888999999999999    999995447999999 67777431             1222    2356999999    7


Q ss_pred             EEecccchhhhhhch
Q 024995          228 EIQLSHSLIRKASKR  242 (259)
Q Consensus       228 ~v~~~~~~i~ls~k~  242 (259)
                      ++|.++++|.||+||
T Consensus        70 ~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2          70 RVDRRKGTVDVSLKK   84 (84)
T ss_dssp             EEETTTTEEEEESSS
T ss_pred             EEECCCCEEEEEEcC
Confidence            999999999999996

>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=99.07  E-value=1.5e-10  Score=83.77  Aligned_cols=64  Identities=11%  Similarity=0.062  Sum_probs=53.1

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCccccc------------ChhhhcCCCCeEEEEEEEEeCCCC
Q 024995           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ------------DIRDILNEGDEVRVKVIKIDREKS  121 (259)
Q Consensus        59 G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~------------~~~~~~~~Gd~V~vkVl~id~~~~  121 (259)
                      ++.++|.     +||+||+|..    .+++||||+|+|++++..            +..+.|++||+|+|+|+++|++++
T Consensus         4 ~~~F~g~Is~v~~~GifV~L~e----~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r   79 (87)
T d2ix0a3           4 DTRFAAEIVDISRGGMRVRLVD----NGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETR   79 (87)
T ss_dssp             CCCEEEEEEEEETTEEEEEETT----TCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTT
T ss_pred             CCEEEEEEEEEEcCeEEEEEec----CCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccC
Confidence            5666666     9999999963    589999999999987532            234569999999999999999999


Q ss_pred             eeEEE
Q 024995          122 RITLS  126 (259)
Q Consensus       122 ri~lS  126 (259)
                      +|.+.
T Consensus        80 ~I~~~   84 (87)
T d2ix0a3          80 SIIAR   84 (87)
T ss_dssp             EEEEE
T ss_pred             eEEEE
Confidence            99764

>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=99.06  E-value=7.7e-12  Score=88.46  Aligned_cols=69  Identities=16%  Similarity=0.216  Sum_probs=54.9

Q ss_pred             cCCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995          151 SDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---  226 (259)
Q Consensus       151 ~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---  226 (259)
                      .++|++++|+|.++++||    +|++|  .+|++||+ .|++++..             ..+    ....+++||.|   
T Consensus         3 ~kvG~iv~G~V~~v~~~G----~fV~l--~~~~~Glv~~sels~~~-------------~~~----~~~~~~~G~~v~v~   59 (76)
T d1sroa_           3 IEVGRVYTGKVTRIVDFG----AFVAI--GGGKEGLVHISQIADKR-------------VEK----VTDYLQMGQEVPVK   59 (76)
T ss_dssp             CCTTSEEEEEEEEEETTE----EEEEC--SSSCCCBCCTTSSCSSC-------------CSC----HHHHCCTTCEEEEE
T ss_pred             CCCCCEEEEEEEEEeCcE----EEEEe--CCCCEEEEEhHHhCccc-------------cCC----HHHccCCCCEEEEE
Confidence            357888999999999999    99988  78999999 77877431             122    33366999999   


Q ss_pred             -EEEecccchhhhhhchh
Q 024995          227 -QEIQLSHSLIRKASKRH  243 (259)
Q Consensus       227 -~~v~~~~~~i~ls~k~~  243 (259)
                       +++|. ++||+||||++
T Consensus        60 Vi~id~-~~ri~LS~k~a   76 (76)
T d1sroa_          60 VLEVDR-QGRIRLSIKEA   76 (76)
T ss_dssp             EEECCT-TCCCEEEECCC
T ss_pred             EEEECC-CCCEEEEEEcC
Confidence             68885 46899999984

>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=99.04  E-value=6.2e-11  Score=88.99  Aligned_cols=91  Identities=12%  Similarity=0.093  Sum_probs=64.5

Q ss_pred             CCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       153 ~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      .|++++|+|++|.+||    +||+|   ++++||+ .|+++++.-....+-..+.  ...+..    .+++||.|    +
T Consensus         3 ~gei~~g~V~~v~~~G----~FVel---~~ieGlv~~s~l~~~~~~~~~~~~~~~--~~~~~~----~~~~Gd~v~vkV~   69 (106)
T d1go3e1           3 MYELIEGEVVDVVEFG----SFVRL---GPLDGLIHVSQIMDDYVSYDPKREAII--GKETGK----VLEIGDYVRARIV   69 (106)
T ss_dssp             TTCEEEEEEEEEETTE----EEEEC---SSSEEEEEGGGSCSSCEEECCC--CEE--ETTTCC----EECTTCEEEEEEE
T ss_pred             CCCEEEEEEEEEeeeE----EEEEe---eCeEEEEEeecccCceeeeccceeEEe--eccccc----ceeecceEEEEEE
Confidence            5888999999999999    99998   4799999 6777643200000000001  012333    56999999    7


Q ss_pred             EEecccch-----hhhhhchhhhhhhHHhhhhcc
Q 024995          228 EIQLSHSL-----IRKASKRHCNEYWNVFHETAI  256 (259)
Q Consensus       228 ~v~~~~~~-----i~ls~k~~~~~p~~~~~~~~~  256 (259)
                      +||.++++     |.||+|+...+||+.+.++++
T Consensus        70 ~vd~~~~~~~~~~i~ls~K~~~~~~~e~~~~~~~  103 (106)
T d1go3e1          70 AISLKAERKRGSKIALTMRQPYLGKLEWIEEEKA  103 (106)
T ss_dssp             EEECCC-----CEEEEECCSTTCEEHHHHHHHHH
T ss_pred             EEchhhccccCceeecccccCCCCcchhhhhHhh
Confidence            89998876     789999999999999988764

>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=99.01  E-value=5.3e-11  Score=87.41  Aligned_cols=73  Identities=10%  Similarity=0.119  Sum_probs=59.0

Q ss_pred             cCCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995          151 SDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---  226 (259)
Q Consensus       151 ~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---  226 (259)
                      .++|+++.|+|.++.++|    +|+.|  .+|++||+ .++++++          |+   ..    ....+++||.|   
T Consensus        16 ~k~G~iv~g~V~~v~~~G----~~V~l--~~~i~G~i~~~~ls~~----------~~---~~----~~~~~~vGq~v~~~   72 (94)
T d3bzka4          16 LKPGMVLEGVVTNVTNFG----AFVDI--GVHQDGLVHISALSEK----------FV---KD----PYEVVKAGDIVKVK   72 (94)
T ss_dssp             CCTTCEEEEEEEEEETTE----EEEEC--SSSSCEEEEGGGGCSS----------CC---SC----HHHHCCTTCEEEEE
T ss_pred             CCCCCEEEEEEEEEECcE----EEEEe--CCCceEEeehhhhhcc----------cc---cC----hhhhhccCcEEEEE
Confidence            356888999999999999    99998  88999999 5676633          11   22    23356999999   


Q ss_pred             -EEEecccchhhhhhchhhhhh
Q 024995          227 -QEIQLSHSLIRKASKRHCNEY  247 (259)
Q Consensus       227 -~~v~~~~~~i~ls~k~~~~~p  247 (259)
                       +++|.++++|.||||+. ++|
T Consensus        73 V~~id~~~~~i~LS~K~~-e~P   93 (94)
T d3bzka4          73 VMEVDIPRNRVGLSMRMS-DTP   93 (94)
T ss_dssp             EEEEETTTTEEEEESCTT-CCC
T ss_pred             EEEEECCCCEEEEEEecc-CCC
Confidence             79999999999999984 676

>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=98.90  E-value=2.1e-09  Score=78.06  Aligned_cols=63  Identities=19%  Similarity=0.200  Sum_probs=54.3

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc----------cChhhhcCCCCeEEEEEEEEeCCCC
Q 024995           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----------QDIRDILNEGDEVRVKVIKIDREKS  121 (259)
Q Consensus        57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~----------~~~~~~~~~Gd~V~vkVl~id~~~~  121 (259)
                      -.|++++|+     +||+||+++      .++||+|+++|++++.          .+..+.|+.||.|++||+++|.+.+
T Consensus         2 f~Gev~~g~I~~v~~~G~fv~lg------~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~   75 (91)
T d1y14b1           2 FKGEVVDGTVVSCSQHGFEVQVG------PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVS   75 (91)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEET------TEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETT
T ss_pred             CCCCEEEEEEEEEEeeEEEEEEc------CeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccC
Confidence            368999998     899999997      6899999999988754          3445579999999999999999999


Q ss_pred             eeEE
Q 024995          122 RITL  125 (259)
Q Consensus       122 ri~l  125 (259)
                      +|..
T Consensus        76 ~i~~   79 (91)
T d1y14b1          76 SIHA   79 (91)
T ss_dssp             EEEE
T ss_pred             ccEE
Confidence            9865

>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=98.86  E-value=4.6e-10  Score=80.24  Aligned_cols=74  Identities=4%  Similarity=-0.063  Sum_probs=57.0

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|.+++++|    +|++|  .+++.||+ .|+++++            ....++    ...+++||.|    
T Consensus         4 k~Gd~V~G~V~~v~~~g----~~V~i--~~~~~g~l~~se~s~~------------~~~~~~----~~~~~vGd~V~~kV   61 (83)
T d2ba0a1           4 SVGDVVIGIIREVAANG----WAVDI--YSPYQAFLPVSENPEM------------KPNKKP----NEVLDIGDAIIAKV   61 (83)
T ss_dssp             CTTCEEEEEEEEECSSE----EEEEC--SSSSCEEEEGGGCTTC------------CTTSCG----GGTCCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEECCE----EEEec--CCCeeEEEeccccccc------------ccccCh----hhhcccccEEEEEE
Confidence            56899999999999999    99988  88999999 5777632            212222    2356999999    


Q ss_pred             EEEecccchhhhhhchhhhhhh
Q 024995          227 QEIQLSHSLIRKASKRHCNEYW  248 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~~~~p~  248 (259)
                      +++|. +++|.||||+....|+
T Consensus        62 ~~vd~-~~~i~LS~k~~~~~k~   82 (83)
T d2ba0a1          62 LNIDP-KMKVTLTMKDRICRPI   82 (83)
T ss_dssp             EEECT-TCCEEEECCSSSCEEE
T ss_pred             EEECC-CCCEEEEecCCCCCCC
Confidence            68875 5689999998765553

>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=98.76  E-value=8.5e-09  Score=75.23  Aligned_cols=63  Identities=14%  Similarity=0.277  Sum_probs=53.8

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccc------------cChhhhcCCCCeEEEEEEEEeCC
Q 024995           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI------------QDIRDILNEGDEVRVKVIKIDRE  119 (259)
Q Consensus        57 ~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~------------~~~~~~~~~Gd~V~vkVl~id~~  119 (259)
                      -.|++++|+     ++|+||+++      .++||+|+++|++++.            .+....|+.||.|++||+++|.+
T Consensus         3 f~Gev~~g~V~~v~~~G~fv~lg------~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~   76 (94)
T d2c35b1           3 FKGEVVDAVVTQVNKVGLFTEIG------PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVD   76 (94)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEET------TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEE
T ss_pred             CCCCEEEEEEEEEEeeEEEEEec------CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecC
Confidence            468999998     899999997      5899999999998752            23345699999999999999999


Q ss_pred             CCeeEE
Q 024995          120 KSRITL  125 (259)
Q Consensus       120 ~~ri~l  125 (259)
                      .++|..
T Consensus        77 ~~~I~~   82 (94)
T d2c35b1          77 KNDIFA   82 (94)
T ss_dssp             TTEEEE
T ss_pred             cCcceE
Confidence            999864

>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=98.68  E-value=5e-09  Score=75.41  Aligned_cols=71  Identities=7%  Similarity=-0.048  Sum_probs=53.9

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|+++++||    +|++|  .++++||+ .|+++++.          ......    ....+++||.|    
T Consensus         6 k~Gdiv~G~V~~i~~~g----~fV~i--~~~~~gll~~s~~~~~~----------~~~~~~----~~~~~~~Gd~v~~kV   65 (87)
T d2je6i1           6 KINDIVIGLVEDVEIYG----WVVDI--KAPYKAYLPASNLLGRS----------INVGED----LRRYLDVGDYVIARI   65 (87)
T ss_dssp             CTTCEEEEEEEEECSSE----EEEEC--SSSSCEEEEHHHHHTSC----------CCTTCC----CSSSCCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEECCE----EEEEe--CCCEEEEEehHHhCCce----------eccccc----cchhhcccceEEEEE
Confidence            46889999999999999    99988  78999999 67776331          111111    22356999999    


Q ss_pred             EEEecccchhhhhhchh
Q 024995          227 QEIQLSHSLIRKASKRH  243 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~  243 (259)
                      ++||.+ +++.||||..
T Consensus        66 ~~vd~~-~~i~LS~k~~   81 (87)
T d2je6i1          66 ENFDRS-IDPVLSVKGK   81 (87)
T ss_dssp             EEEETT-EEEEEECCST
T ss_pred             EEECCC-CCEEEEEecC
Confidence            688854 6899999963

>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=98.66  E-value=5.3e-09  Score=75.40  Aligned_cols=71  Identities=7%  Similarity=0.042  Sum_probs=54.0

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+++.|+|+++++||    +|++|  .++++||+ .|+++...          .   ..+..+....+++||.|    
T Consensus         6 k~GdvV~G~V~~v~~~g----~fV~i--~~~~~g~l~~se~~~~~----------~---~~~~~~~~~~~~vGd~V~~kV   66 (88)
T d2z0sa1           6 QAGDVVIGLIQSVGIMN----WFVDI--NSPYVAVLSVQDFLGRP----------F---NPAVDDMQSLLKVGDYIKAKV   66 (88)
T ss_dssp             CTTCCEEEEEEEECSSE----EEEEC--SSSSCEEEEHHHHHTSC----------C---CTTTTCCTTSSCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEECCe----EEEEe--CCCeEEEEehHHhCccc----------c---cccccchhhhcccCcEEEEEE
Confidence            56888999999999999    99998  88999999 67776332          1   11112233467999999    


Q ss_pred             EEEecccchhhhhhch
Q 024995          227 QEIQLSHSLIRKASKR  242 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~  242 (259)
                      ++||.+ +++.||||+
T Consensus        67 ~~vd~~-~~i~Ls~k~   81 (88)
T d2z0sa1          67 VAFDKT-RSPLLTVQG   81 (88)
T ss_dssp             EEECTT-SCEEEECCS
T ss_pred             EEECCC-CCEEEEEec
Confidence            688855 689999996

>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=98.64  E-value=1.8e-09  Score=82.46  Aligned_cols=74  Identities=7%  Similarity=0.080  Sum_probs=56.6

Q ss_pred             cCCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995          151 SDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---  226 (259)
Q Consensus       151 ~~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---  226 (259)
                      .++|+++.|+|.+|++||    +|++|. .+|++||+ .+++++..           . ...+..    .+++||.|   
T Consensus        19 l~~G~iv~G~V~~i~~~G----~~V~lg-~~~~~G~l~~~els~~~-----------~-~~~~~~----~~~vGq~v~~~   77 (119)
T d1wi5a_          19 LKPGMLLTGTVSSLEDHG----YLVDIG-VDGTRAFLPLLKAQEYI-----------R-QKNKGA----KLKVGQYLNCI   77 (119)
T ss_dssp             CCTTCEEEEEEEEECSSE----EEEECC-CSSCEEEEEHHHHHHHH-----------H-HHSSSC----CCCTTCEEEEE
T ss_pred             cCCCCEEEEEEEEEeccE----EEEEEe-ccccceEEeHHHhcccc-----------c-cCCHHH----hcccceEEEEE
Confidence            357888999999999999    998881 37999999 56665321           0 112333    45999998   


Q ss_pred             -EEEecccchhhhhhchhhh
Q 024995          227 -QEIQLSHSLIRKASKRHCN  245 (259)
Q Consensus       227 -~~v~~~~~~i~ls~k~~~~  245 (259)
                       ++||.++++|.||+|+...
T Consensus        78 V~~vd~~~~~i~LS~k~~~~   97 (119)
T d1wi5a_          78 VEKVKGNGGVVSLSVGHSEV   97 (119)
T ss_dssp             EEECCTTSCEEEEECCCCCS
T ss_pred             EEEEeCCCCEEEEEecHHHh
Confidence             7999999999999998654

>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=98.59  E-value=2.7e-09  Score=72.16  Aligned_cols=57  Identities=16%  Similarity=0.098  Sum_probs=29.7

Q ss_pred             cceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EEEeccc
Q 024995          159 SNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QEIQLSH  233 (259)
Q Consensus       159 G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~v~~~~  233 (259)
                      |+|++|++||    +|++|  .+|++||+ +|+++...         |..++..+..    .+++||.|    ++||.+.
T Consensus         1 G~V~~i~~fG----~FV~l--~~g~~Glihiseis~~~---------~~~~v~~~~~----~~~~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           1 GSVVKTTTFG----AFVSL--LPGKDGLLHISQIRKLA---------GGKRVENVED----VLGVGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             CBEEECC-CS----CEECC--C---CCCCC--------------------------------CCSSCBCCCCCCCCCSSC
T ss_pred             CEEEEEEece----EEEEe--cCCceEEEEHHHccccc---------ccccccCHHH----hcCCCCEEEEEEEEEcCCC
Confidence            7899999999    99988  89999999 89987431         1222333333    67999999    6888665


Q ss_pred             c
Q 024995          234 S  234 (259)
Q Consensus       234 ~  234 (259)
                      |
T Consensus        62 r   62 (62)
T d1e3pa2          62 K   62 (62)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=98.57  E-value=2.2e-08  Score=72.23  Aligned_cols=69  Identities=7%  Similarity=-0.067  Sum_probs=60.4

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      ..++||+|.|+     .+|+||+|+     .+..|+||++++++ ...+....|++||.|.|+|.++|. .+++.||...
T Consensus         3 ~P~~GD~ViG~V~~~~~~~~~VdI~-----s~~~a~L~~~~f~g-~~k~~r~~l~~GD~V~arV~~v~~-~~~~~Lscvd   75 (88)
T d2nn6g1           3 VPVKGDHVIGIVTAKSGDIFKVDVG-----GSEPASLSYLSFEG-ATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVCID   75 (88)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECS-----SSSCCCEESCSSSC-CSSCSSSSSCTTCEEEEEEEECCT-TSCCEEECSB
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEcC-----CCeeEEEeHHHcCc-cccccCcccCCCCEEEEEEEEeCC-CCCEEEEEEc
Confidence            46899999999     789999998     57899999999964 677788899999999999999996 7899998765


Q ss_pred             c
Q 024995          130 L  130 (259)
Q Consensus       130 ~  130 (259)
                      .
T Consensus        76 ~   76 (88)
T d2nn6g1          76 S   76 (88)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=98.30  E-value=3.4e-07  Score=66.04  Aligned_cols=69  Identities=14%  Similarity=0.112  Sum_probs=60.4

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      ..++||+|.|+     ..++||+|+     ....|++|.++.......+....|++||.|.|+|.++|+ .+++.||.+.
T Consensus         4 ~P~~gD~ViG~V~~~~~~~~~vdI~-----~~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~-~~~~~Lsc~~   77 (90)
T d2ja9a1           4 IPSVNDFVIGVIIGTFSDSYKVSLQ-----NFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEK-ELEAEIECFD   77 (90)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESS-----TTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEESSC
T ss_pred             cCCCCCEEEEEEEEEeCCcEEEEcC-----CcchhhhhhhhccCccccccCCccCCCCEEEEEEEEECC-CCCEEEEEec
Confidence            35899999999     789999998     368899998888887888888899999999999999996 7899999754

>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=97.93  E-value=1.7e-06  Score=62.76  Aligned_cols=78  Identities=6%  Similarity=0.069  Sum_probs=52.6

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      .+|+++.|+|+++.++|    +|++|  .++.+|++ +|++++..-   .+    -+.......+....+++||.|    
T Consensus         7 ~vGdiV~G~V~~v~~~g----~~V~I--~~~~~g~l~is~i~~~~~---~~----rr~~~~~~~~~~~~~~~Gd~V~~kV   73 (95)
T d2nn6h1           7 EVGDIVVGRITEVQQKR----WKVET--NSRLDSVLLLSSMNLPGG---EL----RRRSAEDELAMRGFLQEGDLISAEV   73 (95)
T ss_dssp             CSSBCCCEEEEEEETTE----EEEEC--SSSSCEEEESSCCC--------------------CHHHHHHSCSSCEECCEE
T ss_pred             CCCCEEEEEEEEEecCc----EEEEe--CCCceEEEEHHHcccccc---cc----ccccchhhhhhhhhcccccEEEEEE
Confidence            35888999999999999    99988  78899999 688764210   00    000000111234468999999    


Q ss_pred             EEEecccchhhhhhchh
Q 024995          227 QEIQLSHSLIRKASKRH  243 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k~~  243 (259)
                      ++|+.+ .+++||+|.+
T Consensus        74 ~~v~~d-g~i~Ls~r~~   89 (95)
T d2nn6h1          74 QAVFSD-GAVSLHTRSL   89 (95)
T ss_dssp             EEEETT-TEEEEECCSS
T ss_pred             EEECCC-CCEEEEeccc
Confidence            688875 6799999864

>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=97.87  E-value=3.2e-05  Score=53.06  Aligned_cols=59  Identities=19%  Similarity=0.157  Sum_probs=48.2

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCC--eeEEE
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLS  126 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~--ri~lS  126 (259)
                      -++|+++.|+     +..++|+|+      +.+|++|.+|..      |.+.|++||.|+|-|.+++...+  +|.||
T Consensus         6 ~~~geiv~G~V~r~~~~~~~Vdlg------~~eaiLp~~eqi------p~E~~~~Gdrik~~i~~V~~~~kgpqI~lS   71 (72)
T d1hh2p1           6 ELKGTVTTAEVIRVMGEWADIRIG------KLETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVS   71 (72)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEET------TEEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEE
T ss_pred             hccCcEEEEEEEEEcCCCEEEEEC------CcEEECCHHHcC------CCCCCCCCCEEEEEEEEEEEcCCCCeEEEe
Confidence            4789999999     567899997      799999999864      56789999999999999986443  45554

>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=97.84  E-value=8.8e-06  Score=58.01  Aligned_cols=72  Identities=8%  Similarity=-0.006  Sum_probs=48.4

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCC--CcceeeeccCCCee----
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPS--GKKFTLLARAGRQV----  226 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~r~G~~V----  226 (259)
                      ++..+|.|+.|++||    +||+|. +.|++||+ .|.+..+.-.       +......-  ..+-+..++.||.|    
T Consensus         4 ~~~F~g~Is~v~~~G----ifV~L~-e~~~eGlI~~s~L~~d~y~-------~d~~~~~l~~~~~~~~~~~~Gd~V~V~v   71 (87)
T d2ix0a3           4 DTRFAAEIVDISRGG----MRVRLV-DNGAIAFIPAPFLHAVRDE-------LVCSQENGTVQIKGETVYKVTDVIDVTI   71 (87)
T ss_dssp             CCCEEEEEEEEETTE----EEEEET-TTCCEEEEEGGGTCSCGGG-------EEEETTTTEEEETTEEEEETTCEEEEEE
T ss_pred             CCEEEEEEEEEEcCe----EEEEEe-cCCcEEEEEehhCCCceEE-------EeccceEEEEEEcccEEEECCCEEEEEE
Confidence            567999999999999    999993 45899999 6777644211       00000000  00112356999999    


Q ss_pred             EEEecccchhh
Q 024995          227 QEIQLSHSLIR  237 (259)
Q Consensus       227 ~~v~~~~~~i~  237 (259)
                      .+||+++++|.
T Consensus        72 ~~vd~~~r~I~   82 (87)
T d2ix0a3          72 AEVRMETRSII   82 (87)
T ss_dssp             EEEETTTTEEE
T ss_pred             EEEecccCeEE
Confidence            69999999874

>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=97.81  E-value=2.6e-05  Score=59.17  Aligned_cols=74  Identities=20%  Similarity=0.232  Sum_probs=57.6

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCC---CccEEEEEEceecCc--ccccChhhhcCCCCeEEEEEEEEeCCCCeeEE
Q 024995           56 VNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSW--DLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (259)
Q Consensus        56 l~~G~iv~G~-----~~G~fV~l~~~~g---~~gi~glv~isels~--~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~l  125 (259)
                      .++|++|.|+     ...++|+|...++   .....|++|.+++..  ....++.+.|++||.|+|+|+++...+..+.|
T Consensus         5 P~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~~~~L   84 (125)
T d2nn6i1           5 PDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLL   84 (125)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCccEEE
Confidence            5789999999     6789999964333   124679999999843  34557889999999999999999865556888


Q ss_pred             EEec
Q 024995          126 SIKQ  129 (259)
Q Consensus       126 S~K~  129 (259)
                      |.++
T Consensus        85 st~~   88 (125)
T d2nn6i1          85 TTAE   88 (125)
T ss_dssp             ECCS
T ss_pred             EecC
Confidence            8754

>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=97.44  E-value=6.3e-05  Score=53.56  Aligned_cols=71  Identities=4%  Similarity=-0.113  Sum_probs=47.2

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----EE
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----QE  228 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~~  228 (259)
                      |++++|+|+++++||    +|+++   +.++||+ .+.+..+ -..-++-..|...  ....    .++.||.|    +.
T Consensus         4 Gev~~g~I~~v~~~G----~fv~l---g~~eg~i~~~~l~~~-~~~d~~~~~~~~~--~~~~----~~~~Gd~VrvkV~~   69 (91)
T d1y14b1           4 GEVVDGTVVSCSQHG----FEVQV---GPMKVFVTKHLMPQD-LTFNAGSNPPSYQ--SSED----VITIKSRIRVKIEG   69 (91)
T ss_dssp             TCEEEEEEEEEETTE----EEEEE---TTEEEEEEGGGSCTT-CEECC-----CEE--CSSC----EECTTCEEEEEEEE
T ss_pred             CCEEEEEEEEEEeeE----EEEEE---cCeEEEEEhhhcCcc-eEEccccceeEec--ccCe----EEeCCCEEEEEEEE
Confidence            788999999999999    99999   4689999 5555432 1111122222221  1223    45999998    68


Q ss_pred             Eecccchhhh
Q 024995          229 IQLSHSLIRK  238 (259)
Q Consensus       229 v~~~~~~i~l  238 (259)
                      |+.++++|..
T Consensus        70 v~~~~~~i~~   79 (91)
T d1y14b1          70 CISQVSSIHA   79 (91)
T ss_dssp             EEEETTEEEE
T ss_pred             EecccCccEE
Confidence            8999998753

>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=97.34  E-value=0.00036  Score=48.09  Aligned_cols=62  Identities=19%  Similarity=0.252  Sum_probs=46.5

Q ss_pred             CCCCEEEEE----ee-----eEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCC--eeEE
Q 024995           57 NVEDIFVGR----DY-----GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITL  125 (259)
Q Consensus        57 ~~G~iv~G~----~~-----G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~--ri~l  125 (259)
                      ++|+++.|+    +.     -++|+|+...  .+.+|++|.+|.      -|.+.|++||.|+|.|.+++...+  +|.|
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~--~~~EaiLp~~eq------ip~E~y~~Gdrik~~i~~V~~~~kGp~Iil   74 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTET--KASEGVIPAAEQ------VPGESYEHGNRLRCYVVGVTRGAREPLITL   74 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSS--SCEEEEECGGGS------CTTCCCCTTCEEEEEEEEEECCSSSCEEEE
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCC--CCEEEECCHHHc------CCCcccCCCCEEEEEEEEEEecCCCCEEEE
Confidence            689999999    22     2799996211  169999998885      456789999999999999986433  4444


Q ss_pred             E
Q 024995          126 S  126 (259)
Q Consensus       126 S  126 (259)
                      |
T Consensus        75 S   75 (76)
T d2asba1          75 S   75 (76)
T ss_dssp             E
T ss_pred             e
Confidence            4

>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=97.23  E-value=0.00014  Score=52.01  Aligned_cols=71  Identities=6%  Similarity=0.042  Sum_probs=48.2

Q ss_pred             CCccccceeeeccCCCccceeeeecccCCeeEEE-Ecccccccc-ccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKR-VVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       154 g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      |++++|+|++++++|    +|++|   +.++||+ .+.+..+-. ...++...|..  .....    .++.||.|    .
T Consensus         5 Gev~~g~V~~v~~~G----~fv~l---g~~~~~v~~~~l~~d~~y~~~~~~~~~~~--~~~~~----~~~~Gd~VrvkV~   71 (94)
T d2c35b1           5 GEVVDAVVTQVNKVG----LFTEI---GPMSCFISRHSIPSEMEFDPNSNPPCYKT--MDEDI----VIQQDDEIRLKIV   71 (94)
T ss_dssp             TCEEEEEEEEEETTE----EEEEE---TTEEEEEEGGGSCTTEEEESSSSSCEEEE--TTSCS----EEETTCEEEEEEE
T ss_pred             CCEEEEEEEEEEeeE----EEEEe---cCceEEEEhhhcCcceeecccccceEEEc--ccceE----EEeCCCEEEEEEE
Confidence            788999999999999    99999   4689999 555553321 11222223332  22222    56999998    6


Q ss_pred             EEecccchhh
Q 024995          228 EIQLSHSLIR  237 (259)
Q Consensus       228 ~v~~~~~~i~  237 (259)
                      .++.++++|+
T Consensus        72 ~v~~~~~~I~   81 (94)
T d2c35b1          72 GTRVDKNDIF   81 (94)
T ss_dssp             EEEEETTEEE
T ss_pred             EEecCcCcce
Confidence            7888888875

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {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-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=96.22  E-value=0.0037  Score=43.86  Aligned_cols=46  Identities=28%  Similarity=0.511  Sum_probs=36.8

Q ss_pred             eeEEEEEccCCCCccEEEEEEceecCcccc---------cChhhhcCCCCeEEEEEEEEe
Q 024995           67 YGAFIHLRFPDGLYHLTGLVHVSEVSWDLI---------QDIRDILNEGDEVRVKVIKID  117 (259)
Q Consensus        67 ~G~fV~l~~~~g~~gi~glv~isels~~~~---------~~~~~~~~~Gd~V~vkVl~id  117 (259)
                      .+|||+++     .+..||+|++++...+.         .+..+.+++||.|-|.|.+=-
T Consensus        16 ~AAFVDiG-----~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~   70 (87)
T d1smxa_          16 EAAFVDYG-----AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEE   70 (87)
T ss_dssp             TEEEEESS-----SSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECC
T ss_pred             eEEEEEeC-----CCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecc
Confidence            47999998     58899999999876543         245677999999999996643

>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=95.52  E-value=0.01  Score=39.94  Aligned_cols=53  Identities=8%  Similarity=0.026  Sum_probs=38.8

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      +.|++++|+|.++.+-.    ++++|   ++++|+++ +++.                   +..+|    ++||.|    
T Consensus         7 ~~geiv~G~V~r~~~~~----~~Vdl---g~~eaiLp~~eqi-------------------p~E~~----~~Gdrik~~i   56 (72)
T d1hh2p1           7 LKGTVTTAEVIRVMGEW----ADIRI---GKLETRLPKKEWI-------------------PGEEI----KAGDLVKVYI   56 (72)
T ss_dssp             CTTCEEEEEEEEECSSE----EEEEE---TTEEEEEEGGGSC-------------------TTCCC----CTTCEEEEEE
T ss_pred             ccCcEEEEEEEEEcCCC----EEEEE---CCcEEECCHHHcC-------------------CCCCC----CCCCEEEEEE
Confidence            35888999999998766    88888   68999994 4432                   23345    999999    


Q ss_pred             EEEecccc
Q 024995          227 QEIQLSHS  234 (259)
Q Consensus       227 ~~v~~~~~  234 (259)
                      ++|+.+.+
T Consensus        57 ~~V~~~~k   64 (72)
T d1hh2p1          57 IDVVKTTK   64 (72)
T ss_dssp             EEEEEETT
T ss_pred             EEEEEcCC
Confidence            56665554

>d1luza_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Vaccinia virus [TaxId: 10245]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Viral structural mimic of eIF2alpha
species: Vaccinia virus [TaxId: 10245]

Probab=95.37  E-value=0.026  Score=38.51  Aligned_cols=72  Identities=33%  Similarity=0.489  Sum_probs=54.2

Q ss_pred             CCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEEce-ecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           55 RVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        55 ~l~~G~iv~G~----~~G~fV~l~~~~g~~gi~glv~is-els~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      -...|++.+|.    ++-++|.|.+++   |.++++--+ ++..++..+.++.+ +|..|+++|+++|.-+|-|.++.|.
T Consensus         5 lPnigdVtkGiVy~kd~~fyV~L~dY~---g~ea~l~dy~~~~~d~~~klk~kL-VGKtIkvqVIR~d~lKGYIDVr~~~   80 (85)
T d1luza_           5 LPNAGDVIKGRVYEKDYALYIYLFDYP---HFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKR   80 (85)
T ss_dssp             CCCTTCEEEEEEEEETTEEEEEETTCT---TSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEE
T ss_pred             cCCCCceeeeEEEEeCCEEEEEecCCC---CceEEeeehhhhhhHHHHHHHHHh-cCceEEEEEEEEcceeeEEEehhhh
Confidence            46789999999    566789998744   688886321 12223445566666 7999999999999999999999886


Q ss_pred             c
Q 024995          130 L  130 (259)
Q Consensus       130 ~  130 (259)
                      .
T Consensus        81 ~   81 (85)
T d1luza_          81 M   81 (85)
T ss_dssp             E
T ss_pred             h
Confidence            4

>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=94.61  E-value=0.0073  Score=42.32  Aligned_cols=65  Identities=2%  Similarity=-0.258  Sum_probs=44.9

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEE-EccccccccccchhhhhhcccCCCCCcceeeeccCCCee----
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR-ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----  226 (259)
                      ++|+.+-|+|+++..++    .|++|  .++..|++ .+++.           ...++.       .-.+++||.|    
T Consensus         5 ~~GD~ViG~V~~~~~~~----~~VdI--~s~~~a~L~~~~f~-----------g~~k~~-------r~~l~~GD~V~arV   60 (88)
T d2nn6g1           5 VKGDHVIGIVTAKSGDI----FKVDV--GGSEPASLSYLSFE-----------GATKRN-------RPNVQVGDLIYGQF   60 (88)
T ss_dssp             CSSEEEEEEEEEEETTE----EEEEC--SSSSCCCEESCSSS-----------CCSSCS-------SSSSCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEeCCe----EEEEc--CCCeeEEEeHHHcC-----------cccccc-------CcccCCCCEEEEEE
Confidence            46888999999999999    99888  78899988 55542           112211       1256999999    


Q ss_pred             EEEecccchhhhhhc
Q 024995          227 QEIQLSHSLIRKASK  241 (259)
Q Consensus       227 ~~v~~~~~~i~ls~k  241 (259)
                      ++++.. .++.||+.
T Consensus        61 ~~v~~~-~~~~Lscv   74 (88)
T d2nn6g1          61 VVANKD-MEPEMVCI   74 (88)
T ss_dssp             EECCTT-SCCEEECS
T ss_pred             EEeCCC-CCEEEEEE
Confidence            455533 35666654

>d1jjga_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Myxoma virus, m156r [TaxId: 10273]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Viral structural mimic of eIF2alpha
species: Myxoma virus, m156r [TaxId: 10273]

Probab=94.56  E-value=0.028  Score=39.27  Aligned_cols=67  Identities=13%  Similarity=0.150  Sum_probs=48.5

Q ss_pred             ccCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEE-ceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEE
Q 024995           53 SSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (259)
Q Consensus        53 ~~~l~~G~iv~G~----~~G~fV~l~~~~g~~gi~glv~-isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~l  125 (259)
                      ..++-+|++.+|.    ++-++|.|.+++   |.+|++- --++-.++..+..+.+ +|..|+++|+++|.  ..|.+
T Consensus        27 ~~~~~~G~V~kGiVy~rd~~fyV~L~dY~---g~eail~dY~n~~~dr~~klkkkL-VGKTIkVqVIRvDk--lYIDV   98 (102)
T d1jjga_          27 AMDLSPGSVHEGIVYFKDGIFKVRLLGYE---GHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADG--LYVDL   98 (102)
T ss_dssp             CCCCCSSCEEEEEEEEETTEEEEECTTTS---SCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECS--SEEEE
T ss_pred             ecccCCCcEeeeEEEEeCCEEEEEecCCC---CceeeeeehhhhhHHHHHHHHHHh-cCceEEEEEEEecc--EEEEE
Confidence            3478999999999    666789998754   6788842 2233344556666666 79999999999983  34443

>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=92.82  E-value=0.045  Score=38.23  Aligned_cols=67  Identities=7%  Similarity=-0.117  Sum_probs=44.1

Q ss_pred             CCCCccccceeeeccCCCccceeeeecccCCeeEEEEccccccccccchhhhhhcccCCCCCcceeeeccCCCee----E
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV----Q  227 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V----~  227 (259)
                      .+|+.+-|+|.++.+.+    .|++|  .+.-.|++++.+..++         ..++       ..-.+++||.|    +
T Consensus         6 ~~gD~ViG~V~~~~~~~----~~vdI--~~~~~~~L~~~~~f~g---------~~k~-------~r~~l~~GDlV~arV~   63 (90)
T d2ja9a1           6 SVNDFVIGVIIGTFSDS----YKVSL--QNFSSSVSLSYMAFPN---------ASKK-------NRPTLQVGDLVYARVC   63 (90)
T ss_dssp             CTTCEEEEEEEEECSSE----EEEES--STTSCCEEEETTSSTT---------CCSS-------SCCCCCTTCEEEEEEE
T ss_pred             CCCCEEEEEEEEEeCCc----EEEEc--CCcchhhhhhhhccCc---------cccc-------cCCccCCCCEEEEEEE
Confidence            46888999999999999    99988  6677887754333332         1111       12256999999    4


Q ss_pred             EEecccchhhhhhc
Q 024995          228 EIQLSHSLIRKASK  241 (259)
Q Consensus       228 ~v~~~~~~i~ls~k  241 (259)
                      +++.. ..+.||++
T Consensus        64 ~v~~~-~~~~Lsc~   76 (90)
T d2ja9a1          64 TAEKE-LEAEIECF   76 (90)
T ss_dssp             ECCTT-SCCEEESS
T ss_pred             EECCC-CCEEEEEe
Confidence            54433 34666654

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {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-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=92.53  E-value=0.11  Score=36.00  Aligned_cols=64  Identities=19%  Similarity=0.223  Sum_probs=41.9

Q ss_pred             ccccceeeeccCCCccceeeeecccCCeeEEEE-ccccccccccchhhhhhccc-CCCCCcceeeeccCCCee-EEEecc
Q 024995          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI-TRQGFEKRVVSQDLQLWLSN-APPSGKKFTLLARAGRQV-QEIQLS  232 (259)
Q Consensus       156 ~v~G~V~~i~~~G~~~~~fv~l~~~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~r~G~~V-~~v~~~  232 (259)
                      ++.|+|.+|.|  ++.++||++  ..+-.||++ +++..+.         +... ......++...+++||.| ..|..+
T Consensus         3 IY~G~V~~V~p--gl~AAFVDi--G~~k~gFL~~~di~~~~---------~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke   69 (87)
T d1smxa_           3 IYKGKITRIEP--SLEAAFVDY--GAERHGFLPLKEIAREY---------FPANYSAHGRPNIKDVLREGQEVIVQIDKE   69 (87)
T ss_dssp             CEEEEEEEEEG--GGTEEEEES--SSSSCEEEEGGGSCGGG---------CSSCCCSSSCCCGGGTCCTTCEEEEEEEEC
T ss_pred             cEEEEEEEecC--CceEEEEEe--CCCccceeEecccceee---------eccccccccccchhhhccCCCeEEEEEeec
Confidence            48899999986  778899998  788999994 4443211         1110 111223466688999999 355444

>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=89.70  E-value=0.16  Score=34.16  Aligned_cols=60  Identities=8%  Similarity=0.108  Sum_probs=38.1

Q ss_pred             CCCCccccceeeeccCCCccceeeeecc-cCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCCee---
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQ-EDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRQV---  226 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~-~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~~V---  226 (259)
                      +.|++++|+|.++..-.....++++|-. .+|++|+++ +++-                   |..+|    +.||.|   
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqi-------------------p~E~y----~~Gdrik~~   59 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV-------------------PGESY----EHGNRLRCY   59 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC-------------------TTCCC----CTTCEEEEE
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcC-------------------CCccc----CCCCEEEEE
Confidence            4588899999998631101125667722 268999994 4422                   33445    999999   


Q ss_pred             -EEEecccc
Q 024995          227 -QEIQLSHS  234 (259)
Q Consensus       227 -~~v~~~~~  234 (259)
                       ++|....+
T Consensus        60 i~~V~~~~k   68 (76)
T d2asba1          60 VVGVTRGAR   68 (76)
T ss_dssp             EEEEECCSS
T ss_pred             EEEEEecCC
Confidence             57766554

>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=86.79  E-value=0.28  Score=36.02  Aligned_cols=56  Identities=11%  Similarity=0.056  Sum_probs=35.7

Q ss_pred             CCCCccccceeeeccCCCccceeeeecc------cCCeeEEEE-ccccccccccchhhhhhcccCCCCCcceeeeccCCC
Q 024995          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQ------EDGIDDVRI-TRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (259)
Q Consensus       152 ~~g~~v~G~V~~i~~~G~~~~~fv~l~~------~~gv~gl~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~G~  224 (259)
                      ++|+++.|+|+++.+..    +++++..      .....|+++ ++...             ...+  ..+....||+||
T Consensus         6 ~vGDiVig~V~~v~~~~----a~v~I~~v~~~~l~~~~~g~i~~~dvr~-------------te~d--~~~m~~~fr~GD   66 (125)
T d2nn6i1           6 DVGAIVTCKVSSINSRF----AKVHILYVGSMPLKNSFRGTIRKEDVRA-------------TEKD--KVEIYKSFRPGD   66 (125)
T ss_dssp             CTTCEEEEEEEEECSSE----EEEEEEESSSSCCCCSSCSCEEEEGGGT-------------CSSC--CCCGGGTCCSSS
T ss_pred             CCCCEEEEEEEEecCCE----EEEEEeEecCcccccCccccccHHHccc-------------chhh--hhhHHHhcCCCC
Confidence            56888999999999988    7877733      234667764 33221             1111  112345779999


Q ss_pred             ee
Q 024995          225 QV  226 (259)
Q Consensus       225 ~V  226 (259)
                      .|
T Consensus        67 iV   68 (125)
T d2nn6i1          67 IV   68 (125)
T ss_dssp             EE
T ss_pred             EE
Confidence            99

>d1wfqa_ b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {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: Cold shock domain protein E1 (UNR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.60  E-value=3.5  Score=27.90  Aligned_cols=64  Identities=20%  Similarity=0.197  Sum_probs=39.8

Q ss_pred             CCCCCEEEEE------eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEEeCCCCeeEEEEec
Q 024995           56 VNVEDIFVGR------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (259)
Q Consensus        56 l~~G~iv~G~------~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~id~~~~ri~lS~K~  129 (259)
                      -..+....|+      .||+ |.-.+    .+-+-|+|++++...     ...+++||.|...+..-++..+...+.++.
T Consensus        13 ~~~~~r~~G~I~~~~~gfGF-I~~~~----~~~dvF~H~s~~~~~-----~~~l~~G~~VeF~v~~~~kg~k~~Av~V~~   82 (89)
T d1wfqa_          13 TSAALRETGVIEKLLTSYGF-IQCSE----RQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDRRTGKPIAVKLVK   82 (89)
T ss_dssp             SSCCCEEEEEEEEECSSEEE-EEETT----TTEEEEEETTTCSSC-----TTTCCTTCCEEEEEEECSSSCCEEEEEEEE
T ss_pred             CCccceEEEEEEEecCccce-EEeCC----CCceEEEEeehhhcc-----CCcccCCCEEEEEEEECCCCCceEEEEEEE
Confidence            3445556666      5665 44432    267899999998543     245889999999985533323334444443

>d1k3ra1 b.40.4.10 (A:93-163) Hypothetical protein MTH1 (MT0001), insert domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Hypothetical protein MTH1 (MT0001), insert domain
domain: Hypothetical protein MTH1 (MT0001), insert domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=83.34  E-value=0.64  Score=30.44  Aligned_cols=45  Identities=13%  Similarity=0.226  Sum_probs=34.5

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEEE
Q 024995           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI  116 (259)
Q Consensus        54 ~~l~~G~iv~G~-----~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~i  116 (259)
                      ..++.|++-+|.     ..|+||+++       ++-+..+.+           .|+.|+.+.++|.++
T Consensus         6 g~p~vGEiReG~~~rr~~~g~~vDiG-------lD~la~~k~-----------~~~~~~r~tfrIvs~   55 (71)
T d1k3ra1           6 GKPVTGEYRQGLTVKRVKKGTLVDIG-------ADKLALCRE-----------KLTVNRIMSFRVVRL   55 (71)
T ss_dssp             SSCCTTCEEEEEEEEECSSSEEEESS-------SSCEEECSS-----------CCCSSCEEEEEEEEC
T ss_pred             CCCcccceeeEEEEEecCCcEEEEec-------CCceeeeec-----------ccccCcEEEEEEEEc
Confidence            467899999998     678999996       444433222           478899999999987

>d1h95a_ b.40.4.5 (A:) Y-box protein 1 cold shock domain (YB1-CSD) {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: Y-box protein 1 cold shock domain (YB1-CSD)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.12  E-value=1.9  Score=28.72  Aligned_cols=45  Identities=16%  Similarity=0.233  Sum_probs=30.6

Q ss_pred             eeeEEEEEccCCCCccEEEEEEceecCcccccChhhhcCCCCeEEEEEEE
Q 024995           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK  115 (259)
Q Consensus        66 ~~G~fV~l~~~~g~~gi~glv~isels~~~~~~~~~~~~~Gd~V~vkVl~  115 (259)
                      -||+...-+     .+-+-|+|.|.+...-.......+..||.|...+..
T Consensus        21 GfGFI~~dd-----g~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~   65 (79)
T d1h95a_          21 GYGFINRND-----TKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVE   65 (79)
T ss_dssp             TEEEEEEGG-----GTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEE
T ss_pred             CeEEEEECC-----CCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEe
Confidence            466544333     268999999999765322233457889999998754