Citrus Sinensis ID: 026794

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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---
Protein Sequence
MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRCKRYNFHIP
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEEEEEEEEEccccEEEEEcHHHHHHHHHcccccccEEEcEEccEEEEEcccccccccEEEEEEccccccccccHHHHcccccEEEEEEEEEEccccEEEEEccccccccHHHHHHHHccccccEEEEEEEEccccccEEEEcccccHHHHHHHHccccccEEEccccccEEccccEEEEEEEEccccccEEEEEEEcccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccEEEcccEEEEEEEEEccccccEEEEHHHccHHHHHHHcccccEEEccEEEEEEEEcccccccccEEEEEEccccccccccccHEEEcccEEEEEEEEEcccccEEEEEEHcccccHHHHHHHHHcccccEEEEEEEEEcccccEEEEccccccEEEEEEEccccHHHHHHcccccEEEEEcccEEEEEEEccHHHcEEEEEcccccccccEEEcc
Coil and Loop (DISEMBL)
mspshsckepqKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWnkyssrvnvedifvgrdygafihlrfpdglyhlTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKqleedplletlekvipqdgsvisdsssmsssnsntieplpgLGAIFEELLqedgiddvriTRQGFEKRVVSQDLQLwlsnappsgkkfTLLARagrckrynfhip
Flexible Loop (DISEMBL)
mspshsckepQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDilnegdevrvkvikidreksritlsikqleedplleTLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQlwlsnappsgkkftllaragrckrynfhip
Low Complexity Region (SEG)
MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGsvisdsssmsssnsNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRCKRYNFHIP
Disordered region (IsUnstruct)
***************EIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL*************************************PGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRCKRYNF***
Disordered Region (DISOPRED)
*SPS***KEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRCKR*NF*I*
Disordered Region (DISEMBL)
***********KSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGS**************TIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRCKRYNFHIP
Disordered Region (DISPRO)
************SIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRCKRYNFHIP
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRCKRYNFHIP
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	233	2.2.26 [Sep-21-2011]
P73530	328	30S ribosomal protein S1	N/A	no	0.497	0.353	0.338	2e-12
Q89AJ3	566	30S ribosomal protein S1	yes	no	0.493	0.203	0.323	5e-12
P29344	411	30S ribosomal protein S1,	N/A	no	0.622	0.352	0.279	2e-11
P14128	378	30S ribosomal protein S1	N/A	no	0.463	0.285	0.341	3e-11
P37985	557	30S ribosomal protein S1	yes	no	0.463	0.193	0.341	3e-11
P0AG70	557	30S ribosomal protein S1	yes	no	0.463	0.193	0.341	3e-11
P0AG67	557	30S ribosomal protein S1	N/A	no	0.463	0.193	0.341	3e-11
P0AG68	557	30S ribosomal protein S1	yes	no	0.463	0.193	0.341	3e-11
P0AG69	557	30S ribosomal protein S1	N/A	no	0.463	0.193	0.341	3e-11
Q83E09	551	30S ribosomal protein S1	yes	no	0.364	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 = 72.8 bits (177), 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 = 71.2 bits (173), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 43/133 (32%), Positives = 76/133 (57%), Gaps = 18/133 (13%)

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 QLEEDPLLETLEK 141
           QL +DP  +  E+
Sbjct: 261 QLSDDPWTKISER 273

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

 Score = 68.9 bits (167), 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|P37985|RS1_DICD3 30S ribosomal protein S1 OS=Dickeya dadantii (strain 3937) GN=rpsA PE=3 SV=2

 Score = 68.9 bits (167), 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: 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 QLEEDP 134
           QL EDP
Sbjct: 261 QLGEDP 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|P0AG70|RS1_SHIFL 30S ribosomal protein S1 OS=Shigella flexneri GN=rpsA PE=3 SV=1

 Score = 68.9 bits (167), 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: 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 QLEEDP 134
           QL EDP
Sbjct: 261 QLGEDP 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 = 68.9 bits (167), 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: 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 QLEEDP 134
           QL EDP
Sbjct: 261 QLGEDP 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 = 68.9 bits (167), 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: 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 QLEEDP 134
           QL EDP
Sbjct: 261 QLGEDP 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 = 68.9 bits (167), 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: 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 QLEEDP 134
           QL EDP
Sbjct: 261 QLGEDP 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 = 68.9 bits (167), 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	233
225433644	390	PREDICTED: 30S ribosomal protein S1 homo	0.952	0.569	0.759	4e-94
224131510	299	predicted protein [Populus trichocarpa]	0.952	0.742	0.760	2e-93
356569689	378	PREDICTED: 40S ribosomal protein S1-like	0.952	0.587	0.742	1e-90
356538073	383	PREDICTED: 30S ribosomal protein S1 homo	0.952	0.579	0.733	3e-89
147802809	418	hypothetical protein VITISV_006784 [Viti	0.952	0.531	0.677	2e-88
449484641	379	PREDICTED: 30S ribosomal protein S1-like	0.952	0.585	0.703	1e-84
18403854	392	ribosomal protein S1-like RNA-binding do	0.952	0.566	0.720	2e-84
449468800	378	PREDICTED: 30S ribosomal protein S1-like	0.952	0.587	0.698	3e-84
297835412	392	S1 RNA-binding domain-containing protein	0.952	0.566	0.720	8e-84
357462911	399	Polyribonucleotide nucleotidyltransferas	0.952	0.556	0.681	5e-80

>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 =  349 bits (896), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 174/229 (75%), Positives = 199/229 (86%), Gaps = 7/229 (3%)

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 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224
           ELLQE+GI DVRI+RQGFEKRVVSQDLQLWLSNAP   K+FTLLARAGR
Sbjct: 314 ELLQEEGISDVRISRQGFEKRVVSQDLQLWLSNAPAVDKQFTLLARAGR 362

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 =  347 bits (891), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 175/230 (76%), Positives = 199/230 (86%), Gaps = 8/230 (3%)

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 EELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224
           +EL +EDGIDD+RI+RQGFEKRVVSQDLQLWLSNAPP  +KFTLLARAGR
Sbjct: 222 QELTREDGIDDIRISRQGFEKRVVSQDLQLWLSNAPPINRKFTLLARAGR 271

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 =  338 bits (867), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 170/229 (74%), Positives = 194/229 (84%), Gaps = 7/229 (3%)

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 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224
           ELLQEDGI DVRI+RQGFEKRVVSQDLQLWLSNAPP+ ++FTLLARAGR
Sbjct: 302 ELLQEDGIYDVRISRQGFEKRVVSQDLQLWLSNAPPTNQRFTLLARAGR 350

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 =  333 bits (854), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 168/229 (73%), Positives = 193/229 (84%), Gaps = 7/229 (3%)

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 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224
           ELLQEDGI DVRI+RQGFEKRVVSQDLQLWL NAPP+ ++FTLLARAGR
Sbjct: 307 ELLQEDGIYDVRISRQGFEKRVVSQDLQLWLCNAPPTNQRFTLLARAGR 355

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 =  330 bits (847), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 174/257 (67%), Positives = 199/257 (77%), Gaps = 35/257 (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 NAPPSGKKFTLLARAGR 224
           NAP   K+FTLLARAGR
Sbjct: 374 NAPAVDKQFTLLARAGR 390

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 =  318 bits (815), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 161/229 (70%), Positives = 187/229 (81%), Gaps = 7/229 (3%)

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 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224
           ELLQE+GI DVR+ RQGFEKRVVSQDLQLWLSNAPP  KKFTLLARAGR
Sbjct: 303 ELLQEEGIVDVRVNRQGFEKRVVSQDLQLWLSNAPPVEKKFTLLARAGR 351

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 =  317 bits (812), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 165/229 (72%), Positives = 188/229 (82%), Gaps = 7/229 (3%)

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 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224
           ELL+EDGI+ V+I RQGFEKRVVSQDLQLWLSN PPS  KF LLARAGR
Sbjct: 316 ELLKEDGIEAVKINRQGFEKRVVSQDLQLWLSNTPPSDGKFVLLARAGR 364

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  317 bits (811), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 160/229 (69%), Positives = 187/229 (81%), Gaps = 7/229 (3%)

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 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224
           ELLQE+GI DVR+ RQGFEKRVVSQDLQLWLSNAPP  KKFTLLARAGR
Sbjct: 302 ELLQEEGIVDVRVNRQGFEKRVVSQDLQLWLSNAPPVEKKFTLLARAGR 350

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  315 bits (808), Expect = 8e-84,   Method: Compositional matrix adjust.
 Identities = 165/229 (72%), Positives = 188/229 (82%), Gaps = 7/229 (3%)

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 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224
           ELL+EDGI+ V+I RQGFEKRVVSQDLQLWLSN PPS  KF LLARAGR
Sbjct: 316 ELLKEDGIEAVKINRQGFEKRVVSQDLQLWLSNTPPSDGKFVLLARAGR 364

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 =  303 bits (775), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 156/229 (68%), Positives = 189/229 (82%), Gaps = 7/229 (3%)

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 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224
           ELLQEDGI++ RI+RQGFEKRVVSQDLQLWLSNAPP  ++FTLLARAGR
Sbjct: 323 ELLQEDGINEARISRQGFEKRVVSQDLQLWLSNAPPMDQRFTLLARAGR 371

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	233
TAIR|locus:2095203	392	AT3G23700 [Arabidopsis thalian	0.952	0.566	0.698	2.3e-78
TIGR_CMR|SO_2402	555	SO_2402 "ribosomal protein S1"	0.416	0.174	0.390	5.8e-13
TAIR|locus:2145860	416	RPS1 "ribosomal protein S1" [A	0.502	0.281	0.333	3.1e-12
UNIPROTKB|P0AG67	557	rpsA "30S ribosomal subunit pr	0.506	0.211	0.328	5.4e-12
TIGR_CMR|NSE_0408	553	NSE_0408 "ribosomal protein S1	0.459	0.193	0.348	6.9e-12
TIGR_CMR|CBU_0528	551	CBU_0528 "ribosomal protein S1	0.309	0.130	0.443	1.1e-11
TIGR_CMR|CPS_2335	553	CPS_2335 "ribosomal protein S1	0.463	0.195	0.341	1.1e-11
TIGR_CMR|ECH_0402	567	ECH_0402 "putative ribosomal p	0.463	0.190	0.339	1.9e-11
TAIR|locus:2010336	767	AT1G12800 [Arabidopsis thalian	0.879	0.267	0.292	3.9e-11
UNIPROTKB|Q9KQT3	556	VC_1915 "30S ribosomal protein	0.407	0.170	0.359	4e-11

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

 Score = 788 (282.4 bits), Expect = 2.3e-78, P = 2.3e-78
 Identities = 160/229 (69%), Positives = 180/229 (78%)

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 ELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR 224
             ELL+EDGI+ V+I RQGFEKRVVSQDLQLWLSN PPS  KF LLARAGR
Sbjct:   316 ELLKEDGIEAVKINRQGFEKRVVSQDLQLWLSNTPPSDGKFVLLARAGR 364

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

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 = 3.1e-12, P = 3.1e-12
 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 = 5.4e-12, P = 5.4e-12
 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

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

 Score = 170 (64.9 bits), Expect = 6.9e-12, P = 6.9e-12
 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 = 1.1e-11, P = 1.1e-11
 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 = 1.1e-11, P = 1.1e-11
 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 = 1.9e-11, P = 1.9e-11
 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

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

 Score = 165 (63.1 bits), Expect = 3.9e-11, P = 3.9e-11
 Identities = 65/222 (29%), Positives = 95/222 (42%)

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 GIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAG 223
             GI  V  +R  F    ++   Q+++  AP    ++ LLARAG
Sbjct:   700 GIQSVSKSRF-FLSPGLAPTFQVYM--APMFENQYKLLARAG 738

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

UNIPROTKB|Q9KQT3 VC_1915 "30S ribosomal protein S1" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 163 (62.4 bits), Expect = 4.0e-11, P = 4.0e-11
 Identities = 37/103 (35%), Positives = 60/103 (58%)

Query:    44 EKDAVWNKYSSRVNVEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDI 102
             E+D +         V+ I     DYGAF+ L   DGL H+T      +++W  ++   +I
Sbjct:   181 ERDELLETLQEGTEVKGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEI 234

Query:   103 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ 145
             +N GDE+ VKV+K DR+++R++L +KQL EDP +  + K  P+
Sbjct:   235 VNVGDEILVKVLKFDRDRTRVSLGLKQLGEDPWV-AIAKRYPE 276

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

GO:0006412 "translation" 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	233
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	3e-20
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	7e-20
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	5e-19
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	1e-18
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	1e-18
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-18
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	3e-18
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	8e-18
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	3e-17
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	1e-16
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	3e-16
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	6e-16
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	1e-15
PRK08059	123	PRK08059, PRK08059, general stress protein 13; Val	1e-15
COG1098	129	COG1098, VacB, Predicted RNA binding protein (cont	3e-15
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	3e-15
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	4e-15
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	8e-15
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	2e-14
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	2e-14
pfam00575	74	pfam00575, S1, S1 RNA binding domain	8e-14
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	3e-13
PRK05807	136	PRK05807, PRK05807, hypothetical protein; Provisio	5e-13
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	5e-13
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	7e-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	2e-11
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	1e-10
PRK03987	262	PRK03987, PRK03987, translation initiation factor	1e-10
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	3e-10
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	5e-10
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	8e-10
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	9e-10
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	2e-09
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	2e-09
PRK07252	120	PRK07252, PRK07252, hypothetical protein; Provisio	2e-09
cd05691	73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	3e-09
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	4e-09
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	7e-09
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	5e-08
cd05684	79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	7e-08
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	2e-06
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	3e-06
cd05689	72	cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: R	5e-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	2e-05
cd05687	70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	6e-05
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	5e-04
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	0.004

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

 Score = 88.7 bits (221), Expect = 3e-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 = 7e-20
 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 = 85.0 bits (211), Expect = 5e-19
 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|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 83.4 bits (207), Expect = 1e-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|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 83.9 bits (208), Expect = 1e-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|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 82.9 bits (206), Expect = 2e-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 = 3e-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 = 81.5 bits (202), Expect = 8e-18
 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 = 79.5 bits (197), Expect = 3e-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 = 1e-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 = 75.6 bits (186), Expect = 3e-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 = 6e-16
 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 = 1e-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 = 70.1 bits (172), Expect = 1e-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 = 3e-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 = 73.9 bits (183), Expect = 3e-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 = 4e-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 = 8e-15
 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 = 71.3 bits (175), 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 = 2e-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 = 8e-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 = 3e-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|235614 PRK05807, PRK05807, hypothetical protein; Provisional

 Score = 63.6 bits (155), Expect = 5e-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|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

 Score = 67.2 bits (165), Expect = 5e-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 = 61.5 bits (150), 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|236305 PRK08582, PRK08582, hypothetical protein; Provisional

 Score = 61.2 bits (149), 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 = 58.9 bits (143), 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 = 62.8 bits (153), Expect = 2e-11
 Identities = 43/135 (31%), Positives = 64/135 (47%), Gaps = 18/135 (13%)

Query: 23  GSIISVKVIQANEEMK----KLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAF 70
           G  + VKV+      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 = 57.4 bits (139), 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 = 62.5 bits (153), Expect = 2e-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 = 55.6 bits (135), 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 = 59.5 bits (145), Expect = 1e-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 = 3e-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 = 58.5 bits (142), Expect = 5e-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|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 = 8e-10
 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|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 57.8 bits (140), Expect = 9e-10
 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|236126 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 56.6 bits (137), Expect = 2e-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|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|180908 PRK07252, PRK07252, hypothetical protein; Provisional

 Score = 53.2 bits (128), Expect = 2e-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 = 51.9 bits (125), Expect = 3e-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 = 55.9 bits (134), Expect = 4e-09
 Identities = 39/124 (31%), Positives = 64/124 (51%), Gaps = 14/124 (11%)

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 PLLE 137
           P  E
Sbjct: 655 PWEE 658

Length = 863

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

 Score = 55.1 bits (132), Expect = 7e-09
 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 = 52.3 bits (126), Expect = 5e-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 = 7e-08
 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 = 46.8 bits (112), 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 = 2e-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 = 47.2 bits (113), Expect = 3e-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 = 42.9 bits (101), Expect = 5e-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 = 2e-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 = 40.1 bits (94), Expect = 5e-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

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

 Score = 37.8 bits (87), Expect = 0.004
 Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 15/94 (15%)

Query: 49  WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDIL 103
           W +  +R  V   F  R     + GAFI +   +G+    G +HV ++SW  ++  R   
Sbjct: 656 WEEIEARYPVGARFTRRIVKVTNAGAFIEME--EGI---DGFLHVDDLSW--VKRTRPAD 708

Query: 104 NE---GDEVRVKVIKIDREKSRITLSIKQLEEDP 134
           +E   G E+   VI+ D +  RI L +KQL ++P
Sbjct: 709 HELEVGKEIECMVIECDPQARRIRLGVKQLSDNP 742

Length = 863

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	233
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	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
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	99.97
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	99.97
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.96
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.96
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.95
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.95
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.95
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.94
PRK07400	318	30S ribosomal protein S1; Reviewed	99.93
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.93
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.91
PRK07400	318	30S ribosomal protein S1; Reviewed	99.88
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.87
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.79
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.76
PRK08582	139	hypothetical protein; Provisional	99.61
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.61
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.56
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.54
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.54
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.54
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.54
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.54
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.52
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.51
PHA02945	88	interferon resistance protein; Provisional	99.51
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.5
PRK07252	120	hypothetical protein; Provisional	99.49
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.48
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.48
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.47
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.45
PRK08059	123	general stress protein 13; Validated	99.45
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.44
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.44
PRK05807	136	hypothetical protein; Provisional	99.44
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	99.44
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.43
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.43
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.38
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.37
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.37
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.37
PRK03987	262	translation initiation factor IF-2 subunit alpha;	99.32
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.31
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.31
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.3
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.29
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.29
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.29
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.27
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.26
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.25
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.23
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.19
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.19
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	99.16
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.13
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	99.11
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.08
COG2183	780	Tex Transcriptional accessory protein [Transcripti	99.07
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	99.04
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	99.0
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	99.0
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.98
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.97
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.89
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.8
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.78
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.73
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.73
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	98.71
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.68
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	98.61
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.6
COG1098	129	VacB Predicted RNA binding protein (contains ribos	98.57
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.53
TIGR01953	341	NusA transcription termination factor NusA. This m	98.53
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	98.49
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.47
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	98.44
PRK11642	813	exoribonuclease R; Provisional	98.44
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	98.43
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.41
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.4
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	98.38
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	98.23
KOG2916	304	consensus Translation initiation factor 2, alpha s	98.18
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	98.14
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	98.1
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.07
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	97.98
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	97.98
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	97.96
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	97.94
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	97.92
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	97.86
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	97.85
PRK08582	139	hypothetical protein; Provisional	97.84
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	97.82
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.75
PRK07252	120	hypothetical protein; Provisional	97.74
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	97.68
PRK05054	644	exoribonuclease II; Provisional	97.68
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	97.68
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	97.67
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	97.67
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	97.62
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	97.6
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.58
PRK05807	136	hypothetical protein; Provisional	97.58
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.54
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	97.47
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.45
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	97.44
PRK08059	123	general stress protein 13; Validated	97.44
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.43
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	97.42
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.4
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.33
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	97.31
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	97.24
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	97.2
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	97.18
COG0557	706	VacB Exoribonuclease R [Transcription]	97.14
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	97.06
PRK03987	262	translation initiation factor IF-2 subunit alpha;	97.03
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.03
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	97.0
COG2183	780	Tex Transcriptional accessory protein [Transcripti	96.97
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	96.93
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	96.91
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	96.88
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	96.87
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.8
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	96.71
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	96.66
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	96.65
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	96.62
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	96.56
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.52
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	96.32
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.3
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	95.93
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	95.52
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	95.4
PF09876	103	DUF2103: Predicted metal-binding protein (DUF2103)	95.35
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	95.17
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.05
PRK11712	489	ribonuclease G; Provisional	94.96
PRK10811	1068	rne ribonuclease E; Reviewed	94.81
TIGR01953	341	NusA transcription termination factor NusA. This m	94.81
PHA02945	88	interferon resistance protein; Provisional	94.72
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	94.41
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	93.85
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	93.72
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	93.62
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	92.9
PRK11642	813	exoribonuclease R; Provisional	92.52
PRK12327	362	nusA transcription elongation factor NusA; Provisi	89.77
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	88.67
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	88.63
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	86.94
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	85.09
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	84.84
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	83.22
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	81.94
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	80.57

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

Probab=100.00  E-value=3e-38  Score=296.40  Aligned_cols=188  Identities=26%  Similarity=0.488  Sum_probs=171.6

Q ss_pred             hhcccCCCCEEEEEEEEEeCCCCEEEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEE
Q 026794           16 EIAKGLTGSIISVKVIQANEEMKKLVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLT   83 (233)
Q Consensus        16 ~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~~-------~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~   83 (233)
                      ++...++|+++.|+|+++|.+++++++|+|...       .+.+++.+++|+++.|+     +|||||+|+      |++
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            556678999999999999999999999999763       45678999999999999     999999997      799


Q ss_pred             EEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeee
Q 026794           84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNT  163 (233)
Q Consensus        84 Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~  163 (233)
                      ||+|+|+|||.++.+|+++|++||.|+|+|+++|.+++|++||+|++.+|||+ ..++.+++|+.        +.|+|++
T Consensus       217 GLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~-~i~~~~~~g~~--------v~G~Vt~  287 (541)
T COG0539         217 GLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWE-GIEKKYPVGDK--------VEGKVTN  287 (541)
T ss_pred             eEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHH-HHhhhcCCCCE--------EEEEEEE
Confidence            99999999999999999999999999999999999999999999999999996 45566898988        6799999


Q ss_pred             eccCCChhhhhhhhcccCCeeEE----Eeeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          164 IEPLPGLGAIFEELLQEDGIDDV----RITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       164 v~~~~g~~~~~~~l~~~~gv~gl----~~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      ++|      ||+|+++.+||+||    +++|.+...|    .+||+++|+|.++|++++||+|++|+..
T Consensus       288 i~~------~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~  350 (541)
T COG0539         288 LTD------YGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLK  350 (541)
T ss_pred             eec------CcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhh
Confidence            885      58999999999999    3899887766    6899999999999999999999999754

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

Probab=100.00  E-value=1.7e-37  Score=291.42  Aligned_cols=198  Identities=28%  Similarity=0.424  Sum_probs=182.4

Q ss_pred             CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEE
Q 026794            1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIH   72 (233)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~   72 (233)
                      |||.|+ .||+..+.      +||+|+++|+++|++++|++||+|++   +|+.+..++++|+.+.|+     +|||||+
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            789996 79999987      99999999999999999999999987   699999999999999999     9999999


Q ss_pred             EccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeec
Q 026794           73 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISD  152 (233)
Q Consensus        73 l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~  152 (233)
                      +.     +|++||+|+||+||.+...|++++++||.|.|+|+++|++++||+||+|++..|||..+.+. ++.|++    
T Consensus       297 i~-----~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~-~~~g~~----  366 (541)
T COG0539         297 IE-----EGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADK-HPVGDV----  366 (541)
T ss_pred             ec-----CCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhh-cCCCCe----
Confidence            98     59999999999999999889999999999999999999999999999999999999876665 898888    


Q ss_pred             CCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       153 ~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                          ++|.+.+++      ++++|+++++|++|+.    ++|.....+    ..|+++++++..+|.++.||+|++|+..
T Consensus       367 ----v~g~v~~~t------~~g~fv~le~gidG~vh~~d~sw~~~~~~~~~~k~Gd~v~~~vl~vd~~~~~isLgiKql~  436 (541)
T COG0539         367 ----VEGKVKSIT------DFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKERISLGIKQLE  436 (541)
T ss_pred             ----EEEEEeeec------ccceEEccCCCccceEEHHhcCccccCcHHHhhccCcEEEEEEEEEecccceeeeehhhhc
Confidence                789999888      5588899999999995    888765545    4699999999999999999999999876


Q ss_pred             e
Q 026794          225 C  225 (233)
Q Consensus       225 ~  225 (233)
                      .
T Consensus       437 ~  437 (541)
T COG0539         437 E  437 (541)
T ss_pred             c
Confidence            3

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=2.9e-32  Score=257.68  Aligned_cols=197  Identities=25%  Similarity=0.417  Sum_probs=170.5

Q ss_pred             CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCC----CEEEEEechh---hHhhhccCCCCCCEEEEE-----eee
Q 026794            1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM----KKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYG   68 (233)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~----~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G   68 (233)
                      |||+|. .+|...+.      +||.|.|+|+++|.++    +++.||+|++   +|+.+...+++|+++.|+     +||
T Consensus       235 ls~~~~-~~~~~~~~------vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G  307 (491)
T PRK13806        235 LSWSRV-QKADEAVS------VGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFG  307 (491)
T ss_pred             CCCccc-cChhHhcC------CCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCce
Confidence            355554 35555444      9999999999999876    4799999987   598999999999999999     999


Q ss_pred             EEEEEccCCCCccEEEEEEccccCc-ccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCC
Q 026794           69 AFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDG  147 (233)
Q Consensus        69 ~fV~l~~~~~~~gv~Glv~~sels~-~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~  147 (233)
                      +||++.     +|++||+|+|+++| .++.++.+.|++||.|+|+|+++|+++++|.||+|++.++||....+ .+++|+
T Consensus       308 ~fV~l~-----~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~-~~~vG~  381 (491)
T PRK13806        308 AFVEIL-----PGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAE-RFAPGT  381 (491)
T ss_pred             EEEEeC-----CCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhh-hCCCCC
Confidence            999997     48999999999999 57889999999999999999999999999999999999999976655 467788


Q ss_pred             eeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794          148 SVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL  219 (233)
Q Consensus       148 ~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls  219 (233)
                      +        ++|+|+++++      +|+|+++++|++||+    +++.+.+++    .+||+++++|.++|++++|++||
T Consensus       382 ~--------v~G~V~~i~~------~G~FV~l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls  447 (491)
T PRK13806        382 T--------VTGTVEKRAQ------FGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA  447 (491)
T ss_pred             E--------EEEEEEEEec------CceEEEcCCCcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEEE
Confidence            7        6799999985      478888899999995    666655433    68999999999999999999999


Q ss_pred             Ecccc
Q 026794          220 ARAGR  224 (233)
Q Consensus       220 ~r~~~  224 (233)
                      .|+..
T Consensus       448 ~~~~~  452 (491)
T PRK13806        448 PAGAA  452 (491)
T ss_pred             eehhh
Confidence            99653

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=4.5e-32  Score=268.68  Aligned_cols=196  Identities=26%  Similarity=0.437  Sum_probs=170.4

Q ss_pred             CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEE
Q 026794            1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIH   72 (233)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~   72 (233)
                      |||+|. .+|...+.      +||++.|+|+++|++++++.||+|+.   +|+.+.+.+++|++++|+     +||+||+
T Consensus       525 iS~~~v-~~~~~~~k------vGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVe  597 (863)
T PRK12269        525 MSWGHV-ARPREFVK------KGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIE  597 (863)
T ss_pred             cccccc-CCHHHhcc------CCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEE
Confidence            456664 45655443      89999999999999999999999976   588888999999999999     9999999


Q ss_pred             EccCCCCccEEEEEEccccCc-ccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeee
Q 026794           73 LRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVIS  151 (233)
Q Consensus        73 l~~~~~~~gv~Glv~~sels~-~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~  151 (233)
                      |.     +|++||+|+||++| .++.+|.+.|++||+|+|+|+++|.+++|++||+|++.+|||....+ .++.|++   
T Consensus       598 L~-----~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~-~~~vG~~---  668 (863)
T PRK12269        598 LA-----EGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEA-RYPVGAR---  668 (863)
T ss_pred             ec-----CCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHH-hCCCCCE---
Confidence            97     48999999999999 57899999999999999999999999999999999999999976544 5788888   


Q ss_pred             cCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc-----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR-----VVSQDLQLWLSNAPPSGKKFTLLARA  222 (233)
Q Consensus       152 ~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~-----~vg~~~~v~i~~~d~~~~ki~Ls~r~  222 (233)
                           ++|+|++++++      |+|+++++||+|+.    ++|.+...+     .+||.++++|.++|++++|++||.|+
T Consensus       669 -----v~G~V~~i~~~------G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~  737 (863)
T PRK12269        669 -----FTRRIVKVTNA------GAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQ  737 (863)
T ss_pred             -----EEEEEEEEecc------eEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEecc
Confidence                 67999999854      78888899999995    566443222     58999999999999999999999986


Q ss_pred             c
Q 026794          223 G  223 (233)
Q Consensus       223 ~  223 (233)
                      .
T Consensus       738 l  738 (863)
T PRK12269        738 L  738 (863)
T ss_pred             c
Confidence            5

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.98  E-value=1.2e-31  Score=252.05  Aligned_cols=188  Identities=22%  Similarity=0.396  Sum_probs=165.8

Q ss_pred             hcccCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEE
Q 026794           17 IAKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTG   84 (233)
Q Consensus        17 ~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~G   84 (233)
                      +++.++|++|.|+|+++|++++++.||+|..       .|+.+...+++|++++|+     +||+||+|+      |++|
T Consensus       160 ~~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlg------gv~G  233 (486)
T PRK07899        160 DLQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG------GVDG  233 (486)
T ss_pred             ChhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEE
Confidence            3445799999999999999999999999853       377788899999999999     999999996      7999


Q ss_pred             EEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeee
Q 026794           85 LVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTI  164 (233)
Q Consensus        85 lv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v  164 (233)
                      |||+|+++|.++.++.+.|++||.|+|+|+++|++++||.||+|++.++||..+.++ ++.|++        ++|+|+++
T Consensus       234 lv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~-~~vG~v--------v~G~V~~I  304 (486)
T PRK07899        234 LVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFART-HAIGQI--------VPGKVTKL  304 (486)
T ss_pred             EEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHh-cCCCCE--------EEEEEEEE
Confidence            999999999999999999999999999999999999999999999999999766554 567777        67999998


Q ss_pred             ccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          165 EPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       165 ~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      .+      +|+|+++.+|++||.    ++++++..+    .+||.++|+|.++|.+++|++||.|+...
T Consensus       305 ~~------fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~  367 (486)
T PRK07899        305 VP------FGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQANE  367 (486)
T ss_pred             ec------cEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEEEccc
Confidence            85      477888899999995    666665444    58999999999999999999999986543

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=99.97  E-value=2.2e-30  Score=256.74  Aligned_cols=200  Identities=18%  Similarity=0.296  Sum_probs=170.5

Q ss_pred             CCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEE
Q 026794            2 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHL   73 (233)
Q Consensus         2 ~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~l   73 (233)
                      ||.+-..+|...+.      +||+|+|+|+++|.+++++.||+|++   +|+.+.+++++|++++|+     +||+||++
T Consensus       612 s~~~~~~~p~~~~k------vGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l  685 (863)
T PRK12269        612 SWVKKTSKPSDMVK------IGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEM  685 (863)
T ss_pred             cCccccCCHHHcCC------CCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEe
Confidence            45322356666655      99999999999999999999999976   599999999999999999     99999999


Q ss_pred             ccCCCCccEEEEEEccccCcccc-cCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeec
Q 026794           74 RFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISD  152 (233)
Q Consensus        74 ~~~~~~~gv~Glv~~sels~~~~-~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~  152 (233)
                      .     +|++||||+|+++|.+. .++.+.|++||.|+|+|+++|++++||.||+|++..|||..+. +.++.|+.    
T Consensus       686 ~-----~gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~-~~~~vG~i----  755 (863)
T PRK12269        686 E-----EGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFA-NAYGVGST----  755 (863)
T ss_pred             C-----CCcEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHH-hhCCCCCE----
Confidence            8     48999999999999765 4556689999999999999999999999999999999997654 44778888    


Q ss_pred             CCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc-------cccCceEEEEeecCCCCCEEEEEEc
Q 026794          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR-------VVSQDLQLWLSNAPPSGKKFTLLAR  221 (233)
Q Consensus       153 ~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~-------~vg~~~~v~i~~~d~~~~ki~Ls~r  221 (233)
                          ++|+|+++++      +|+|+++++||+|+.    +++++...+       .+||.++++|.++|++++||+||.|
T Consensus       756 ----V~GkV~~v~~------~GvFVeL~~gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~LSlk  825 (863)
T PRK12269        756 ----VEGEVSSVTD------FGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVR  825 (863)
T ss_pred             ----EEEEEEEEec------CeEEEEcCCCeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEEEEEe
Confidence                6799999885      477888899999995    666654322       5899999999999999999999999


Q ss_pred             ccceee
Q 026794          222 AGRCKR  227 (233)
Q Consensus       222 ~~~~vq  227 (233)
                      +.++.+
T Consensus       826 ~~~~~~  831 (863)
T PRK12269        826 DYQRKV  831 (863)
T ss_pred             chhhHH
Confidence            776543

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=99.97  E-value=1.1e-29  Score=240.18  Aligned_cols=187  Identities=24%  Similarity=0.415  Sum_probs=162.6

Q ss_pred             cccCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEE
Q 026794           18 AKGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL   85 (233)
Q Consensus        18 ~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Gl   85 (233)
                      ++.++|+++.|+|+++|++++++.+|+++.       .|+.+...+++|++++|+     +||+||+|+     .|++||
T Consensus       155 ~~~~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~-----~gv~g~  229 (491)
T PRK13806        155 PESYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELA-----PGVEGM  229 (491)
T ss_pred             hHHcCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcC-----CCcEEE
Confidence            345699999999999999999999999975       366777889999999998     999999997     389999


Q ss_pred             EEccccCcccccCcccccCCCCEEEEEEEEEeCCC----CeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCe
Q 026794           86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK----SRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNS  161 (233)
Q Consensus        86 v~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~----~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v  161 (233)
                      ||+|+++|.++.++.+.|++||.|+|+|+++|.++    +|++||+|++.++||....+ .++.|++        +.|+|
T Consensus       230 v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~-~~~~G~~--------v~G~V  300 (491)
T PRK13806        230 VHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGD-RLKAGDK--------VTGKV  300 (491)
T ss_pred             EEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhc-cCCCCCE--------EEEEE
Confidence            99999999999999999999999999999999876    48999999999999975544 4677887        67999


Q ss_pred             eeeccCCChhhhhhhhcccCCeeEEE----eec-cccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          162 NTIEPLPGLGAIFEELLQEDGIDDVR----ITR-QGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       162 ~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~-~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      +.+.+      +|+|+++.+|++|+.    ++| .++.++    .+||.++++|.++|++++|+.||.|+..
T Consensus       301 ~~v~~------~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~  366 (491)
T PRK13806        301 VRLAP------FGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAE  366 (491)
T ss_pred             EEEeC------ceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecc
Confidence            99885      478888899999995    566 334333    6899999999999999999999998653

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.96  E-value=3.6e-28  Score=233.31  Aligned_cols=183  Identities=26%  Similarity=0.454  Sum_probs=161.3

Q ss_pred             cCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEE
Q 026794           20 GLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVH   87 (233)
Q Consensus        20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~   87 (233)
                      .++|+++.|+|+++|++++++.+|+|++       .|+.++..+++|++++|+     +||+||+++      |++||+|
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            5699999999999999999999999975       266778899999999999     999999996      7999999


Q ss_pred             ccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccC
Q 026794           88 VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL  167 (233)
Q Consensus        88 ~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~  167 (233)
                      +++++|.++.++.+.|++||.|+|+|+++|.+++++.||+|++.++||....+ .++.|++        ++|+|+++.+ 
T Consensus       230 ~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~-~~~~G~~--------v~g~V~~i~~-  299 (565)
T PRK06299        230 ITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEK-KYPVGSK--------VKGKVTNITD-  299 (565)
T ss_pred             HHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHh-hCCCCCE--------EEEEEEEEeC-
Confidence            99999999999999999999999999999999999999999999999976544 4777887        6799999875 


Q ss_pred             CChhhhhhhhcccCCeeEEE----eeccc-cccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          168 PGLGAIFEELLQEDGIDDVR----ITRQG-FEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       168 ~g~~~~~~~l~~~~gv~gl~----~~~~~-~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                           +|+|+++.+|+.|+.    ++|.. ..+|    .+||+++|+|.++|++++++.||.|+.
T Consensus       300 -----~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~ls~k~~  359 (565)
T PRK06299        300 -----YGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQC  359 (565)
T ss_pred             -----CeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEehHHh
Confidence                 477888899999995    45432 3333    589999999999999999999999865

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.96  E-value=7.9e-28  Score=221.44  Aligned_cols=186  Identities=23%  Similarity=0.385  Sum_probs=162.0

Q ss_pred             ccCCCCEEEEEEEEEeCCCCEEEEEechh-------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEE
Q 026794           19 KGLTGSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLV   86 (233)
Q Consensus        19 ~~~vG~~v~~~Vi~id~~~~~i~lS~k~~-------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv   86 (233)
                      +.++|+.+.|+|+++|++++++.+|+|..       .|..++..+++|++++|+     ++|+||+++      +++|||
T Consensus       146 ~~~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~------~v~g~v  219 (390)
T PRK06676        146 SDFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG------GVDGLV  219 (390)
T ss_pred             HHcCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC------CeEEEE
Confidence            34699999999999999999999999974       356677889999999998     999999996      799999


Q ss_pred             EccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeecc
Q 026794           87 HVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEP  166 (233)
Q Consensus        87 ~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~  166 (233)
                      |+|+++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++.++||....+ .++.|++        +.|.|+.+.+
T Consensus       220 ~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~-~~~~G~~--------v~g~V~~i~~  290 (390)
T PRK06676        220 HISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEE-KLPEGDV--------IEGTVKRLTD  290 (390)
T ss_pred             EHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchh-hhcCCcE--------EEEEEEEEeC
Confidence            999999999999999999999999999999999999999999999999976555 4667777        6799998875


Q ss_pred             CCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          167 LPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       167 ~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                            +|+|+++.+|++|+.    +++.+..++    .+||.++++|.++|+++++++||+|+...
T Consensus       291 ------~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~  351 (390)
T PRK06676        291 ------FGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEE  351 (390)
T ss_pred             ------ceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEeccc
Confidence                  477788899999994    555554433    58999999999999999999999986543

>TIGR00717 rpsA ribosomal protein S1

Probab=99.95  E-value=3.4e-27  Score=224.15  Aligned_cols=180  Identities=23%  Similarity=0.465  Sum_probs=158.2

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCc
Q 026794           22 TGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW   93 (233)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~   93 (233)
                      +||.+.|+|+++|++++++.||++++   +|+.+.+.+++|+++.|+     ++|+||+++     .+++||+|+++++|
T Consensus       320 vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~-----~~v~glv~~s~ls~  394 (516)
T TIGR00717       320 KGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELE-----GGIDGLIHLSDISW  394 (516)
T ss_pred             CCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEECC-----CCCEEEEEHHHCcC
Confidence            99999999999999999999999875   588888889999999999     999999997     48999999999999


Q ss_pred             ccc-cCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhh
Q 026794           94 DLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA  172 (233)
Q Consensus        94 ~~~-~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~  172 (233)
                      .+. .++...|++||.|.|+|+++|.++++|.||+|++.+|||....+ .++.|++        ++|.|..+++      
T Consensus       395 ~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~-~~~~G~~--------v~g~V~~v~~------  459 (516)
T TIGR00717       395 DKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAA-KYKVGSV--------VKGKVTEIKD------  459 (516)
T ss_pred             cccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhh-ccCcceE--------EEEEEEEEec------
Confidence            764 56778899999999999999999999999999999999975544 3567777        6799999885      


Q ss_pred             hhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794          173 IFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR  221 (233)
Q Consensus       173 ~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r  221 (233)
                      +|+|+++.+|++|+.    +++++.+++    .+||.++++|.++|.+++|++||.|
T Consensus       460 ~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~k  516 (516)
T TIGR00717       460 FGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK  516 (516)
T ss_pred             ceEEEEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            477888899999995    566554333    6899999999999999999999986

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.

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.95  E-value=5e-27  Score=225.42  Aligned_cols=184  Identities=29%  Similarity=0.517  Sum_probs=161.6

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCc
Q 026794           22 TGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW   93 (233)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~   93 (233)
                      +|+.|.|+|+++|++++++.||+|+.   +|..+...+++|+++.|+     ++|+||+|+     .+++||+|+++++|
T Consensus       334 ~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~-----~~v~g~i~~s~l~~  408 (565)
T PRK06299        334 VGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLE-----GGIDGLVHLSDISW  408 (565)
T ss_pred             CCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceEEEECC-----CCCEEEEEHHHcCc
Confidence            89999999999999999999999976   588888889999999999     999999997     38999999999999


Q ss_pred             ccc-cCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhh
Q 026794           94 DLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA  172 (233)
Q Consensus        94 ~~~-~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~  172 (233)
                      .+. .++.+.|++||.|+|+|+++|.++++|.||+|++..+||....+. ++.|++        +.|+|.++.+      
T Consensus       409 ~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~-~~~G~v--------V~G~V~~v~~------  473 (565)
T PRK06299        409 DKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKK-HKKGSI--------VTGTVTEVKD------  473 (565)
T ss_pred             cccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhh-cCCCCE--------EEEEEEEEec------
Confidence            887 889999999999999999999999999999999999999766554 577887        6799999885      


Q ss_pred             hhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          173 IFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       173 ~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      +|+|+.+.+|+.|++    ++..++.++    .+||.+++++.++|.+++|++||.+....
T Consensus       474 ~G~fV~l~~gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS~k~~~~  534 (565)
T PRK06299        474 KGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDE  534 (565)
T ss_pred             CceEEecCCCcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEccccCEEEEEeeehhh
Confidence            477788889999995    444444332    68999999999999999999999986544

>TIGR00717 rpsA ribosomal protein S1

Probab=99.95  E-value=8.3e-27  Score=221.53  Aligned_cols=196  Identities=28%  Similarity=0.425  Sum_probs=166.2

Q ss_pred             CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE-----eeeEEEE
Q 026794            1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIH   72 (233)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~   72 (233)
                      |+|++. .+|+..+.      +|+.+.|+|+.+|++++++.+|+|..   +|+.+...+++|+++.|+     ++|+||+
T Consensus       219 ~s~~~~-~~~~~~~~------vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~  291 (516)
T TIGR00717       219 MSWKRV-KHPSEYVK------VGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVE  291 (516)
T ss_pred             cCCCCC-CCHHHhcc------CCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccCCCEEEEEEEEeeCCcEEEE
Confidence            355553 45554444      89999999999999999999999975   588888889999999998     9999999


Q ss_pred             EccCCCCccEEEEEEccccCcc-cccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeee
Q 026794           73 LRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVIS  151 (233)
Q Consensus        73 l~~~~~~~gv~Glv~~sels~~-~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~  151 (233)
                      ++     ++++||+|+|+++|. ...++.+.|++||.|+|+|+++|++++++.||+|++..+||....+. ++.|+.   
T Consensus       292 l~-----~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~-~~~G~~---  362 (516)
T TIGR00717       292 IE-----EGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEK-HPVGDR---  362 (516)
T ss_pred             eC-----CCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHh-CCCCCE---
Confidence            97     489999999999986 46778888999999999999999999999999999999999766554 677777   


Q ss_pred             cCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccc-cc----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794          152 DSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFE-KR----VVSQDLQLWLSNAPPSGKKFTLLARA  222 (233)
Q Consensus       152 ~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~-~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~  222 (233)
                           +.|+|.++.+      +|+|+++.+|++|+.    ++|.... ++    .+||.+.++|.++|.+++|+.||+|.
T Consensus       363 -----v~g~V~~v~~------~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~  431 (516)
T TIGR00717       363 -----VTGKIKKITD------FGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ  431 (516)
T ss_pred             -----EEEEEEEEec------ceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeecc
Confidence                 6799998874      578888899999995    5554321 11    58999999999999999999999997


Q ss_pred             c
Q 026794          223 G  223 (233)
Q Consensus       223 ~  223 (233)
                      .
T Consensus       432 ~  432 (516)
T TIGR00717       432 L  432 (516)
T ss_pred             c
Confidence            4

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.

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

Probab=99.94  E-value=3.6e-26  Score=222.55  Aligned_cols=187  Identities=27%  Similarity=0.462  Sum_probs=163.2

Q ss_pred             hcccCCCCEEEEEEEEEeCCCCE-EEEEechhh-------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEE
Q 026794           17 IAKGLTGSIISVKVIQANEEMKK-LVFSEKDAV-------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLT   83 (233)
Q Consensus        17 ~~~~~vG~~v~~~Vi~id~~~~~-i~lS~k~~~-------~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~   83 (233)
                      +++.++|+.+.|+|+++|+++++ +.+|+|...       ++..++.+++|+++.|+     ++|+||+++      +++
T Consensus       428 d~~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~------gv~  501 (647)
T PRK00087        428 DLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIG------GVD  501 (647)
T ss_pred             CHHHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEEC------CEE
Confidence            34456999999999999999988 999998762       45677789999999999     999999995      799


Q ss_pred             EEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeee
Q 026794           84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNT  163 (233)
Q Consensus        84 Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~  163 (233)
                      ||+|+|+++|.++.++.+.|++||.|+|+|+++|++++++.||+|++.++||....++ ++.|+.        +.|.|..
T Consensus       502 Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~-~~~G~~--------v~g~V~~  572 (647)
T PRK00087        502 GLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEK-YPVGSI--------VLGKVVR  572 (647)
T ss_pred             EEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhh-ccCCeE--------EEEEEEE
Confidence            9999999999999999999999999999999999999999999999999999765544 566776        6799999


Q ss_pred             eccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          164 IEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       164 v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      +.++      |+|+++.+|+.|+.    +++.+++.+    .+||.+++++.++|.+++|+.||.|+..
T Consensus       573 i~~~------G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~  635 (647)
T PRK00087        573 IAPF------GAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVE  635 (647)
T ss_pred             EECC------eEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence            8854      77788899999994    566555444    6899999999999999999999998754

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.93  E-value=5.3e-25  Score=197.87  Aligned_cols=174  Identities=15%  Similarity=0.260  Sum_probs=147.7

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccC
Q 026794           22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (233)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels   92 (233)
                      +|+++.|+|+++|.+++++.||+|+.    .|+.+.+.++.|++++|+     ++|+||+++      |++||||+|++|
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            89999999999999999999999975    488888888899999998     899999996      899999999999


Q ss_pred             cccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhh
Q 026794           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGA  172 (233)
Q Consensus        93 ~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~  172 (233)
                      |.+..   +.+ +|+.+.++|+++|+++++|.||+|.+..++   ... .++.|++        +.|+|+++.++     
T Consensus       152 ~~~~~---~~~-vG~~i~~kVl~id~~~~~i~lS~K~~~~~~---~~~-~~k~G~v--------v~G~V~~I~~~-----  210 (318)
T PRK07400        152 TRKPK---EEL-VGEELPLKFLEVDEERNRLVLSHRRALVER---KMN-RLEVGEV--------VVGTVRGIKPY-----  210 (318)
T ss_pred             ccCCc---ccc-CCCEEEEEEEEEEcccCEEEEEhhHhhhhh---hhc-cCCCCCE--------EEEEEEEEECC-----
Confidence            96533   334 899999999999999999999999765543   222 3667777        67999998854     


Q ss_pred             hhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          173 IFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       173 ~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                       |+|+++ .|++|+.    ++++++.++    .+||.+++++.++|.++++++||.|+..
T Consensus       211 -G~fV~i-~gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~  268 (318)
T PRK07400        211 -GAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLE  268 (318)
T ss_pred             -eEEEEE-CCEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccc
Confidence             777777 4899994    777776555    6899999999999999999999999765

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.93  E-value=4.1e-25  Score=207.89  Aligned_cols=178  Identities=17%  Similarity=0.316  Sum_probs=154.1

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccC
Q 026794           22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (233)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels   92 (233)
                      +|+.|+|+|+++|.+++++.||+|++    .|+.+.+.++.|++++|+     ++|+||++       |++||||.|+++
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            99999999999999999999999976    477777777899999998     89999999       489999999999


Q ss_pred             cccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccc----cChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCC
Q 026794           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE----EDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLP  168 (233)
Q Consensus        93 ~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~----~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~  168 (233)
                      +.++.++.++  +||.|+|+|+++|.+++++.||+|.+.    .++|....+. ++.|++        ++|+|.+++++ 
T Consensus       155 ~~~~~~~~~~--vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~-lk~G~i--------v~G~V~~i~~~-  222 (486)
T PRK07899        155 MRRVRDLQPY--IGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQ-LQKGQV--------RKGVVSSIVNF-  222 (486)
T ss_pred             ccccCChhhc--CCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHh-ccCCCE--------EEEEEEEEECC-
Confidence            9988888774  799999999999999999999999643    3678666554 677887        77999998854 


Q ss_pred             ChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          169 GLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       169 g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                           |+|+++. |++|+.    ++|.++.++    .+||.++++|.++|++++||+||.|+..
T Consensus       223 -----G~FVdlg-gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~  280 (486)
T PRK07899        223 -----GAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQ  280 (486)
T ss_pred             -----eEEEEEC-CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence                 7778774 899994    788777666    4899999999999999999999999653

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.91  E-value=1.7e-23  Score=192.74  Aligned_cols=180  Identities=18%  Similarity=0.325  Sum_probs=152.9

Q ss_pred             CCCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEcccc
Q 026794           21 LTGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV   91 (233)
Q Consensus        21 ~vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sel   91 (233)
                      .+|+.|.|+|+.+|.+++++.||++..    .|+.+...++.|++++|+     ++|+||+++      |++||||++++
T Consensus        64 ~vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~------G~~gflp~~el  137 (390)
T PRK06676         64 KVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVE------GVRGFIPASLI  137 (390)
T ss_pred             CCCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHc
Confidence            399999999999999999999999974    488888888999999999     899999996      68999999999


Q ss_pred             CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecccc----ChhhHHhhhhcCCCCeeeecCCccccCCeeeeccC
Q 026794           92 SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE----DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL  167 (233)
Q Consensus        92 s~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~----dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~  167 (233)
                      +|.+..++.++  +||.++|+|+++|.+++++.||+|.+..    ++|...... ++.|++        ++|+|..+.++
T Consensus       138 ~~~~~~~~~~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~-~~~G~~--------v~g~V~~v~~~  206 (390)
T PRK06676        138 STRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSS-LKEGDV--------VEGTVARLTDF  206 (390)
T ss_pred             CCccCCChHHc--CCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhh-CCCCCE--------EEEEEEEEecc
Confidence            99998888774  8999999999999999999999998765    466554443 567777        67999988754


Q ss_pred             CChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          168 PGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       168 ~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                            |+|+++ .|++|+.    +++.++.++    .+||.++++|.++|.+++++.||.|+..
T Consensus       207 ------G~fV~l-~~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~  264 (390)
T PRK06676        207 ------GAFVDI-GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTL  264 (390)
T ss_pred             ------eEEEEe-CCeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence                  667777 4899994    666555544    5799999999999999999999998543

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.88  E-value=3.2e-22  Score=179.87  Aligned_cols=111  Identities=37%  Similarity=0.649  Sum_probs=106.5

Q ss_pred             cCCCCEEEEEEEEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc
Q 026794           20 GLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD   94 (233)
Q Consensus        20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~   94 (233)
                      .++|+.+.|+|+++|++++++.||+|.+.++.....+++|+++.|+     +||+||++.      |++||+|+|+++|+
T Consensus       158 ~~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i~------gv~Gllhisels~~  231 (318)
T PRK07400        158 ELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIG------GVSGLLHISEISHE  231 (318)
T ss_pred             ccCCCEEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEEC------CEEEEEEHHHcccc
Confidence            4699999999999999999999999998888888999999999999     999999996      79999999999999


Q ss_pred             cccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhh
Q 026794           95 LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLL  136 (233)
Q Consensus        95 ~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~  136 (233)
                      ++.++.+.|++||.|+|+|+++|.++++|.||+|++++|||+
T Consensus       232 ~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~  273 (318)
T PRK07400        232 HIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGD  273 (318)
T ss_pred             cccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhh
Confidence            999999999999999999999999999999999999999995

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

Probab=99.87  E-value=2.1e-21  Score=189.27  Aligned_cols=178  Identities=21%  Similarity=0.362  Sum_probs=152.4

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccC
Q 026794           22 TGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (233)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels   92 (233)
                      +|++++|+|+++|.+++++.||++..    .|+.+.+.++.|+++.|+     ++|+||+++      +++||+|.++++
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            99999999999999999999999865    477888888999999998     889999997      699999999999


Q ss_pred             cccccCcccccCCCCEEEEEEEEEeCCCCe-EEEEEecccc----ChhhHHhhhhcCCCCeeeecCCccccCCeeeeccC
Q 026794           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSR-ITLSIKQLEE----DPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPL  167 (233)
Q Consensus        93 ~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~r-i~LS~k~~~~----dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~  167 (233)
                      +.+..++..+  +||.++|+|+++|.++++ +.+|+|.+..    ++|....+. ++.|+.        +.|+|..+.+ 
T Consensus       423 ~~~~~d~~~~--vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~-l~~G~i--------V~g~V~~v~~-  490 (647)
T PRK00087        423 LGYVEDLSEY--KGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNS-LEEGDV--------VEGEVKRLTD-  490 (647)
T ss_pred             ccccCCHHHh--CCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHh-CCCCCE--------EEEEEEEEeC-
Confidence            9998888764  899999999999999998 9999999753    566555554 566777        6799998875 


Q ss_pred             CChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          168 PGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       168 ~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                           +|+|+++ +|++|+.    ++|.++.++    .+||.++++|.++|++++++.||.|..
T Consensus       491 -----~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~  548 (647)
T PRK00087        491 -----FGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKL  548 (647)
T ss_pred             -----CcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeecc
Confidence                 4778888 7999995    566555444    589999999999999999999999853

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.79  E-value=3.4e-19  Score=159.02  Aligned_cols=101  Identities=25%  Similarity=0.386  Sum_probs=89.0

Q ss_pred             cCCC-CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           54 SRVN-VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        54 ~~~~-~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      ++++ +|+++.|+     +||+||+|.+++   |++||||+||+||+++.++++++++||.|.|+|+++|+++++|.||+
T Consensus        12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~---gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~   88 (319)
T PTZ00248         12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYD---DIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSK   88 (319)
T ss_pred             hhCCCCCCEEEEEEEEEeCCeEEEEecCCC---CcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEe
Confidence            4555 89999998     999999996433   79999999999999999999999999999999999999999999999


Q ss_pred             eccccChhhHHhhhhcCCCCeeeecCCccccCCeeeecc
Q 026794          128 KQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEP  166 (233)
Q Consensus       128 k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~  166 (233)
                      |++.++||..+.++ ++.|+.        +.|.|..+..
T Consensus        89 K~v~~~pw~~~~e~-~~~g~~--------v~~~V~~ia~  118 (319)
T PTZ00248         89 KRVSPEDIEACEEK-FSKSKK--------VHSIMRHIAQ  118 (319)
T ss_pred             eecccchHHHHHHh-CcCCCE--------EEEEEEEchh
Confidence            99999999766655 777887        5678877753

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

Probab=99.76  E-value=5.6e-19  Score=135.91  Aligned_cols=75  Identities=45%  Similarity=0.751  Sum_probs=71.2

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .+++|++++|+     +|||||+|++     |-.|||||||++++|++|+.+++++||.|+|+|+++|. +++|+||+|+
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            47899999998     9999999984     78999999999999999999999999999999999997 9999999999


Q ss_pred             cccChh
Q 026794          130 LEEDPL  135 (233)
Q Consensus       130 ~~~dp~  135 (233)
                      ++..|-
T Consensus        76 ~~e~pe   81 (129)
T COG1098          76 LEEEPE   81 (129)
T ss_pred             hhhCcc
Confidence            999885

>PRK08582 hypothetical protein; Provisional

Probab=99.61  E-value=3e-15  Score=119.69  Aligned_cols=77  Identities=40%  Similarity=0.679  Sum_probs=71.9

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .+++|++|.|+     +||+||+|.     ++++||||+|+++|+++.++.+.|++||.|+|+|+++|. +++|.||+|+
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            36899999998     999999998     489999999999999999999999999999999999997 5999999999


Q ss_pred             cccChhhH
Q 026794          130 LEEDPLLE  137 (233)
Q Consensus       130 ~~~dp~~~  137 (233)
                      +.++||.+
T Consensus        76 ~~~~~~~~   83 (139)
T PRK08582         76 AKDRPKRQ   83 (139)
T ss_pred             cccCchhh
Confidence            99999964

>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=99.61  E-value=2.2e-15  Score=107.91  Aligned_cols=66  Identities=26%  Similarity=0.423  Sum_probs=60.9

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCc---ccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~---~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      +++|+++.|+     +||+||+|.     ++++|++|++++||+++.++   .+.|++||.++|+|+++|+++++|.||
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     999999997     48999999999999997775   588999999999999999999999986

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.56  E-value=1.4e-14  Score=143.59  Aligned_cols=88  Identities=27%  Similarity=0.423  Sum_probs=78.5

Q ss_pred             HhhhccCCCCCCEEE-EE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCe
Q 026794           49 WNKYSSRVNVEDIFV-GR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR  122 (233)
Q Consensus        49 ~~~~~~~~~~G~vv~-g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~r  122 (233)
                      .+.+....++|++|. |+     +||+||+|.     +|++||||+|+++|+++.++.+.|++||.|+|+|+++|. ++|
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            345556789999995 45     999999998     489999999999999999999999999999999999997 899


Q ss_pred             EEEEEeccccChhhHHhhhh
Q 026794          123 ITLSIKQLEEDPLLETLEKV  142 (233)
Q Consensus       123 i~LS~k~~~~dp~~~~~~~~  142 (233)
                      |.||+|++.++||++..++.
T Consensus       818 I~LSlK~l~~~Pw~~~~~~~  837 (891)
T PLN00207        818 LRLSRRALLPEANSEKSSQK  837 (891)
T ss_pred             EEEEEeccccCchhhhhhhh
Confidence            99999999999998766543

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

Probab=99.54  E-value=2.5e-14  Score=101.53  Aligned_cols=69  Identities=43%  Similarity=0.731  Sum_probs=65.0

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      ++++|+++.|+     ++|+||+|+     .+++||||++++++.+..++.+.|++||+++|+|+++|.+++++.||+|
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            47899999999     899999998     3899999999999999999999999999999999999999999999986

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=99.54  E-value=2.2e-14  Score=104.42  Aligned_cols=71  Identities=31%  Similarity=0.389  Sum_probs=66.4

Q ss_pred             hccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        52 ~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      .+.++++|+++.|+     +||+||++.+     +++||+|+++++++++.++.+.|++||.|+|+|+++|.+++++.||
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 NFSDLKPGMVVHGYVRNITPYGVFVEFLG-----GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS   82 (83)
T ss_pred             hHHhCCCCCEEEEEEEEEeeceEEEEcCC-----CCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEe
Confidence            35668999999999     9999999973     8999999999999999999999999999999999999999999998


Q ss_pred             E
Q 026794          127 I  127 (233)
Q Consensus       127 ~  127 (233)
                      +
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.

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

Probab=99.54  E-value=4.2e-14  Score=100.71  Aligned_cols=67  Identities=33%  Similarity=0.541  Sum_probs=60.4

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      ++.|++++|+     +||+||++.+    .+.+||+|+|+++|.++.++.+.|++||+|+|+|+++|.++ ++.||+
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l~~----~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~   72 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKIPG----CRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL   72 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEECC----CCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence            3589999998     9999999962    23799999999999999999999999999999999999865 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.

>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=99.54  E-value=2.5e-14  Score=101.72  Aligned_cols=66  Identities=20%  Similarity=0.305  Sum_probs=61.1

Q ss_pred             CCCCCEEEEE-----e-eeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           56 VNVEDIFVGR-----D-YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        56 ~~~G~vv~g~-----~-~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      +++|+++.|+     + ||+|++|.     ++.+|++|+|+++|++..++.+.|++||.|+|+|+++|.  +++.||+|
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            4789999998     4 89999998     489999999999999999999999999999999999984  89999986

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.

>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=99.54  E-value=3.2e-14  Score=101.56  Aligned_cols=65  Identities=17%  Similarity=0.305  Sum_probs=60.7

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccc--ccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~--~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      |++++|+     ++|+||+|.     ++++|+||+++++|.+  ..++.+.|++||.|+|+|+++|+++++|.||+|
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            7888888     999999997     4899999999999874  889999999999999999999999999999987

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.

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

Probab=99.52  E-value=9.6e-14  Score=98.86  Aligned_cols=71  Identities=34%  Similarity=0.489  Sum_probs=64.4

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      ++.|+++.|+     ++|+||++.+.   .+++||+|+|+++++++.++.+.|++||.|+|+|+++|.+++++.||+|+
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            3679999998     99999999631   15999999999999999999999999999999999999999999999985

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

>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=99.51  E-value=6e-14  Score=98.55  Aligned_cols=65  Identities=29%  Similarity=0.387  Sum_probs=60.9

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      |+++.|+     ++|+||++.+     +++||+|+|++++++..++.+.|++||.++|+|+++|.+++++.||+|
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 GLKTHGTIVKVKPNGCIVSFYN-----NVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECC-----CCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            6788888     9999999983     799999999999999999999999999999999999999999999986

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.

>PHA02945 interferon resistance protein; Provisional

Probab=99.51  E-value=1e-13  Score=100.96  Aligned_cols=75  Identities=31%  Similarity=0.396  Sum_probs=68.1

Q ss_pred             cCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEEcccc--CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVSEV--SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        54 ~~~~~G~vv~g~----~~G~fV~l~~~~~~~gv~Glv~~sel--s~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      .-+.+|+++.|+    +||+||.|.+++   |.+||||+|++  +..++++ ++++ .||++.|||+++|+.++.|.||+
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            446899999999    999999999754   79999999955  9999999 9999 99999999999999999999999


Q ss_pred             eccccC
Q 026794          128 KQLEED  133 (233)
Q Consensus       128 k~~~~d  133 (233)
                      |+..++
T Consensus        82 K~V~~~   87 (88)
T PHA02945         82 KRMCRH   87 (88)
T ss_pred             eEcccC
Confidence            997653

>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=99.50  E-value=1.3e-13  Score=97.68  Aligned_cols=68  Identities=26%  Similarity=0.418  Sum_probs=63.4

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      +++|+++.|+     ++|+||+|+     .+++|++|++++++++..++.+.|++||.++|+|+++|.+++++.||+|
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            4789999998     999999998     4899999999999999888899999999999999999999999999985

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.

>PRK07252 hypothetical protein; Provisional

Probab=99.49  E-value=1.6e-13  Score=107.03  Aligned_cols=75  Identities=36%  Similarity=0.657  Sum_probs=69.4

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccc
Q 026794           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (233)
Q Consensus        57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~  131 (233)
                      ++|+++.|+     ++|+||+|.     .+++||+|+++++++++.++.+.|++||.|+|+|+++|.+++++.||+|+++
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            579999998     999999997     3799999999999999999999999999999999999999999999999998


Q ss_pred             cCh-hh
Q 026794          132 EDP-LL  136 (233)
Q Consensus       132 ~dp-~~  136 (233)
                      +++ |.
T Consensus        77 ~~~~~~   82 (120)
T PRK07252         77 EEKQHF   82 (120)
T ss_pred             cCcccc
Confidence            865 64

>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=99.48  E-value=1.8e-13  Score=96.07  Aligned_cols=64  Identities=22%  Similarity=0.437  Sum_probs=59.9

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      |++++|+     ++|+||++.     .+++||+|+++++|.+..++.+.|++||.++|+|+++|.+++++.||+
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     389999999999999999999999999999999999999999999985

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=99.48  E-value=1.6e-13  Score=97.34  Aligned_cols=57  Identities=26%  Similarity=0.402  Sum_probs=54.1

Q ss_pred             eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      +||+||+|.     +|++||+|+|++++.+..++.+.|++||.++|+|+++|+.++++.||+
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            799999997     389999999999999999999999999999999999999999999985

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=99.47  E-value=3.5e-13  Score=96.47  Aligned_cols=68  Identities=16%  Similarity=0.166  Sum_probs=61.3

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .+++|+++.|+     ++|+||+++-    .|++||+|.++++|.      +.+++||.+.|+|+++|.+++++.||+|+
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            36899999999     9999999951    279999999999986      77999999999999999999999999998


Q ss_pred             ccc
Q 026794          130 LEE  132 (233)
Q Consensus       130 ~~~  132 (233)
                      +.+
T Consensus        71 ~~~   73 (74)
T cd05694          71 SKV   73 (74)
T ss_pred             ccc
Confidence            765

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.

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

Probab=99.45  E-value=4.2e-13  Score=94.61  Aligned_cols=68  Identities=34%  Similarity=0.562  Sum_probs=62.9

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccc
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~  131 (233)
                      |+++.|+     ++|+||++.     .+++|++|+++++++++.++.+.|++||.++|+|+++|.+++++.||+|+++
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~-----~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~~   73 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLG-----DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE   73 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeC-----CCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEcC
Confidence            6788887     999999998     3799999999999999999999999999999999999999999999999763

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.

>PRK08059 general stress protein 13; Validated

Probab=99.45  E-value=5.1e-13  Score=104.65  Aligned_cols=77  Identities=45%  Similarity=0.796  Sum_probs=72.2

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      .+.+++|+++.|+     ++|+||++.     .+++||+|+++++++++.++.+.|++||.|+|+|+++|.+++++.||+
T Consensus         2 ~~~~k~G~iv~G~V~~i~~~G~fV~i~-----~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lsl   76 (123)
T PRK08059          2 MSQYEVGSVVTGKVTGIQPYGAFVALD-----EETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSI   76 (123)
T ss_pred             cccCCCCCEEEEEEEEEecceEEEEEC-----CCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEE
Confidence            3568899999999     999999998     479999999999999999999999999999999999999999999999


Q ss_pred             eccccCh
Q 026794          128 KQLEEDP  134 (233)
Q Consensus       128 k~~~~dp  134 (233)
                      |++..+|
T Consensus        77 k~~~~~~   83 (123)
T PRK08059         77 RATEEAP   83 (123)
T ss_pred             EEcccCc
Confidence            9999888

>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=99.44  E-value=7.4e-13  Score=94.19  Aligned_cols=70  Identities=41%  Similarity=0.643  Sum_probs=64.1

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (233)
Q Consensus        57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~  130 (233)
                      ++|+++.|+     ++|+||++.+    .+.+|++|++++++++..++.+.|++||.|+|+|+++|.+++++.||+|+.
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            368999998     9999999973    269999999999999999999999999999999999999999999999975

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.

>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=99.44  E-value=7.2e-13  Score=95.50  Aligned_cols=72  Identities=35%  Similarity=0.666  Sum_probs=62.6

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc-cCcccccCCCCEEEEEEEEEeCCCCeEEEEEecccc
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE  132 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~-~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~  132 (233)
                      |+++.|+     +||+||+|.+.-  .+.+||+|+++++|++. .++.+.|++||.|+|+|+++|  ++++.||+|++++
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  15899999999999986 899999999999999999999  8999999999877


Q ss_pred             Ch
Q 026794          133 DP  134 (233)
Q Consensus       133 dp  134 (233)
                      +.
T Consensus        77 ~~   78 (79)
T cd05684          77 DT   78 (79)
T ss_pred             CC
Confidence            53

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.

>PRK05807 hypothetical protein; Provisional

Probab=99.44  E-value=5.4e-13  Score=106.29  Aligned_cols=70  Identities=46%  Similarity=0.722  Sum_probs=65.8

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .+++|++++|+     +||+||+|.      +..||||+|++++.++.++.++|++||.|+|+|+++|. +++|.||+|+
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            36789999999     999999995      68999999999999999999999999999999999997 7999999999


Q ss_pred             cc
Q 026794          130 LE  131 (233)
Q Consensus       130 ~~  131 (233)
                      +.
T Consensus        75 ~~   76 (136)
T PRK05807         75 AM   76 (136)
T ss_pred             cc
Confidence            86

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

Probab=99.44  E-value=1.3e-13  Score=118.73  Aligned_cols=77  Identities=35%  Similarity=0.623  Sum_probs=72.3

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      -+.+|++|-|+     +||+||.|.+++   |++||+|+||++.+++.+++++++.||.+-|+||++|+.++.|.||+|.
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     999999999876   6999999999999999999999999999999999999999999999999


Q ss_pred             cccCh
Q 026794          130 LEEDP  134 (233)
Q Consensus       130 ~~~dp  134 (233)
                      ..++.
T Consensus        85 V~~~q   89 (269)
T COG1093          85 VTEHQ   89 (269)
T ss_pred             CCHHH
Confidence            87664

>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=99.43  E-value=3.6e-13  Score=94.24  Aligned_cols=63  Identities=29%  Similarity=0.470  Sum_probs=58.8

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      |+++.|+     ++|+||+|.     .+++||+|++++++++..++.+.|++||.++|+|+++|++++++.||
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     37999999999999999999999999999999999999999999886

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.

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

Probab=99.43  E-value=5.1e-13  Score=93.35  Aligned_cols=63  Identities=37%  Similarity=0.748  Sum_probs=57.2

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCc-ccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~-~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      |+++.|+     +||+||+|.     ++++||+|+++++| .+..++.+.|++||.|+|+|+++|.+++++.||
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            6778887     999999998     38999999999997 577889999999999999999999999999875

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.

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

Probab=99.38  E-value=2.2e-12  Score=90.65  Aligned_cols=65  Identities=32%  Similarity=0.532  Sum_probs=60.6

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      |+++.|+     ++|+||++.     .+.+|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+|
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     899999997     3799999999999999999999999999999999999988899999986

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=99.37  E-value=2.9e-12  Score=88.66  Aligned_cols=64  Identities=44%  Similarity=0.830  Sum_probs=59.3

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      |+++.|+     ++|+||++.     .+.+||+|.++++++++.++.+.|++||.++|+|+++|. ++++.||+|
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            6778887     999999998     379999999999999999999999999999999999998 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=99.37  E-value=2.7e-12  Score=90.61  Aligned_cols=66  Identities=39%  Similarity=0.674  Sum_probs=58.9

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc-cccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~-~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      +++|+++.|+     +||+||+|.     ++++||+|+++++|. +..++.+.|++||.|+|+|+++|.+++++.||
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            5789999998     999999998     379999999999985 55577788999999999999999999999874

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.

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

Probab=99.37  E-value=1.2e-12  Score=132.09  Aligned_cols=124  Identities=23%  Similarity=0.355  Sum_probs=106.1

Q ss_pred             CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechhhHh------hhccCCCCCCEEEEE-----eeeE
Q 026794            1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWN------KYSSRVNVEDIFVGR-----DYGA   69 (233)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~------~~~~~~~~G~vv~g~-----~~G~   69 (233)
                      +++.|++.||...+...  ..+|..+..+|+.++.+.+++.+++|.+..+      .-.....+|.++.|+     ++||
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 LPKEHLSDHPLQPPLRD--FKVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGA  615 (1710)
T ss_pred             cChHhhhhcccccccce--eeeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCe
Confidence            46778877777655432  2478888889999999999999999987532      234456789999999     9999


Q ss_pred             EEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccc
Q 026794           70 FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (233)
Q Consensus        70 fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~  131 (233)
                      ||.+.+     |++||.|.|+++++++.++++.|.+||++.|+|.++|.+++||.||+|+..
T Consensus       616 ~V~F~g-----~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~  672 (1710)
T KOG1070|consen  616 FVTFTG-----GLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASS  672 (1710)
T ss_pred             EEEecC-----ccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhh
Confidence            999985     899999999999999999999999999999999999999999999999864

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

Probab=99.32  E-value=8.4e-12  Score=109.53  Aligned_cols=77  Identities=36%  Similarity=0.614  Sum_probs=70.4

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .+++|+++.|+     ++|+||+|.+++   |++||+|+|+++++++.++.+.|++||.|.|+|+++|.+++++.||+|+
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            46889999998     999999997422   6999999999999999999999999999999999999999999999998


Q ss_pred             cccCh
Q 026794          130 LEEDP  134 (233)
Q Consensus       130 ~~~dp  134 (233)
                      +.++.
T Consensus        82 v~~~e   86 (262)
T PRK03987         82 VNEHQ   86 (262)
T ss_pred             cccch
Confidence            87765

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.31  E-value=6.3e-12  Score=122.65  Aligned_cols=111  Identities=23%  Similarity=0.448  Sum_probs=85.6

Q ss_pred             CCCchhHhhhcccCCCCEEE--------------EEEEEEeCCCCEEEEEechhh--------Hhhhcc--CCCCCCEEE
Q 026794            8 KEPQKSIHEIAKGLTGSIIS--------------VKVIQANEEMKKLVFSEKDAV--------WNKYSS--RVNVEDIFV   63 (233)
Q Consensus         8 ~~p~~~~~~~~~~~vG~~v~--------------~~Vi~id~~~~~i~lS~k~~~--------~~~~~~--~~~~G~vv~   63 (233)
                      ..|+....+...+.+|+.|-              ++ |+++. .+.+.++-....        .+.+..  .+++|++|+
T Consensus       575 ~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~-Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~  652 (719)
T TIGR02696       575 YAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAE-ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFL  652 (719)
T ss_pred             CCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCE-EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEE
Confidence            45665555555555665553              23 77775 677777765431        233444  489999999


Q ss_pred             EE-----eeeEEEEEccCCCCccEEEEEEccccC----cccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           64 GR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS----WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        64 g~-----~~G~fV~l~~~~~~~gv~Glv~~sels----~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      |+     +||+||+|.     +|.+||+|+|+++    |.++.++.++|++||.|+|||+++|. ++||+|+
T Consensus       653 GkV~~I~dfGaFVel~-----~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~  718 (719)
T TIGR02696       653 GTVVKTTAFGAFVSLL-----PGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV  718 (719)
T ss_pred             EEEEEEECceEEEEec-----CCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence            99     999999997     4899999999996    46899999999999999999999995 8899986

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.

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

Probab=99.31  E-value=2.3e-11  Score=123.13  Aligned_cols=185  Identities=17%  Similarity=0.183  Sum_probs=147.5

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechhh-----------HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEE
Q 026794           22 TGSIISVKVIQANEEMKKLVFSEKDAV-----------WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL   85 (233)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~~-----------~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Gl   85 (233)
                      .++.+.+++|.++..++.+.+|.+...           --+..++++.|+++.|.     +.|+|+.+.     ++++++
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            579999999999998888999988321           12356789999999999     899999998     699999


Q ss_pred             EEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHH--hhhhcCCCCeeeecCCccccCCeee
Q 026794           86 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET--LEKVIPQDGSVISDSSSMSSSNSNT  163 (233)
Q Consensus        86 v~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~--~~~~~~~g~~~~~~~~~~~~g~v~~  163 (233)
                      +|+|+++..+...++..|++||.|.++|++++...+|+.|++|.....--...  ....+..|+.        ..|.+..
T Consensus      1190 v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~--------~~g~v~~ 1261 (1710)
T KOG1070|consen 1190 VPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDR--------EDGTVEV 1261 (1710)
T ss_pred             EEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhcccc--------ccceEEE
Confidence            99999999999999999999999999999999999999999998544322111  1223566777        6799998


Q ss_pred             eccCCChhhhhhhhcccCCe--eEE----Eeeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          164 IEPLPGLGAIFEELLQEDGI--DDV----RITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       164 v~~~~g~~~~~~~l~~~~gv--~gl----~~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      +.|+      |.|+++..++  .|+    +++.++.+..    ..|+.+...+.+.+.++++|+|.+++...
T Consensus      1262 ~~~~------G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~~~V~a~~lk~~~ek~rIsl~~k~s~~ 1327 (1710)
T KOG1070|consen 1262 VDPF------GLFIKLDVTVNMVGLCHISEEADDRGENITALYYAGDRVKACVLKEDSEKKRISLGLKSSYL 1327 (1710)
T ss_pred             ecCC------ceEEEecCcceecccccceeecchhhhhcccceeccceeeeEeeeccchhhhhhhhhhhhcc
Confidence            8865      5566666665  676    3444443322    56899999999999999999999776543

>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=99.30  E-value=5.6e-12  Score=95.39  Aligned_cols=70  Identities=30%  Similarity=0.478  Sum_probs=62.4

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc-------------------cCcccccCCCCEEEE
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDEVRV  111 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~-------------------~~~~~~~~~Gd~V~v  111 (233)
                      +++|+++.|+     ++|+||.|.+     +++|++|+++++|++.                   .++.+.|++||.|+|
T Consensus         1 L~~G~vV~G~V~~v~~~gl~v~L~~-----g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~   75 (100)
T cd05693           1 LSEGMLVLGQVKEITKLDLVISLPN-----GLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRC   75 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECCC-----CcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEE
Confidence            5789999999     9999999983     8999999999999763                   347889999999999


Q ss_pred             EEEEEeCC---CCeEEEEEecc
Q 026794          112 KVIKIDRE---KSRITLSIKQL  130 (233)
Q Consensus       112 kVi~vd~e---~~ri~LS~k~~  130 (233)
                      +|+++|.+   +++|.||+|..
T Consensus        76 kVi~~d~~~~~~~~i~LSlr~~   97 (100)
T cd05693          76 KVVSLDKSKSGKKRIELSLEPE   97 (100)
T ss_pred             EEEEccCCcCCCcEEEEEecHH
Confidence            99999987   79999999864

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.

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

Probab=99.29  E-value=1.5e-11  Score=85.76  Aligned_cols=62  Identities=27%  Similarity=0.545  Sum_probs=56.2

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      |++++|+     ++|+||+++      |++||+|.|++++.+..++.+.  +||.++|+|+++|.+++++.||+|
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     999999994      7999999999999988877774  799999999999999999999985

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.

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

Probab=99.29  E-value=1.6e-11  Score=84.97  Aligned_cols=63  Identities=44%  Similarity=0.865  Sum_probs=58.4

Q ss_pred             CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        58 ~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      +|+++.|+     ++|+||++.      +.+|++|.+++++.+..++.+.|++||.|+|+|+++|.+++++.||
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     999999996      6999999999999999999999999999999999999999999886

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.

>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=99.29  E-value=1e-11  Score=85.73  Aligned_cols=63  Identities=38%  Similarity=0.670  Sum_probs=57.7

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      |+++.|+     ++|+||++.     ++.+||+|.+++++.++.++.+.|++||.++|+|+++|.+++++.||
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     999999997     47999999999999999999999999999999999999999999886

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.

>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=99.27  E-value=1.5e-11  Score=86.01  Aligned_cols=61  Identities=20%  Similarity=0.328  Sum_probs=54.2

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      |++++|+     ++|+||+|.+     +++||+|.++++..+..  .+.|++||.++|+|+++|+++++|.||
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 GMLVNARVKKVLSNGLILDFLS-----SFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcC-----CceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            6788888     9999999973     79999999999866544  778999999999999999999999886

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.

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

Probab=99.26  E-value=2.2e-11  Score=89.00  Aligned_cols=70  Identities=23%  Similarity=0.363  Sum_probs=62.3

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCc----ccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW----DLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~----~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~L  125 (233)
                      .+++|+++.|+     ++|+||++.     ++.+|++|++++++    .+..++.+.+++||.++|+|+++|++ +++.|
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            35899999999     999999998     48999999999997    45577888899999999999999975 99999


Q ss_pred             EEecc
Q 026794          126 SIKQL  130 (233)
Q Consensus       126 S~k~~  130 (233)
                      |+|+.
T Consensus        77 S~~~~   81 (86)
T cd05789          77 HTRSL   81 (86)
T ss_pred             EeCcc
Confidence            99875

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".

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

Probab=99.25  E-value=3e-11  Score=83.73  Aligned_cols=63  Identities=44%  Similarity=0.783  Sum_probs=57.5

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      |+++.|+     ++|+||++.     .+.+||+|.++++++++.++.+.|++||.++|+|+++|. ++++.||+
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     999999997     379999999999999998999999999999999999998 99999985

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=99.23  E-value=4.5e-11  Score=117.67  Aligned_cols=93  Identities=34%  Similarity=0.615  Sum_probs=78.0

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc
Q 026794           31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (233)
Q Consensus        31 i~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~   97 (233)
                      ++++ +++.+.++....        ..+.+...+++|+++.|+     +||+||+|.     ++.+||+|+|+++|.++.
T Consensus       587 idi~-d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~-----~~~~GllhiSels~~~v~  660 (693)
T PRK11824        587 IDIE-DDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEIL-----PGKDGLVHISEIADERVE  660 (693)
T ss_pred             cccC-CCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEEC-----CCCEEEEEeeeccCcccc
Confidence            4444 356666665432        134455678999999999     999999998     489999999999999999


Q ss_pred             CcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (233)
Q Consensus        98 ~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~  130 (233)
                      ++.+.|++||.|+|+|+++|.+ +++.||+|.+
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 9999999976

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

Probab=99.19  E-value=1.2e-10  Score=80.37  Aligned_cols=67  Identities=43%  Similarity=0.725  Sum_probs=61.5

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      ++|+++.|+     ++|+||+++     +++.|++|.+++++.+..++.+.|++||.++|+|+++|.+++++.||++
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            468999998     899999998     3799999999999998888889999999999999999998899999975

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

Probab=99.19  E-value=9.8e-11  Score=86.55  Aligned_cols=70  Identities=26%  Similarity=0.404  Sum_probs=59.8

Q ss_pred             cCCCCCCEEEEE-----ee--eEEEEEccCCCCccEEEEEEccccCc---ccccCcccccCCCCEEEEEEEEEeCCCCeE
Q 026794           54 SRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSW---DLIQDIRDILNEGDEVRVKVIKIDREKSRI  123 (233)
Q Consensus        54 ~~~~~G~vv~g~-----~~--G~fV~l~~~~~~~gv~Glv~~sels~---~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri  123 (233)
                      .+++.|++|.|+     +|  ||||+|.     .|.+||||+||+||   .++.++.+.+++||.|.|+|++......-.
T Consensus         3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~-----~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~   77 (88)
T cd04453           3 REPIVGNIYLGRVKKIVPGLQAAFVDIG-----LGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGP   77 (88)
T ss_pred             CcCCCCCEEEEEEEEeccCCcEEEEEeC-----CCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCc
Confidence            357899999999     65  9999998     37999999999999   678889999999999999999987766555


Q ss_pred             EEEEe
Q 026794          124 TLSIK  128 (233)
Q Consensus       124 ~LS~k  128 (233)
                      .|+.+
T Consensus        78 ~lt~~   82 (88)
T cd04453          78 RLTTN   82 (88)
T ss_pred             eEEEE
Confidence            55544

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=99.16  E-value=2.4e-10  Score=82.39  Aligned_cols=66  Identities=30%  Similarity=0.610  Sum_probs=56.2

Q ss_pred             CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc-----------CcccccCCCCEEEEEEEEEeCCCC
Q 026794           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREKS  121 (233)
Q Consensus        58 ~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~-----------~~~~~~~~Gd~V~vkVi~vd~e~~  121 (233)
                      +|++++|+     ++|+||++..    ++++|++|.++++++++.           +....|++||.|+|+|+++|.+++
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     9999999972    379999999999976532           345789999999999999999999


Q ss_pred             eEEEEE
Q 026794          122 RITLSI  127 (233)
Q Consensus       122 ri~LS~  127 (233)
                      ++.|++
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=99.13  E-value=1.4e-10  Score=111.59  Aligned_cols=94  Identities=36%  Similarity=0.631  Sum_probs=81.8

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc
Q 026794           31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (233)
Q Consensus        31 i~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~   97 (233)
                      ++++ +.+.+.++-...        ..+.+...+++|++|.|+     +||+||+|.     +|-+||||+|++++.++.
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 667777665542        245677889999999999     999999998     589999999999999999


Q ss_pred             CcccccCCCCEEEEEEEEEeCCCCeEEEEEeccc
Q 026794           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (233)
Q Consensus        98 ~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~  131 (233)
                      ...+.+++||.+.||++++|. ++|+.||+|...
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            999999999999999999995 899999999764

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=99.11  E-value=4.3e-10  Score=94.26  Aligned_cols=101  Identities=23%  Similarity=0.315  Sum_probs=82.8

Q ss_pred             CCCEEEEEE---EEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE-----eeeEEEEEccCC--C---CccEEEEEEc
Q 026794           22 TGSIISVKV---IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPD--G---LYHLTGLVHV   88 (233)
Q Consensus        22 vG~~v~~~V---i~id~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~--~---~~gv~Glv~~   88 (233)
                      .+..+.+.+   +++|.+++++.+.    +|..+...+++|++|.|+     ++|+||+|...+  +   ..+++|++|+
T Consensus        29 ~~~~i~as~~G~~~id~~~~~Isv~----P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~  104 (189)
T PRK09521         29 DNGEVYASVVGKVFIDDINRKISVI----PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHI  104 (189)
T ss_pred             eCCEEEEEeeEEEEEcCCCCEEEEe----cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEh
Confidence            456666554   5668888888885    466666788999999999     999999996321  0   1268999999


Q ss_pred             cccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           89 SEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        89 sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      +++++.+..++.+.|++||.|+|+|++++   +++.||+|+
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            99999999999999999999999999998   789999985

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

Probab=99.08  E-value=5.7e-10  Score=80.88  Aligned_cols=69  Identities=22%  Similarity=0.208  Sum_probs=63.5

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~  130 (233)
                      +++|+++.|+     +.+++|++.     .+.+|++|.++++..+..++.+.|++||.+.|+|+++|.+ +++.||++..
T Consensus         4 p~~GdiV~G~V~~v~~~~~~V~i~-----~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~~   77 (82)
T cd04454           4 PDVGDIVIGIVTEVNSRFWKVDIL-----SRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADN   77 (82)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEeC-----CCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECCC
Confidence            5899999999     899999997     3799999999999988889999999999999999999986 8999999873

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".

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=99.07  E-value=2.2e-10  Score=111.66  Aligned_cols=75  Identities=37%  Similarity=0.648  Sum_probs=70.0

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      +..+++|++++|+     +||+||+|+     -+.+|+||+|++|..++.+|.+++++||.|+|+|+++|..++||.|||
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     999999997     478999999999999999999999999999999999999999999999


Q ss_pred             ecccc
Q 026794          128 KQLEE  132 (233)
Q Consensus       128 k~~~~  132 (233)
                      +.-..
T Consensus       728 r~~~~  732 (780)
T COG2183         728 RLDEE  732 (780)
T ss_pred             eccCC
Confidence            97544

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=99.04  E-value=7.3e-10  Score=109.05  Aligned_cols=88  Identities=34%  Similarity=0.649  Sum_probs=73.2

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc
Q 026794           31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (233)
Q Consensus        31 i~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~   97 (233)
                      |+++. ++.+.++....        ..+.+...+++|++|.|+     +||+||++.     ++.+||+|+|+++|.++.
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            66764 56776665432        133455678999999999     999999998     489999999999999999


Q ss_pred             CcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794           98 DIRDILNEGDEVRVKVIKIDREKSRITL  125 (233)
Q Consensus        98 ~~~~~~~~Gd~V~vkVi~vd~e~~ri~L  125 (233)
                      ++.+.|++||.|+|+|+++|. +++++|
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 787764

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).

>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=99.00  E-value=1.1e-09  Score=77.04  Aligned_cols=58  Identities=21%  Similarity=0.260  Sum_probs=51.8

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccc--ccCcccccCCCCEEEEEEEEEeCCCC
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKS  121 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~--~~~~~~~~~~Gd~V~vkVi~vd~e~~  121 (233)
                      |+++.|+     ++|+||+++     .+++|++|++++++++  ..++.+.|++||.|+|+|+++|.++.
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~-----~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~   65 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLA-----DNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT   65 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeC-----CCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence            6788887     899999998     4899999999999985  78899999999999999999997543

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.

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

Probab=99.00  E-value=1.1e-09  Score=74.10  Aligned_cols=56  Identities=45%  Similarity=0.781  Sum_probs=52.2

Q ss_pred             eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      ++|+||++.     .+.+|++|.+++++.+..++.+.|++||.|+|+|+++|.+++++.||
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     47999999999999988888999999999999999999999998875

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.

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

Probab=98.98  E-value=3.7e-09  Score=75.95  Aligned_cols=61  Identities=34%  Similarity=0.578  Sum_probs=54.3

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      ...++.|+.++|+     +||+||++.     .+.+||+|.|++.        +.|++||+++++|.++ .+++++.||+
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            4568999999999     999999998     3799999999973        5599999999999999 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.

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

Probab=98.97  E-value=3e-09  Score=79.93  Aligned_cols=65  Identities=31%  Similarity=0.584  Sum_probs=56.9

Q ss_pred             eeeEEEEEccCCCCccEEEEEEccccCcccccC-----------cccccCCCCEEEEEEEEEeCCC-----CeEEEEEec
Q 026794           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-----------IRDILNEGDEVRVKVIKIDREK-----SRITLSIKQ  129 (233)
Q Consensus        66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~-----------~~~~~~~Gd~V~vkVi~vd~e~-----~ri~LS~k~  129 (233)
                      ++|+||++.      +++||+|++++++++...           ....|++||.|+|+|.++|.+.     .++.||+|+
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            999999996      599999999999887653           3477999999999999999764     589999999


Q ss_pred             cccChhh
Q 026794          130 LEEDPLL  136 (233)
Q Consensus       130 ~~~dp~~  136 (233)
                      ....||.
T Consensus        86 ~~~g~~~   92 (99)
T cd04460          86 PGLGKLE   92 (99)
T ss_pred             CCCCcHH
Confidence            9999974

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.

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

Probab=98.89  E-value=7.6e-09  Score=86.00  Aligned_cols=129  Identities=22%  Similarity=0.452  Sum_probs=87.2

Q ss_pred             CCCCCCCCCCchhHhhhcc-cCCCCEEE-----EEEEEEeC-CCCEEEEEe----chhhHhhhccCCCCCCEEEEE----
Q 026794            1 MSPSHSCKEPQKSIHEIAK-GLTGSIIS-----VKVIQANE-EMKKLVFSE----KDAVWNKYSSRVNVEDIFVGR----   65 (233)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~-~~vG~~v~-----~~Vi~id~-~~~~i~lS~----k~~~~~~~~~~~~~G~vv~g~----   65 (233)
                      ++|+++.+++.....+.++ .+.|+.+.     +.|.++.. +.+++.-.-    -......+.-+...|++++|+    
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            4577776666655544433 34444332     34444433 344443111    011233344567789999999    


Q ss_pred             -eeeEEEEEccCCCCccEEEEEEccccCccccc-----------CcccccCCCCEEEEEEEEEe-----CCCCeEEEEEe
Q 026794           66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKID-----REKSRITLSIK  128 (233)
Q Consensus        66 -~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~-----------~~~~~~~~Gd~V~vkVi~vd-----~e~~ri~LS~k  128 (233)
                       ++|+||+++      .++|++|.+++.+++..           +....|+.||.|+++|+++|     ++..+|.+|+|
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      59999999999876542           23467999999999999998     56789999999


Q ss_pred             ccccChh
Q 026794          129 QLEEDPL  135 (233)
Q Consensus       129 ~~~~dp~  135 (233)
                      +...-|+
T Consensus       167 ~~~LG~~  173 (179)
T TIGR00448       167 QPLLGKL  173 (179)
T ss_pred             cCcCCcc
Confidence            9766664

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

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.80  E-value=6.1e-09  Score=98.26  Aligned_cols=98  Identities=18%  Similarity=0.275  Sum_probs=79.8

Q ss_pred             cccCCCCEEEEEEEEEeCCCCEEEEE-echh--------hHhhhccCCC--CCCEEEEE-----eeeEEEEEccCCCCcc
Q 026794           18 AKGLTGSIISVKVIQANEEMKKLVFS-EKDA--------VWNKYSSRVN--VEDIFVGR-----DYGAFIHLRFPDGLYH   81 (233)
Q Consensus        18 ~~~~vG~~v~~~Vi~id~~~~~i~lS-~k~~--------~~~~~~~~~~--~G~vv~g~-----~~G~fV~l~~~~~~~g   81 (233)
                      ++..+|+.+.+.|...+  .+++.++ .|+.        .++.++..|+  .|++++|+     ++|+||+++      +
T Consensus        85 ~~~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLg------g  156 (470)
T PRK09202         85 PDAEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLG------R  156 (470)
T ss_pred             ccccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEEC------C
Confidence            44579999999998877  3444333 2332        2446777887  99999999     899999996      7


Q ss_pred             EEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCC--eEEEEEec
Q 026794           82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ  129 (233)
Q Consensus        82 v~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~--ri~LS~k~  129 (233)
                      ++||+|.++++      |.+.|++||.|+|.|++++.+++  +|.||.+.
T Consensus       157 vea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~  200 (470)
T PRK09202        157 AEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH  200 (470)
T ss_pred             eEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence            99999999985      78889999999999999999877  89999875

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

Probab=98.78  E-value=3.7e-08  Score=82.30  Aligned_cols=128  Identities=21%  Similarity=0.433  Sum_probs=86.1

Q ss_pred             CCCCCCCCCCchhHhhhccc-CCCCEE-----EEEEEEEeC-CCCEEEEEec----hhhHhhhccCCCCCCEEEEE----
Q 026794            1 MSPSHSCKEPQKSIHEIAKG-LTGSII-----SVKVIQANE-EMKKLVFSEK----DAVWNKYSSRVNVEDIFVGR----   65 (233)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~-~vG~~v-----~~~Vi~id~-~~~~i~lS~k----~~~~~~~~~~~~~G~vv~g~----   65 (233)
                      ++|+++.+++.....+.++. +.|+.+     -+.|++++. +.+++.-.--    .+....+..+...|+++.|+    
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            35777766666555444433 334433     245555554 3444431111    11234445568899999999    


Q ss_pred             -eeeEEEEEccCCCCccEEEEEEccccCccccc-----------CcccccCCCCEEEEEEEEEeCCC-----CeEEEEEe
Q 026794           66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREK-----SRITLSIK  128 (233)
Q Consensus        66 -~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~-----------~~~~~~~~Gd~V~vkVi~vd~e~-----~ri~LS~k  128 (233)
                       ++|+||+++      .++|++|.+++.+++..           +....+++||.|+++|.+++.+.     .+|.+|++
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             999999996      59999999999876532           34567999999999999999754     38999999


Q ss_pred             ccccCh
Q 026794          129 QLEEDP  134 (233)
Q Consensus       129 ~~~~dp  134 (233)
                      +.-.-+
T Consensus       167 ~~~LG~  172 (187)
T PRK08563        167 QPGLGK  172 (187)
T ss_pred             CCCCCc
Confidence            854444

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

Probab=98.73  E-value=7.8e-09  Score=97.41  Aligned_cols=76  Identities=29%  Similarity=0.458  Sum_probs=69.4

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .+..|.+|+|+     +||+||+|.     ++..||+|+|+|+..++.+|++.+++||.|.+|.++.|+ ++.+.+|.|.
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            56777888888     999999998     588999999999999999999999999999999999997 7788889999


Q ss_pred             cccChhh
Q 026794          130 LEEDPLL  136 (233)
Q Consensus       130 ~~~dp~~  136 (233)
                      +.++|-.
T Consensus       739 lLp~p~~  745 (760)
T KOG1067|consen  739 LLPDPAT  745 (760)
T ss_pred             hcCCccc
Confidence            9999954

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.73  E-value=3.8e-08  Score=85.26  Aligned_cols=70  Identities=27%  Similarity=0.370  Sum_probs=62.6

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc----cCcccccCCCCEEEEEEEEEeCCCCeEE
Q 026794           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRIT  124 (233)
Q Consensus        54 ~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~----~~~~~~~~~Gd~V~vkVi~vd~e~~ri~  124 (233)
                      ..+++||+|.|+     ++|+||+|.     .+..|++|+++++|.++    .++++.|++||.|+|+|++++. .+++.
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            456999999999     999999997     37899999999999987    7899999999999999999996 44699


Q ss_pred             EEEec
Q 026794          125 LSIKQ  129 (233)
Q Consensus       125 LS~k~  129 (233)
                      ||+|+
T Consensus       133 LS~k~  137 (235)
T PRK04163        133 LTLKG  137 (235)
T ss_pred             EEEcC
Confidence            99975

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=98.71  E-value=9.4e-10  Score=98.65  Aligned_cols=100  Identities=13%  Similarity=0.132  Sum_probs=84.0

Q ss_pred             CCCCCCCCCCchhHhhhcccCCCCEEEEEEEEEeCCCCEEEEEechh---hHhhhccCCCCCCEEEEE------eeeEEE
Q 026794            1 MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA---VWNKYSSRVNVEDIFVGR------DYGAFI   71 (233)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~---~~~~~~~~~~~G~vv~g~------~~G~fV   71 (233)
                      |||.|. ++|+..+.      +||++.|+|+.+|+++++|.||.|+.   +|+.+...++.|++++|+      +||+|+
T Consensus        52 lS~~ri-~~i~d~vk------vGd~v~vkVl~VD~ekg~IdLS~K~v~~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~  124 (319)
T PTZ00248         52 LSKRRI-RSINKLIR------VGRHEVVVVLRVDKEKGYIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSV  124 (319)
T ss_pred             hccccc-CCHHHhcC------CCCEEEEEEEEEeCCCCEEEEEeeecccchHHHHHHhCcCCCEEEEEEEEchhhcCCCH
Confidence            578775 78887776      99999999999999999999999986   599999999999999999      699999


Q ss_pred             E------EccCCCCccEEEEEEccccCcccccCcccccC---CCCEEEEE
Q 026794           72 H------LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILN---EGDEVRVK  112 (233)
Q Consensus        72 ~------l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~---~Gd~V~vk  112 (233)
                      +      ..     +..++|.|+.++....+.++.+.|+   +++.+..+
T Consensus       125 eely~~i~~-----pl~~~~gh~y~af~~~v~~~~evl~~l~i~~ev~~~  169 (319)
T PTZ00248        125 EELYTKIIW-----PLYKKYGHALDALKEALTNPDNVFEGLDIPEEVKES  169 (319)
T ss_pred             HHHHHHHHH-----HHHHhcCCHHHHHHHHhcCchhhhccCCCCHHHHHH
Confidence            8      33     4789999999998888888877765   55544433

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

Probab=98.68  E-value=1.1e-07  Score=66.48  Aligned_cols=59  Identities=17%  Similarity=0.281  Sum_probs=49.7

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEEEE
Q 026794           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITLSI  127 (233)
Q Consensus        57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~--~ri~LS~  127 (233)
                      +.|++++|+     ++|+||+++      +.+|++|.+|++.      .+.|++||.++|.|++++.++  .+|.||.
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig------~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lSr   67 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLG------KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILSR   67 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcC------CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence            468999998     889999996      5999999999973      456899999999999999654  4677773

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.

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=98.61  E-value=1.1e-07  Score=68.84  Aligned_cols=70  Identities=24%  Similarity=0.327  Sum_probs=64.2

Q ss_pred             ccCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEE-ccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           53 SSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        53 ~~~~~~G~vv~g~----~~G~fV~l~~~~~~~gv~Glv~-~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      ..-+++|+++.|.    +.|+||.|.+    ++++|+|. .+|++.+++.++.+.+ +|..+.|+|+.+|.++|.|.||.
T Consensus        11 y~~P~v~dvv~~Vv~i~d~~~YV~Lle----Y~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         11 YVFPNINEVTKGIVFVKDNIFYVKLID----YGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             EecCCCCeEEEEEEEEeccEEEEEEec----CccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence            4457899999987    9999999986    67999998 9999999999999999 99999999999999999999985

>TIGR02063 RNase_R ribonuclease R

Probab=98.60  E-value=1.8e-07  Score=92.80  Aligned_cols=70  Identities=27%  Similarity=0.535  Sum_probs=59.6

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc-----------cCcccccCCCCEEEEEEEEEe
Q 026794           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKID  117 (233)
Q Consensus        54 ~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~-----------~~~~~~~~~Gd~V~vkVi~vd  117 (233)
                      -..++|++++|+     +||+||+|.+    ++++||+|+|+++++++           .+....|++||.|+|+|.++|
T Consensus       623 l~~~iG~~~~g~V~~v~~fGifV~L~~----~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd  698 (709)
T TIGR02063       623 MSEKIGEEFEGVISGVTSFGLFVELEN----NTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKAD  698 (709)
T ss_pred             hhccCCcEEEEEEEEEEeCCEEEEecC----CceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEe
Confidence            345789999998     9999999973    36999999999997653           234567999999999999999


Q ss_pred             CCCCeEEEEE
Q 026794          118 REKSRITLSI  127 (233)
Q Consensus       118 ~e~~ri~LS~  127 (233)
                      .++++|.|++
T Consensus       699 ~~~~~I~~~l  708 (709)
T TIGR02063       699 LDTGKIDFEL  708 (709)
T ss_pred             cccCeEEEEE
Confidence            9999999986

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.

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

Probab=98.57  E-value=2.5e-08  Score=77.26  Aligned_cols=65  Identities=17%  Similarity=0.080  Sum_probs=52.5

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      |+.++|+++.+++      ||||++++.|=+||.    ++...++.-    .+||+|+|+|.++|. ++|++||+|+...
T Consensus         6 G~~l~GkItgI~~------yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~~~e   78 (129)
T COG1098           6 GSKLKGKITGITP------YGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRKLEE   78 (129)
T ss_pred             cceEEEEEEeeEe------cceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHHhhh
Confidence            3338899998885      589999999999993    455445433    689999999999997 9999999998765

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

Probab=98.53  E-value=3.2e-07  Score=75.93  Aligned_cols=82  Identities=27%  Similarity=0.529  Sum_probs=65.4

Q ss_pred             HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc----------C-cccccCCCCEEEEE
Q 026794           49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----------D-IRDILNEGDEVRVK  112 (233)
Q Consensus        49 ~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~----------~-~~~~~~~Gd~V~vk  112 (233)
                      ...+.-++..|+++.|.     +||+||.++      ..+||+|.|++.++++.          . ...++++||.|++|
T Consensus        72 f~al~fkP~~gEVV~GeVv~~~~~G~fV~ig------p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~R  145 (183)
T COG1095          72 FRALVFKPFRGEVVEGEVVEVVEFGAFVRIG------PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRAR  145 (183)
T ss_pred             EEEEEEEeccccEEEEEEEEEeecceEEEec------cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEE
Confidence            44556678889999998     999999997      69999999999988542          1 23369999999999


Q ss_pred             EEEEeCCC-----CeEEEEEeccccC--hhh
Q 026794          113 VIKIDREK-----SRITLSIKQLEED--PLL  136 (233)
Q Consensus       113 Vi~vd~e~-----~ri~LS~k~~~~d--p~~  136 (233)
                      |+..+...     .+|.+++|+.-..  +|.
T Consensus       146 Iv~~s~~~~~~~~~~I~lTmrq~~LGklew~  176 (183)
T COG1095         146 IVGVSLKSRRPRESKIGLTMRQPGLGKLEWI  176 (183)
T ss_pred             EEEEecccCccccceEEEEeccccCCcchhh
Confidence            99998654     6899999985443  464

>TIGR01953 NusA transcription termination factor NusA

Probab=98.53  E-value=2.7e-07  Score=83.96  Aligned_cols=98  Identities=16%  Similarity=0.273  Sum_probs=73.4

Q ss_pred             cccCCCCEEEEEEEEEeCCCCEEEEE-ech--------hhHhhhccCC--CCCCEEEEE-----eee-EEEEEccCCCCc
Q 026794           18 AKGLTGSIISVKVIQANEEMKKLVFS-EKD--------AVWNKYSSRV--NVEDIFVGR-----DYG-AFIHLRFPDGLY   80 (233)
Q Consensus        18 ~~~~vG~~v~~~Vi~id~~~~~i~lS-~k~--------~~~~~~~~~~--~~G~vv~g~-----~~G-~fV~l~~~~~~~   80 (233)
                      ++..+|+.+.+.+..-+  -+++.++ .|+        +.++.++..|  +.|++++|+     +.| +||+++      
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            55679999998875433  2333333 233        1255666677  599999999     546 699996      


Q ss_pred             cEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCC--CCeEEEEEec
Q 026794           81 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDRE--KSRITLSIKQ  129 (233)
Q Consensus        81 gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e--~~ri~LS~k~  129 (233)
                      +++|++|.+|..      +.+.|++||.++|.|++++.+  ..+|.||.+.
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      456699999999999999954  3579999875

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=98.49  E-value=1.4e-06  Score=76.01  Aligned_cols=100  Identities=15%  Similarity=0.196  Sum_probs=78.4

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEEechhh-HhhhccCCCC---CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccC
Q 026794           22 TGSIISVKVIQANEEMKKLVFSEKDAV-WNKYSSRVNV---EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS   92 (233)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS~k~~~-~~~~~~~~~~---G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels   92 (233)
                      +|+.+-+. +.+|+.+ |+....+... .+......-.   ++.++|+     ..|.||-+++     ++-||||-||.-
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-RIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITEN-----GYLGFIHKSERF  189 (287)
T ss_pred             CCCEEEEE-EEEccCC-cEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcC-----CeEEEEcchhhc
Confidence            89999999 8888765 7776665443 4445555444   8888888     8899999973     899999999963


Q ss_pred             cccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhH
Q 026794           93 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLE  137 (233)
Q Consensus        93 ~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~  137 (233)
                              ...+.||.++++|+.+.+ .++|.||++....+-.++
T Consensus       190 --------~~prlG~~l~~rVi~~re-Dg~lnLSl~p~~~E~l~~  225 (287)
T COG2996         190 --------AEPRLGERLTARVIGVRE-DGKLNLSLRPRAHEMLDE  225 (287)
T ss_pred             --------ccccCCceEEEEEEEEcc-CCeeecccccccHHhhhh
Confidence                    336789999999999996 999999999876555443

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.47  E-value=2.3e-07  Score=85.02  Aligned_cols=98  Identities=16%  Similarity=0.236  Sum_probs=71.6

Q ss_pred             cccCCCCEEEEEEEEEeCCCCEEEEEechh--------hHhhhccCC--CCCCEEEEE-----eeeEEEEEccCCCCccE
Q 026794           18 AKGLTGSIISVKVIQANEEMKKLVFSEKDA--------VWNKYSSRV--NVEDIFVGR-----DYGAFIHLRFPDGLYHL   82 (233)
Q Consensus        18 ~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~--------~~~~~~~~~--~~G~vv~g~-----~~G~fV~l~~~~~~~gv   82 (233)
                      ++..+|+.+.+.+...+..+ +...+.|+.        ..+..+..|  +.|++++|+     ++|+||+++      ++
T Consensus        85 ~~~~vGD~i~~~I~~~~fgR-~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg------~v  157 (362)
T PRK12327         85 PAYELGDVIEIEVTPKDFGR-IAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG------KI  157 (362)
T ss_pred             ccccCCCEEEEecCcCCCCh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC------Ce
Confidence            45578999998876544322 111112221        245566777  999999999     889999996      79


Q ss_pred             EEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCC--eEEEEEe
Q 026794           83 TGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLSIK  128 (233)
Q Consensus        83 ~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~--ri~LS~k  128 (233)
                      +|++|.+++.      +.+.|++||.++|.|++++.+++  +|.||.-
T Consensus       158 Ea~LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt  199 (362)
T PRK12327        158 EAVLPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT  199 (362)
T ss_pred             EEEecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence            9999998874      36779999999999999996554  4666653

>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=98.44  E-value=2.6e-07  Score=65.75  Aligned_cols=61  Identities=16%  Similarity=0.125  Sum_probs=49.7

Q ss_pred             ccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccc--cccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794          155 SMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQG--FEKR----VVSQDLQLWLSNAPPSGKKFTLLAR  221 (233)
Q Consensus       155 ~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~--~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r  221 (233)
                      ..++|+|.++.      ++|+++++++||+|+.    +++..  .+++    .+||.++++|.++|++++|++||.|
T Consensus         2 ~~V~g~V~~i~------~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k   72 (73)
T cd05703           2 QEVTGFVNNVS------KEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CEEEEEEEEEe------CCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            34779999887      4578888899999995    56542  3333    6899999999999999999999986

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.

>PRK11642 exoribonuclease R; Provisional

Probab=98.44  E-value=7e-07  Score=89.58  Aligned_cols=71  Identities=30%  Similarity=0.511  Sum_probs=60.4

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc-----------CcccccCCCCEEEEEEEEEeCCC
Q 026794           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREK  120 (233)
Q Consensus        57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~-----------~~~~~~~~Gd~V~vkVi~vd~e~  120 (233)
                      ++|++++|+     +||+||+|.+    .+++||||+++++++++.           +....|++||.|+|+|.++|.++
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            689999998     9999999973    359999999999987432           23467999999999999999999


Q ss_pred             CeEEEEEeccc
Q 026794          121 SRITLSIKQLE  131 (233)
Q Consensus       121 ~ri~LS~k~~~  131 (233)
                      ++|.|++-...
T Consensus       718 rkI~f~l~~~~  728 (813)
T PRK11642        718 RKIDFSLISSE  728 (813)
T ss_pred             CeEEEEEeccc
Confidence            99999996443

>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=98.43  E-value=2.7e-07  Score=65.83  Aligned_cols=60  Identities=7%  Similarity=-0.096  Sum_probs=50.2

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc-------cccCceEEEEeecCCCCCEEEEE
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR-------VVSQDLQLWLSNAPPSGKKFTLL  219 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~-------~vg~~~~v~i~~~d~~~~ki~Ls  219 (233)
                      |..+.|+|.++.+      +|+|+.+.+|++|+.    +++..+.++       .+||.++++|.++|.+++++.||
T Consensus         4 G~~V~g~V~~i~~------~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~LS   74 (74)
T cd05705           4 GQLLRGYVSSVTK------QGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCEEEEEEEEEeC------CcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            3347899999884      578888899999995    788775553       68999999999999999999986

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.

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

Probab=98.41  E-value=9.7e-07  Score=86.83  Aligned_cols=68  Identities=26%  Similarity=0.485  Sum_probs=58.5

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc-----------cCcccccCCCCEEEEEEEEEeCC
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDRE  119 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~-----------~~~~~~~~~Gd~V~vkVi~vd~e  119 (233)
                      -+.|++++|+     +||+||+|.+    ++++||||++++.|++.           .+....|++||.|+|+|.++|.+
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            3679999998     9999999974    47999999999998752           22346799999999999999999


Q ss_pred             CCeEEEEE
Q 026794          120 KSRITLSI  127 (233)
Q Consensus       120 ~~ri~LS~  127 (233)
                      +++|.+++
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.

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

Probab=98.40  E-value=1e-06  Score=65.54  Aligned_cols=74  Identities=22%  Similarity=0.259  Sum_probs=58.0

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCC---CccEEEEEEccccCccccc--CcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRITL  125 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~---~~gv~Glv~~sels~~~~~--~~~~~~~~Gd~V~vkVi~vd~e~~ri~L  125 (233)
                      +++|++|.|+     ...+++++...++   .....|++|+|++...+..  ++.+.|++||.|+|||++++. .+.+.|
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            5788998888     5568888821111   0367899999999887776  789999999999999999984 566889


Q ss_pred             EEecc
Q 026794          126 SIKQL  130 (233)
Q Consensus       126 S~k~~  130 (233)
                      |+++-
T Consensus        83 st~~~   87 (92)
T cd05791          83 STAEN   87 (92)
T ss_pred             EecCC
Confidence            98763

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".

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

Probab=98.38  E-value=5.5e-06  Score=72.36  Aligned_cols=172  Identities=16%  Similarity=0.145  Sum_probs=112.6

Q ss_pred             CCCCEEEEEEEEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE-eeeEEEEEccCCCCccEEEEEEccccCcccccCc
Q 026794           21 LTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI   99 (233)
Q Consensus        21 ~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~-~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~   99 (233)
                      -+|++|++- +..|.+ +++.++.+....  ....+--+.++.-. +-|+|++.+     -.-+-++|.++++..+    
T Consensus        45 evGdev~vF-iY~D~~-~rl~aTt~~p~~--tvg~~g~~~Vv~v~~~lGaFlD~G-----l~KDl~vp~~elp~~~----  111 (287)
T COG2996          45 EVGDEVTVF-IYVDSE-DRLIATTREPKA--TVGEYGWLKVVEVNKDLGAFLDWG-----LPKDLLVPLDELPTLK----  111 (287)
T ss_pred             ccCcEEEEE-EEECCC-CceeheeecceE--eecceeEEEEEEEcCCcceEEecC-----CCcceeeehhhccccc----
Confidence            489999988 777854 456555543210  01122223344444 789999996     3478999999986531    


Q ss_pred             ccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcC--CCCeeeecCCccccCCeeeeccCCChhhhhhhh
Q 026794          100 RDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP--QDGSVISDSSSMSSSNSNTIEPLPGLGAIFEEL  177 (233)
Q Consensus       100 ~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~--~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l  177 (233)
                      +-..++||.+-|.+ .+|. ++||.-.++.  +.+.+..+...+.  .+..        +.|+|-+..      ..|.|+
T Consensus       112 ~~wpq~Gd~l~v~l-~~Dk-k~Ri~g~~a~--~~~l~~l~~~~~~~l~nq~--------v~~tVYr~~------~~G~fv  173 (287)
T COG2996         112 SLWPQKGDKLLVYL-YVDK-KGRIWGTLAI--EKILENLATPAYNNLKNQE--------VDATVYRLL------ESGTFV  173 (287)
T ss_pred             ccCCCCCCEEEEEE-EEcc-CCcEEEEecc--hhHHHhcCCccchhhhcCe--------eeeEEEEEe------ccceEE
Confidence            23478999998775 5675 5577765542  2222222222111  1222        556766654      345555


Q ss_pred             cccCCeeEEEeeccccccccccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          178 LQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       178 ~~~~gv~gl~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      -.++|.-|++....+..+|.+|+.++.+|..+.. |++++||.|...
T Consensus       174 ~~e~~~~GfIh~sEr~~~prlG~~l~~rVi~~re-Dg~lnLSl~p~~  219 (287)
T COG2996         174 ITENGYLGFIHKSERFAEPRLGERLTARVIGVRE-DGKLNLSLRPRA  219 (287)
T ss_pred             EEcCCeEEEEcchhhcccccCCceEEEEEEEEcc-CCeeeccccccc
Confidence            5599999998888888889999999999999775 999999997543

>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=98.23  E-value=1.6e-06  Score=61.18  Aligned_cols=59  Identities=8%  Similarity=0.063  Sum_probs=47.0

Q ss_pred             cc-CCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEE
Q 026794          157 SS-SNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLA  220 (233)
Q Consensus       157 ~~-g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~  220 (233)
                      ++ |+|+++.     .++|+++++.+|++|+.    +++.+.+.+    .+||+++++|.++|+++++|+||.
T Consensus         4 ~~~g~V~~v~-----~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~   71 (71)
T cd05696           4 VDSVKVTKVE-----PDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             eeeeEEEEEc-----cCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            44 7887762     15688899999999995    556555544    689999999999999999999984

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.

>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=98.18  E-value=1.4e-06  Score=75.62  Aligned_cols=85  Identities=26%  Similarity=0.437  Sum_probs=76.1

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .+.++++|-+.     +.|+||.|-+++   .++|+|-.||||.+|+.++....++|..=.|.|+.+|.++|.|.||.+.
T Consensus        13 yPev~e~VmvnV~sIaemGayv~LlEYn---niEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrr   89 (304)
T KOG2916|consen   13 YPEVEEIVMVNVRSIAEMGAYVKLLEYN---NIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRR   89 (304)
T ss_pred             CCCcccEEEEEeeEehhccceEeeeecC---CcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhcc
Confidence            35778888776     899999998876   6999999999999999999999999999999999999999999999999


Q ss_pred             cccChhhHHhhhh
Q 026794          130 LEEDPLLETLEKV  142 (233)
Q Consensus       130 ~~~dp~~~~~~~~  142 (233)
                      +.++.-.++.+++
T Consensus        90 Vs~ed~~kC~Er~  102 (304)
T KOG2916|consen   90 VSPEDKEKCEERF  102 (304)
T ss_pred             CCHHHHHHHHHHH
Confidence            9887766666665

>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=98.14  E-value=4.3e-06  Score=59.69  Aligned_cols=64  Identities=17%  Similarity=0.051  Sum_probs=49.9

Q ss_pred             CccccCCeeeeccCCChhhhhhhhccc-CCeeEEE----eeccccccccccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVR----ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~-~gv~gl~----~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      |..+.|.|.++++      +|+++++. +|++|+.    +++.  +.=.+||.+.++|.++|.+++++.||.|+.+.
T Consensus         5 G~~v~g~V~si~d------~G~~v~~g~~gv~Gfl~~~~~~~~--~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~   73 (74)
T cd05694           5 GMVLSGCVSSVED------HGYILDIGIPGTTGFLPKKDAGNF--SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV   73 (74)
T ss_pred             CCEEEEEEEEEeC------CEEEEEeCCCCcEEEEEHHHCCcc--cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            3347899998884      57778776 6899995    4442  11267999999999999999999999997654

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.

>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=98.10  E-value=4.7e-06  Score=58.09  Aligned_cols=60  Identities=8%  Similarity=0.087  Sum_probs=48.4

Q ss_pred             cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR  221 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r  221 (233)
                      .+.|+|..+.+      +|+++++.++++|+.    +++++..++    .+||.+++++.++|++.+++.||.|
T Consensus         3 ~~~g~V~~v~~------~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k   70 (70)
T cd05698           3 KTHGTIVKVKP------NGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             EEEEEEEEEec------CcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            36788888874      578888899999995    555444433    6799999999999999999999975

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.

>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=98.07  E-value=4.8e-06  Score=58.03  Aligned_cols=58  Identities=9%  Similarity=0.078  Sum_probs=47.9

Q ss_pred             cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL  219 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls  219 (233)
                      .++|+|..+.      ++|+++++++|++|+.    ++++...++    .+||.+++++.++|.+++++.||
T Consensus         3 ~v~g~V~~v~------~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls   68 (69)
T cd05697           3 VVKGTIRKLR------PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT   68 (69)
T ss_pred             EEEEEEEEEe------ccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence            3678998887      4588888899999995    666655443    67999999999999999999987

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.

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

Probab=97.98  E-value=1e-05  Score=57.17  Aligned_cols=61  Identities=10%  Similarity=0.030  Sum_probs=48.7

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR  221 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r  221 (233)
                      |..+.|+|.++.+     .+++|+++.+|.+|+.    +++++++++    .+||.+++++.+++.  +|+.||.|
T Consensus         4 G~iv~G~V~~i~~-----~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl~   72 (72)
T cd05704           4 GAVTLGMVTKVIP-----HSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR   72 (72)
T ss_pred             CCEEEEEEEEeeC-----CcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence            3447899999874     3577888899999994    777777665    579999999988874  89999986

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.

>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=97.98  E-value=1.5e-05  Score=56.03  Aligned_cols=62  Identities=8%  Similarity=0.025  Sum_probs=49.1

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR  221 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r  221 (233)
                      |..+.|.|..+.+      +++++++++|++|+.    ++++..+++    .+||.+++++.++|.+++++.||.|
T Consensus         4 G~iv~g~V~~v~~------~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~   73 (73)
T cd05706           4 GDILPGRVTKVND------RYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCEEEEEEEEEeC------CeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            3347799988874      577888899999994    555544332    6899999999999999999999975

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.

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

Probab=97.96  E-value=1.3e-05  Score=56.36  Aligned_cols=59  Identities=8%  Similarity=0.143  Sum_probs=47.3

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR  221 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r  221 (233)
                      ++|+|..+.++      +.++++..|++|+.    +++.....+    .+||.+++++.++|.+++++.||.|
T Consensus         8 v~g~V~~v~~~------g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k   74 (74)
T PF00575_consen    8 VEGKVTSVEDF------GVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             EEEEEEEEETT------EEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             EEEEEEEEECC------EEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            77999998854      67788889999995    443322223    6899999999999999999999986

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 ....

>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=97.94  E-value=8.4e-06  Score=56.62  Aligned_cols=58  Identities=10%  Similarity=0.045  Sum_probs=47.0

Q ss_pred             cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL  219 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls  219 (233)
                      .+.|.|.++.+      +++++++.++++|+.    ++++..+++    .+||.+++++.++|++.+++.||
T Consensus         3 ~v~g~V~~v~~------~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls   68 (68)
T cd05707           3 VVRGFVKNIAN------NGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             EEEEEEEEEEC------ccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            36788888874      578888899999995    555555544    68999999999999999999876

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.

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

Probab=97.92  E-value=1.6e-05  Score=57.49  Aligned_cols=64  Identities=11%  Similarity=0.059  Sum_probs=51.8

Q ss_pred             cCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCC
Q 026794          143 IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGK  214 (233)
Q Consensus       143 ~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~  214 (233)
                      ++.|++        +.|+|..+.+      +++|+++.+|++|+.    +++++..++    .+||+++|+|.++|.+++
T Consensus        12 ~~~G~i--------~~g~V~~v~~------~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~   77 (83)
T cd04461          12 LKPGMV--------VHGYVRNITP------YGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQ   77 (83)
T ss_pred             CCCCCE--------EEEEEEEEee------ceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCC
Confidence            566777        6799998885      577888899999994    666655444    579999999999999999


Q ss_pred             EEEEEE
Q 026794          215 KFTLLA  220 (233)
Q Consensus       215 ki~Ls~  220 (233)
                      ++.||+
T Consensus        78 ~i~lsl   83 (83)
T cd04461          78 RFLLSL   83 (83)
T ss_pred             EEEEeC
Confidence            999984

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.

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

Probab=97.86  E-value=1.3e-05  Score=55.43  Aligned_cols=57  Identities=18%  Similarity=0.139  Sum_probs=44.8

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eec-cccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITR-QGFEKR----VVSQDLQLWLSNAPPSGKKFTLL  219 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~-~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls  219 (233)
                      +.|.|..+.++      |.|+++++|++|+.    ++| .+..++    .+||.+++++.++|.+++|++|+
T Consensus         4 ~~g~V~~i~~~------G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690           4 VSGKIKSITDF------GIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             EEEEEEEEEee------eEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence            66888888754      77888899999995    443 233333    68999999999999999999875

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.

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

Probab=97.85  E-value=2.4e-05  Score=54.19  Aligned_cols=59  Identities=10%  Similarity=0.054  Sum_probs=45.8

Q ss_pred             cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc--cccCceEEEEeecCCCCCEEEEEEc
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR--VVSQDLQLWLSNAPPSGKKFTLLAR  221 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~--~vg~~~~v~i~~~d~~~~ki~Ls~r  221 (233)
                      .++|+|.++.+      .|.++++ +|++|+.    +++...+.+  .+||.++++|.++|.+++++.||.|
T Consensus         3 iv~g~V~~v~~------~G~~v~l-~g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd~~~~~i~lS~k   67 (67)
T cd04465           3 IVEGKVTEKVK------GGLIVDI-EGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             EEEEEEEEEEC------CeEEEEE-CCEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            36788888874      4677777 7999995    444443322  5899999999999999999999975

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.

>PRK08582 hypothetical protein; Provisional

Probab=97.84  E-value=3.1e-05  Score=61.93  Aligned_cols=63  Identities=10%  Similarity=0.056  Sum_probs=49.9

Q ss_pred             cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      .+.|.|+.+++      +++|+++.+|++|+.    +++..+...    .+||.++|+|.+++. +++|.||.++...
T Consensus         8 iv~G~V~~I~~------fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~~~   78 (139)
T PRK08582          8 KLQGKVTGITN------FGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKAKD   78 (139)
T ss_pred             EEEEEEEEEEC------CeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEeccc
Confidence            37799999885      478888899999994    555555433    579999999999997 4899999987543

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

Probab=97.82  E-value=2e-05  Score=54.77  Aligned_cols=58  Identities=12%  Similarity=-0.003  Sum_probs=44.6

Q ss_pred             cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc--cccCceEEEEeecCCCCCEEEEE
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR--VVSQDLQLWLSNAPPSGKKFTLL  219 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~--~vg~~~~v~i~~~d~~~~ki~Ls  219 (233)
                      .++|+|.++.+      +|+++++.+|++|+.    ++..+....  .+||+++++|..+|++++++.||
T Consensus         3 ~V~g~V~~i~~------~G~~v~l~~~v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~id~~~~~i~LS   66 (66)
T cd05695           3 LVNARVKKVLS------NGLILDFLSSFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             EEEEEEEEEeC------CcEEEEEcCCceEEEEHHHcCCccCcccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            36789988874      578888888999995    333222211  68999999999999999999886

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.

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

Probab=97.75  E-value=0.0001  Score=61.20  Aligned_cols=123  Identities=16%  Similarity=0.202  Sum_probs=75.0

Q ss_pred             CCCCCCCCCCchhHhhhcc-cCCCCEE-----EEEEEEEeC-CCCEEEEEech----hhHhhhccCCCCCCEEEEE----
Q 026794            1 MSPSHSCKEPQKSIHEIAK-GLTGSII-----SVKVIQANE-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR----   65 (233)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~-~~vG~~v-----~~~Vi~id~-~~~~i~lS~k~----~~~~~~~~~~~~G~vv~g~----   65 (233)
                      |.|+++..+......+.++ .+.|+.+     -+.|++++. +.+++.-.--.    .....+.-++..|++++|+    
T Consensus        13 i~P~~f~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf~gEVv~g~V~~v   92 (176)
T PTZ00162         13 LKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDV   92 (176)
T ss_pred             ECHHHcCccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecCCCCEEEEEEEEE
Confidence            3566666555555544443 2334322     234444433 33444321111    1234556678999999999    


Q ss_pred             -eeeEEEEEccCCCCccEEEEEEccccCcccc------------cCcccccCCCCEEEEEEEEEeCCCC--eEEEEEec
Q 026794           66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI------------QDIRDILNEGDEVRVKVIKIDREKS--RITLSIKQ  129 (233)
Q Consensus        66 -~~G~fV~l~~~~~~~gv~Glv~~sels~~~~------------~~~~~~~~~Gd~V~vkVi~vd~e~~--ri~LS~k~  129 (233)
                       ++|+||.++      ..++|+|.+.+..+..            .+-...++.|+.|++||..+..+.+  ++..++|+
T Consensus        93 ~~~G~~v~~G------p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~i~T~~~  165 (176)
T PTZ00162         93 NKLGFFAQAG------PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAIATINS  165 (176)
T ss_pred             ecceEEEEee------CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEEEEEecC
Confidence             999999997      6889999999974321            1123468999999999988865433  34445544

>PRK07252 hypothetical protein; Provisional

Probab=97.74  E-value=4.3e-05  Score=59.62  Aligned_cols=66  Identities=14%  Similarity=0.061  Sum_probs=52.3

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      |..+.|.|+.+.+      +|+|+++.++++|+.    +++.++..+    .+||.++|+|.++|.+.+++.||.+....
T Consensus         4 G~iv~G~V~~V~~------~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~   77 (120)
T PRK07252          4 GDKLKGTITGIKP------YGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEE   77 (120)
T ss_pred             CCEEEEEEEEEeC------cEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeeccc
Confidence            3347799998875      477888899999994    565555444    68999999999999999999999986543

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

Probab=97.68  E-value=7.2e-05  Score=52.73  Aligned_cols=62  Identities=8%  Similarity=0.044  Sum_probs=47.7

Q ss_pred             ccccCCeeeeccCCChhhhhhhhccc--CCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794          155 SMSSSNSNTIEPLPGLGAIFEELLQE--DGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARA  222 (233)
Q Consensus       155 ~~~~g~v~~v~~~~g~~~~~~~l~~~--~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~  222 (233)
                      ..+.|+|..+.+      +++++++.  +|++|+.    +++++...+    .+||.+++++.++|.+++++.||.|+
T Consensus         5 ~~~~g~V~~v~~------~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~   76 (76)
T cd04452           5 ELVVVTVKSIAD------MGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             CEEEEEEEEEEc------cEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence            336799988874      46777776  3699994    555554433    58999999999999999999999874

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

>PRK05054 exoribonuclease II; Provisional

Probab=97.68  E-value=0.00015  Score=71.45  Aligned_cols=65  Identities=14%  Similarity=0.111  Sum_probs=52.5

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc--cc-c--C-------cccccCCCCEEEEEEEEEeCCCC
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD--LI-Q--D-------IRDILNEGDEVRVKVIKIDREKS  121 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~--~~-~--~-------~~~~~~~Gd~V~vkVi~vd~e~~  121 (233)
                      |+.+.|.     +||+||+|..    .+++||||++.+..+  +. -  +       -...|+.||.|+|+|.++|.+++
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            4488887     9999999974    589999999999653  11 1  1       12469999999999999999999


Q ss_pred             eEEEEE
Q 026794          122 RITLSI  127 (233)
Q Consensus       122 ri~LS~  127 (233)
                      +|.+.+
T Consensus       638 ~i~~~~  643 (644)
T PRK05054        638 SIIARP  643 (644)
T ss_pred             eEEEEE
Confidence            999865

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

Probab=97.68  E-value=7e-05  Score=52.24  Aligned_cols=62  Identities=15%  Similarity=0.283  Sum_probs=48.8

Q ss_pred             cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                      .+.|+|..+.+      .+.++++.++++|+.    ++.+...++    .+||.+++++.++|.+++++.||.|..
T Consensus         3 ~v~g~V~~v~~------~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~   72 (73)
T cd05691           3 IVTGKVTEVDA------KGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK   72 (73)
T ss_pred             EEEEEEEEEEC------CeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence            36788888874      477788889999995    444444333    589999999999999999999998764

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.

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

Probab=97.67  E-value=5.9e-05  Score=52.80  Aligned_cols=57  Identities=5%  Similarity=0.070  Sum_probs=43.7

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecc-ccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQ-GFEKR----VVSQDLQLWLSNAPPSGKKFTLL  219 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~-~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls  219 (233)
                      ..|.|..+.++      |.|+++.+|++|+.    ++|. ...++    .+||.++|++.++|.+++++.|+
T Consensus         7 ~~g~V~~i~~~------G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           7 LFGKVTNLTDY------GCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             EEEEEEEEEee------EEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence            67999988854      77788899999994    4432 11111    67999999999999999999764

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.

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

Probab=97.67  E-value=0.00041  Score=57.66  Aligned_cols=75  Identities=28%  Similarity=0.331  Sum_probs=59.3

Q ss_pred             hccCCCCCCEEEEE-----eeeEEEEEccCCCC-----ccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCC
Q 026794           52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDGL-----YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS  121 (233)
Q Consensus        52 ~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~-----~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~  121 (233)
                      ....++.|++|-|.     .-.+.|++.+.++-     ....|-+|+|+++..++++.++.|++||.|+|+|++.-   .
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            45678999999998     55677777654331     12578899999999999999999999999999999973   4


Q ss_pred             eEEEEEec
Q 026794          122 RITLSIKQ  129 (233)
Q Consensus       122 ri~LS~k~  129 (233)
                      .+.||.+.
T Consensus       135 ~~~Lst~~  142 (188)
T COG1096         135 PIQLSTKG  142 (188)
T ss_pred             CeEEEecC
Confidence            46777654

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

Probab=97.62  E-value=8.1e-05  Score=52.58  Aligned_cols=59  Identities=7%  Similarity=0.007  Sum_probs=45.9

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCC--eeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEE
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDG--IDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLA  220 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~g--v~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~  220 (233)
                      |...+|+|+++.+      +|+|+++ +|  ++|+.    ++++++.++    .+||++.|++.++|.++ |++||.
T Consensus         4 g~~~~g~V~~i~~------fG~fv~l-~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~   72 (73)
T cd05686           4 YQIFKGEVASVTE------YGAFVKI-PGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL   72 (73)
T ss_pred             CCEEEEEEEEEEe------eeEEEEE-CCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence            3447799998885      4778887 45  68883    777766554    57999999999999976 899885

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.

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

Probab=97.60  E-value=0.00011  Score=51.66  Aligned_cols=64  Identities=9%  Similarity=0.074  Sum_probs=48.6

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccC-CeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~-gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                      |..+.|.|..+.++      ++|+++.+ +++|+.    +++++...+    .+||.+++++.++|.+++++.|+.|+.
T Consensus         3 g~~v~g~V~~i~~~------g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~   75 (77)
T cd05708           3 GQKIDGTVRRVEDY------GVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCEEEEEEEEEEcc------eEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            33477999888754      67777774 799995    444443322    689999999999999999999998863

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.58  E-value=9.6e-05  Score=72.96  Aligned_cols=59  Identities=17%  Similarity=0.111  Sum_probs=47.1

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----ee----ccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----IT----RQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL  219 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~----~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls  219 (233)
                      |..++|+|+++.      +||+|+++.+|++||.    ++    +.++.++    .+||+++|+|.++| +++|++|+
T Consensus       648 G~i~~GkV~~I~------dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID-~~gKI~L~  718 (719)
T TIGR02696       648 GERFLGTVVKTT------AFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADID-DRGKLSLV  718 (719)
T ss_pred             CCEEEEEEEEEE------CceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEEC-CCCCeeec
Confidence            444789999998      4588899999999994    43    3456555    57999999999999 47899986

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.

>PRK05807 hypothetical protein; Provisional

Probab=97.58  E-value=0.00013  Score=58.19  Aligned_cols=60  Identities=7%  Similarity=0.010  Sum_probs=47.5

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      ++|+|..+.++      |+|+++ +|.+|+.    +++..+...    .+||.++|+|.+++. +++|.||.|+..
T Consensus         9 v~G~Vt~i~~~------GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~~~   76 (136)
T PRK05807          9 LEGTVVNITNF------GAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQAM   76 (136)
T ss_pred             EEEEEEEEECC------eEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence            77999988754      777888 6889994    555444333    689999999999998 799999998754

>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=97.54  E-value=0.00029  Score=49.98  Aligned_cols=64  Identities=19%  Similarity=0.222  Sum_probs=50.6

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccC--cccccCCCCEE-EEEEEEEeCCCCeEEEEEe
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD--IRDILNEGDEV-RVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~--~~~~~~~Gd~V-~vkVi~vd~e~~ri~LS~k  128 (233)
                      |++++|+     +-+++|++.+    .++.|++|...+|++.-++  .-..+++||++ .+.|+  +...+.|.||.|
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            6778887     6679999984    4899999999999933333  23348899999 99999  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.

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

Probab=97.47  E-value=0.00018  Score=49.09  Aligned_cols=58  Identities=9%  Similarity=0.130  Sum_probs=45.3

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR  221 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r  221 (233)
                      +.|+|..+.+      +++|+++.++++|+.    ++++.+.++    .+||.+++++.+++. ++++.||.|
T Consensus         4 ~~g~V~~i~~------~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~k   69 (69)
T cd05692           4 VEGTVTRLKP------FGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK   69 (69)
T ss_pred             EEEEEEEEEe------eeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence            5688888774      477888899999994    444443332    579999999999998 889999875

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.

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

Probab=97.45  E-value=0.00075  Score=49.73  Aligned_cols=58  Identities=17%  Similarity=0.236  Sum_probs=46.0

Q ss_pred             CCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCc-----------ccccCCCCEEEEEEEEEeCCCC
Q 026794           58 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----------RDILNEGDEVRVKVIKIDREKS  121 (233)
Q Consensus        58 ~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~-----------~~~~~~Gd~V~vkVi~vd~e~~  121 (233)
                      .|++++|+     ++|+||.++      ++++|+|.+.+..+...++           ...++.|+.|++||+.+..+.+
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            47889998     999999997      7999999998876544332           3448899999999999876543

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.

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

Probab=97.44  E-value=0.0002  Score=49.82  Aligned_cols=60  Identities=7%  Similarity=0.067  Sum_probs=46.5

Q ss_pred             cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEc
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLAR  221 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r  221 (233)
                      .++|+|.++.+      .++++++..+++|+.    +++...+.+    .+||.++++|.+++.+++++.||.+
T Consensus         3 iv~g~V~~i~~------~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           3 IVKGTVVSVDD------DEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             EEEEEEEEEeC------CEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            36789888874      477888888899994    444433323    6799999999999988999999875

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.

>PRK08059 general stress protein 13; Validated

Probab=97.44  E-value=0.00024  Score=55.55  Aligned_cols=68  Identities=13%  Similarity=0.116  Sum_probs=53.2

Q ss_pred             cCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCC
Q 026794          143 IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGK  214 (233)
Q Consensus       143 ~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~  214 (233)
                      ++.|++        +.|.|..+.+      +|+++++.++++|+.    ++++.+.++    .+||.++|+|.++|.+++
T Consensus         5 ~k~G~i--------v~G~V~~i~~------~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~   70 (123)
T PRK08059          5 YEVGSV--------VTGKVTGIQP------YGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKG   70 (123)
T ss_pred             CCCCCE--------EEEEEEEEec------ceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCC
Confidence            455666        6799988875      477888899999995    444444333    579999999999999999


Q ss_pred             EEEEEEcccc
Q 026794          215 KFTLLARAGR  224 (233)
Q Consensus       215 ki~Ls~r~~~  224 (233)
                      ++.||.|...
T Consensus        71 ~i~lslk~~~   80 (123)
T PRK08059         71 KISLSIRATE   80 (123)
T ss_pred             eEEEEEEEcc
Confidence            9999998653

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.43  E-value=0.00036  Score=65.28  Aligned_cols=59  Identities=29%  Similarity=0.469  Sum_probs=48.9

Q ss_pred             ccCCCCCCEEEEE-----ee--eEEEEEccCCCCccEEEEEEccccCcc------------cccCcccccCCCCEEEEEE
Q 026794           53 SSRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKV  113 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~--G~fV~l~~~~~~~gv~Glv~~sels~~------------~~~~~~~~~~~Gd~V~vkV  113 (233)
                      .....+|++|.|+     ++  ||||+++     .+-.||+|++++.+.            +..++.+.+++||.|.|+|
T Consensus        20 ~~~~~vGnIY~GrV~~i~p~l~aAFVdiG-----~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV   94 (414)
T TIGR00757        20 KSRQLKGNIYKGRVTRILPSLQAAFVDIG-----LEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQV   94 (414)
T ss_pred             cCcCCCCCEEEEEEeeecCCCceEEEEcC-----CCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEE
Confidence            4456799999999     66  8999998     478999999999763            2345677899999999999


Q ss_pred             EEE
Q 026794          114 IKI  116 (233)
Q Consensus       114 i~v  116 (233)
                      ..-
T Consensus        95 ~Ke   97 (414)
T TIGR00757        95 VKE   97 (414)
T ss_pred             eeC
Confidence            983

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.

>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=97.42  E-value=0.00016  Score=49.31  Aligned_cols=57  Identities=5%  Similarity=-0.063  Sum_probs=44.1

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL  219 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls  219 (233)
                      ..|+|+.+.+      +|.|+++.++++|+.    +++....++    .+||.++|++.++|.+++++.||
T Consensus         4 ~~g~V~~i~~------~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           4 LEGVVTNVTD------FGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             EEEEEEEEec------ccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            5688888875      477788899999995    443333222    67999999999999999999875

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.40  E-value=0.00018  Score=72.53  Aligned_cols=60  Identities=13%  Similarity=0.083  Sum_probs=50.5

Q ss_pred             c-cCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          157 S-SSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       157 ~-~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                      + .|+|+++.      +||+|+++.+|++||.    ++|+++..+    .+||.++|++.++|. ++||+||.|+.
T Consensus       757 y~~g~V~~I~------~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSlK~l  825 (891)
T PLN00207        757 YRNCEIKSIA------PYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSRRAL  825 (891)
T ss_pred             EECcEEEEEe------ccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEEecc
Confidence            5 36888887      5588899999999994    888877666    579999999999997 78999999874

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

Probab=97.33  E-value=0.00079  Score=58.11  Aligned_cols=98  Identities=23%  Similarity=0.330  Sum_probs=72.3

Q ss_pred             CCCEEEEEEEEE-eCCCCEEEEEechhhHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccc
Q 026794           22 TGSIISVKVIQA-NEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL   95 (233)
Q Consensus        22 vG~~v~~~Vi~i-d~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~   95 (233)
                      -|+++...+... +..++.+.+=.    .+. ...++.||+|-|+     ..+..|+|..     ...+++|.|++-++.
T Consensus        32 ~~~~iyssv~G~~~~~~~~v~VIp----l~g-~YiP~~gD~VIG~I~~v~~~~W~VDI~s-----p~~A~L~ls~~~~r~  101 (239)
T COG1097          32 EGGKIYSSVVGLLDVKGKLVRVIP----LEG-RYIPEVGDVVIGKIIEVGPSGWKVDIGS-----PYPALLSLSDFLRRK  101 (239)
T ss_pred             cCCEEEEEEEeEEEEeCCEEEEEe----CCC-cccCCCCCEEEEEEEEEcccceEEEcCC-----ccceEeehhhhhccc
Confidence            566666666542 32233332221    222 3457899999998     8899999983     689999999997766


Q ss_pred             c----cCcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794           96 I----QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (233)
Q Consensus        96 ~----~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~  130 (233)
                      +    .+++.+|++||-|.|+|.++|. .+...|++|..
T Consensus       102 ~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~k~~  139 (239)
T COG1097         102 FENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTLKDE  139 (239)
T ss_pred             ccccccccccccccCCEEEEEEEEccC-CCceEEEeecC
Confidence            4    4688899999999999999996 78889988543

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

Probab=97.31  E-value=0.00026  Score=53.39  Aligned_cols=63  Identities=16%  Similarity=0.075  Sum_probs=48.9

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecccc----------------------ccc-cccCceEEEE
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGF----------------------EKR-VVSQDLQLWL  206 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~----------------------~~~-~vg~~~~v~i  206 (233)
                      |..+.|+|..+.++      +.++.+..|++|+.    +++.+.                      .+. .+||.+.++|
T Consensus         4 G~vV~G~V~~v~~~------gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kV   77 (100)
T cd05693           4 GMLVLGQVKEITKL------DLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKV   77 (100)
T ss_pred             CCEEEEEEEEEcCC------CEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEE
Confidence            44478999998754      67778899999994    665331                      111 6899999999


Q ss_pred             eecCCC---CCEEEEEEcc
Q 026794          207 SNAPPS---GKKFTLLARA  222 (233)
Q Consensus       207 ~~~d~~---~~ki~Ls~r~  222 (233)
                      .++|.+   +++|.||.|.
T Consensus        78 i~~d~~~~~~~~i~LSlr~   96 (100)
T cd05693          78 VSLDKSKSGKKRIELSLEP   96 (100)
T ss_pred             EEccCCcCCCcEEEEEecH
Confidence            999997   7899999985

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.

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

Probab=97.24  E-value=0.00049  Score=49.12  Aligned_cols=61  Identities=10%  Similarity=0.048  Sum_probs=46.4

Q ss_pred             cccCCeeeeccCCChhhhhhhhccc---CCeeEEE----eecccc-ccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQE---DGIDDVR----ITRQGF-EKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~---~gv~gl~----~~~~~~-~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                      .+.|.|+.+.++      ++|+++.   .|++|+.    +++++. .++    .+||+++|++.++|  .+++.+|.|+.
T Consensus         3 ~~~g~V~~v~~~------G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~   74 (79)
T cd05684           3 IYKGKVTSIMDF------GCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDV   74 (79)
T ss_pred             EEEEEEEEEEee------eEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEec
Confidence            366888888854      7777777   5799994    555543 434    58999999999999  78999999864


Q ss_pred             c
Q 026794          224 R  224 (233)
Q Consensus       224 ~  224 (233)
                      .
T Consensus        75 ~   75 (79)
T cd05684          75 D   75 (79)
T ss_pred             c
Confidence            3

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.

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

Probab=97.20  E-value=0.00083  Score=47.94  Aligned_cols=63  Identities=8%  Similarity=0.067  Sum_probs=48.0

Q ss_pred             cCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEEeeccccccccccCceEEEEeecCCCCCEEEEEE
Q 026794          143 IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLA  220 (233)
Q Consensus       143 ~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~  220 (233)
                      ++.|+.        .+|++..+.+      +|.|++++++++|+....+-.+.-.+||.+++++.++ .+++|+.++.
T Consensus        14 ~~~G~~--------~~g~V~~i~~------~G~fV~l~~~~~Glv~~se~~~~~~iGd~v~v~I~~i-~e~~~i~l~~   76 (77)
T cd04473          14 LEVGKL--------YKGKVNGVAK------YGVFVDLNDHVRGLIHRSNLLRDYEVGDEVIVQVTDI-PENGNIDLIP   76 (77)
T ss_pred             CCCCCE--------EEEEEEeEec------ceEEEEECCCcEEEEEchhccCcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence            566777        6689988875      4777888999999953332222237899999999999 8999999875

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.

>TIGR02062 RNase_B exoribonuclease II

Probab=97.18  E-value=0.0011  Score=65.27  Aligned_cols=64  Identities=14%  Similarity=0.165  Sum_probs=50.4

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCc--ccc---cCc-------ccccCCCCEEEEEEEEEeCCCC
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI---QDI-------RDILNEGDEVRVKVIKIDREKS  121 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~--~~~---~~~-------~~~~~~Gd~V~vkVi~vd~e~~  121 (233)
                      |+.+.|.     ++|+||+|..    .|++||||++.+..  ++.   .+.       ...|+.||.|+|+|.++|.+++
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            4478887     8999999974    58999999999965  221   111       1259999999999999999999


Q ss_pred             eEEEE
Q 026794          122 RITLS  126 (233)
Q Consensus       122 ri~LS  126 (233)
                      +|.+.
T Consensus       634 ~i~~~  638 (639)
T TIGR02062       634 SIIAR  638 (639)
T ss_pred             cEeee
Confidence            98863

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.

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=97.14  E-value=0.0011  Score=66.06  Aligned_cols=72  Identities=31%  Similarity=0.499  Sum_probs=58.6

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc-----------CcccccCCCCEEEEEEEEE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKI  116 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~-----------~~~~~~~~Gd~V~vkVi~v  116 (233)
                      +-.-.+|+.++|+     .||+||.|.+    .+++|++|++.+..++..           .....|+.||.|+|++.++
T Consensus       617 ~m~~~vg~~f~g~V~~v~~~g~~V~l~~----~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v  692 (706)
T COG0557         617 YMKKRVGEEFDGVVTGVTSFGFFVELPE----LGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSV  692 (706)
T ss_pred             HHHHhcCCEEEEEEEEEEeccEEEEecc----cccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEE
Confidence            3345788888888     8999999985    579999999999965432           2233589999999999999


Q ss_pred             eCCCCeEEEEEe
Q 026794          117 DREKSRITLSIK  128 (233)
Q Consensus       117 d~e~~ri~LS~k  128 (233)
                      +...+++.+++-
T Consensus       693 ~~~~~~i~~~~v  704 (706)
T COG0557         693 DLDERKIDFELV  704 (706)
T ss_pred             cccccceEEEec
Confidence            999999998764

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=97.06  E-value=0.0022  Score=53.68  Aligned_cols=95  Identities=11%  Similarity=0.084  Sum_probs=63.2

Q ss_pred             cCCCCEEEEEEEE---EeCCCCeEEEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcc
Q 026794          103 LNEGDEVRVKVIK---IDREKSRITLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ  179 (233)
Q Consensus       103 ~~~Gd~V~vkVi~---vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~  179 (233)
                      |..++.+.+.+..   +|.++++|+|       +||.... ...+.|++        +.|+|+++.+.      ++++++
T Consensus        27 y~~~~~i~as~~G~~~id~~~~~Isv-------~P~~~~~-~~~~~Gdi--------V~GkV~~i~~~------g~~V~I   84 (189)
T PRK09521         27 YEDNGEVYASVVGKVFIDDINRKISV-------IPFKKTP-PLLKKGDI--------VYGRVVDVKEQ------RALVRI   84 (189)
T ss_pred             EeeCCEEEEEeeEEEEEcCCCCEEEE-------ecCcCCC-CCCCCCCE--------EEEEEEEEcCC------eEEEEE
Confidence            4446667665544   4767777877       5885432 23567777        67999998754      444443


Q ss_pred             ----------cCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794          180 ----------EDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARA  222 (233)
Q Consensus       180 ----------~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~  222 (233)
                                .++++|+.    +++...++.    .+||.+.++|.+++   +++.||.|.
T Consensus        85 ~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~k~  142 (189)
T PRK09521         85 VSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLSTKG  142 (189)
T ss_pred             EEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEEec
Confidence                      45788884    333222211    57999999998888   689999985

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

Probab=97.03  E-value=0.00086  Score=59.10  Aligned_cols=63  Identities=6%  Similarity=0.004  Sum_probs=49.9

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccC--CeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQED--GIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~--gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      +.|+|..+.+      +|+|+++.+  |++|+.    ++++++...    .+||.+.+++.++|.+++++.||.|....
T Consensus        12 V~G~V~~I~~------~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~   84 (262)
T PRK03987         12 VVGTVKEVKD------FGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNE   84 (262)
T ss_pred             EEEEEEEEEC------CEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEeccc
Confidence            6799998875      477777775  899995    555555433    58999999999999999999999986553

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.03  E-value=0.00068  Score=67.37  Aligned_cols=63  Identities=13%  Similarity=0.060  Sum_probs=51.8

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                      |..+.|+|+.+.+      +|+|+++.+|++|+.    +++.+++++    .+||.++|++.++|.+ +|+.||.|+.
T Consensus       622 G~v~~G~V~~I~~------fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~  692 (693)
T PRK11824        622 GEIYEGKVVRIVD------FGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV  692 (693)
T ss_pred             CeEEEEEEEEEEC------CeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence            4447899999884      588888899999993    677766655    6899999999999987 9999999864

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

Probab=97.00  E-value=0.0013  Score=47.52  Aligned_cols=62  Identities=6%  Similarity=-0.107  Sum_probs=46.2

Q ss_pred             ccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecc----cccc----ccccCceEEEEeecCCCCCEEEEEEcc
Q 026794          155 SMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQ----GFEK----RVVSQDLQLWLSNAPPSGKKFTLLARA  222 (233)
Q Consensus       155 ~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~----~~~~----~~vg~~~~v~i~~~d~~~~ki~Ls~r~  222 (233)
                      ..+.|+|..+.+      .++++++.++++|+.    ++++    ..++    -.+||.+.++|.+++.+ +++.||.|.
T Consensus         8 diV~g~V~~i~~------~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~~~   80 (86)
T cd05789           8 DVVIGRVTEVGF------KRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTRS   80 (86)
T ss_pred             CEEEEEEEEECC------CEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeCc
Confidence            337899998874      467788899999995    3321    1111    15899999999999876 889999986


Q ss_pred             c
Q 026794          223 G  223 (233)
Q Consensus       223 ~  223 (233)
                      .
T Consensus        81 ~   81 (86)
T cd05789          81 L   81 (86)
T ss_pred             c
Confidence            4

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".

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=96.97  E-value=0.00062  Score=67.32  Aligned_cols=67  Identities=7%  Similarity=-0.001  Sum_probs=55.7

Q ss_pred             CCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       153 ~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      +|+.++|.|.+++      +||+|+++.-..+|+.    ++...+..|    .+||.++||+.++|..++||+||+|.-.
T Consensus       658 ~Gm~leg~Vrnv~------~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~  731 (780)
T COG2183         658 PGMILEGTVRNVV------DFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDE  731 (780)
T ss_pred             CCCEEEEEEEEee------eccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence            4555899999998      5588887777778884    778778777    5899999999999999999999998654


Q ss_pred             e
Q 026794          225 C  225 (233)
Q Consensus       225 ~  225 (233)
                      .
T Consensus       732 ~  732 (780)
T COG2183         732 E  732 (780)
T ss_pred             C
Confidence            3

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

Probab=96.93  E-value=0.0012  Score=45.13  Aligned_cols=57  Identities=12%  Similarity=0.098  Sum_probs=43.8

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEE
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLA  220 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~  220 (233)
                      ..|.|..+.+      +++++++.++++|+.    ++++....+    .+||.+.|++.++|+ .+++.||.
T Consensus         4 ~~g~V~~v~~------~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls~   68 (68)
T cd04472           4 YEGKVVKIKD------FGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR   68 (68)
T ss_pred             EEEEEEEEEE------eEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence            5688888875      477888888999994    444443322    579999999999999 88898873

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.

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

Probab=96.91  E-value=0.0057  Score=44.98  Aligned_cols=68  Identities=19%  Similarity=0.073  Sum_probs=54.0

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .+++||.|-|+     ....+|+|..     ...|++|.+++... .+..+..|++||-|.|+|.++|+ .....||+..
T Consensus         3 ~P~~gD~VIG~V~~~~~~~~~VdI~s-----~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~-~~~~eLtc~~   75 (86)
T cd05790           3 VPAKGDHVIGIVVAKAGDFFKVDIGG-----SEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANR-DMEPELSCVD   75 (86)
T ss_pred             cCCCCCEEEEEEEEEcCCeEEEEcCC-----CcceEechHHcccc-cccccccCCCCCEEEEEEEecCC-CCCeEEEEeC
Confidence            35789999998     5678999973     57899999887543 34456779999999999999997 4567888765

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".

>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=96.88  E-value=0.0026  Score=46.36  Aligned_cols=36  Identities=25%  Similarity=0.438  Sum_probs=25.0

Q ss_pred             cEEEEEEccccCccccc--CcccccCCCCEEEEEEEEE
Q 026794           81 HLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKI  116 (233)
Q Consensus        81 gv~Glv~~sels~~~~~--~~~~~~~~Gd~V~vkVi~v  116 (233)
                      ...|+||.+++.....+  ++.+.|++||.|+|+|+++
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            57899999999766554  4688899999999999974

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.

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

Probab=96.87  E-value=0.0021  Score=45.72  Aligned_cols=60  Identities=3%  Similarity=0.067  Sum_probs=44.4

Q ss_pred             ccccCCeeeeccCCChhhhhhhhcccC-CeeEEE----eeccccc-----------c--c--cccCceEEEEeecCCCCC
Q 026794          155 SMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR----ITRQGFE-----------K--R--VVSQDLQLWLSNAPPSGK  214 (233)
Q Consensus       155 ~~~~g~v~~v~~~~g~~~~~~~l~~~~-gv~gl~----~~~~~~~-----------~--~--~vg~~~~v~i~~~d~~~~  214 (233)
                      ...+|.|+++.+      +|+|+++++ |++|+.    ++++.+.           .  .  .+||.++|++.++|.+++
T Consensus         3 ~~~~g~V~~v~~------~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~   76 (83)
T cd04471           3 EEFDGVISGVTS------FGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRR   76 (83)
T ss_pred             CEEEEEEEeEEe------eeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccC
Confidence            346788888875      477787788 899994    3332110           1  1  579999999999999999


Q ss_pred             EEEEEE
Q 026794          215 KFTLLA  220 (233)
Q Consensus       215 ki~Ls~  220 (233)
                      ++.++.
T Consensus        77 ~i~~~l   82 (83)
T cd04471          77 KIDFEL   82 (83)
T ss_pred             EEEEEE
Confidence            998874

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=96.80  E-value=0.0017  Score=63.35  Aligned_cols=94  Identities=12%  Similarity=0.134  Sum_probs=67.2

Q ss_pred             EEEeCCCCeEEEEEeccccC----hhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE--
Q 026794          114 IKIDREKSRITLSIKQLEED----PLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR--  187 (233)
Q Consensus       114 i~vd~e~~ri~LS~k~~~~d----p~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~--  187 (233)
                      ++++ +++.+..+-......    .|-+...+..++|.+        ..|+|+++.+      ||+|+++-+|=+|++  
T Consensus       585 Idie-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~i--------y~G~V~ri~~------fGaFv~l~~gkdgl~hi  649 (692)
T COG1185         585 IDIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEV--------YEGTVVRIVD------FGAFVELLPGKDGLVHI  649 (692)
T ss_pred             EEec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccE--------EEEEEEEEee------cceEEEecCCcceeEEe
Confidence            4555 678888777553221    132333344667776        6799999984      688999999988883  


Q ss_pred             --eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          188 --ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       188 --~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                        ++++++++.    .+||.+.||+.++|. ++|+.||+++.
T Consensus       650 S~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~  690 (692)
T COG1185         650 SQLAKERVEKVEDVLKEGDEVKVKVIEIDK-QGRIRLSIKAV  690 (692)
T ss_pred             hhhhhhhhhcccceeecCceEEEEEeeecc-cCCccceehhc
Confidence              777776655    579999999988884 47799998864

>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]

Probab=96.71  E-value=0.0021  Score=61.78  Aligned_cols=68  Identities=29%  Similarity=0.496  Sum_probs=58.1

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      .+.++.|..+.|+     .||+||+|+     ..+.||+|.++++..      .-|.+|+.+-|++..+-++++.|.|..
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     489999999999862      237899999999999999889888876


Q ss_pred             eccc
Q 026794          128 KQLE  131 (233)
Q Consensus       128 k~~~  131 (233)
                      ..+.
T Consensus       186 ~~~~  189 (715)
T COG1107         186 VGLD  189 (715)
T ss_pred             cCCc
Confidence            6554

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

Probab=96.66  E-value=0.0033  Score=46.24  Aligned_cols=59  Identities=15%  Similarity=0.012  Sum_probs=43.2

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eec---cccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITR---QGFEKR----VVSQDLQLWLSNAPPSGKKFTLL  219 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~---~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls  219 (233)
                      ..|+|+++.++    -+++|+++.+|.+|+.    ++|   .++.++    .+||++.|++...+...+--.|+
T Consensus        11 y~g~V~~i~~~----~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt   80 (88)
T cd04453          11 YLGRVKKIVPG----LQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLT   80 (88)
T ss_pred             EEEEEEEeccC----CcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEE
Confidence            67999999864    3489999999999994    555   233222    57999999999977665544444

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

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

Probab=96.65  E-value=0.002  Score=43.83  Aligned_cols=58  Identities=10%  Similarity=0.135  Sum_probs=43.1

Q ss_pred             ccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794          155 SMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL  219 (233)
Q Consensus       155 ~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls  219 (233)
                      ..+.|+|..+.++      +.++++. +++|+.    +++.+...+    .+||.+++++.++|.+++++.||
T Consensus         3 ~~~~g~V~~v~~~------g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05688           3 DVVEGTVKSITDF------GAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CEEEEEEEEEEee------eEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence            3467888888754      5666665 688985    344344333    68999999999999999999876

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=96.62  E-value=0.0039  Score=42.21  Aligned_cols=62  Identities=8%  Similarity=0.136  Sum_probs=45.6

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEEe----ecccccc----ccccCceEEEEeecCCCCCEEEEEEc
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI----TRQGFEK----RVVSQDLQLWLSNAPPSGKKFTLLAR  221 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~~----~~~~~~~----~~vg~~~~v~i~~~d~~~~ki~Ls~r  221 (233)
                      |..+.|.|..+.+      .+.++++.+++.|+..    ++....+    -.+||.+.+++.+++.+++++.|+.|
T Consensus         3 G~~v~g~V~~v~~------~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        3 GDVVEGTVTEITP------FGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCEEEEEEEEEEc------cEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            3447789988875      3667777889999952    2221111    15799999999999999999999875

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

Probab=96.56  E-value=0.0027  Score=42.16  Aligned_cols=56  Identities=13%  Similarity=0.203  Sum_probs=40.4

Q ss_pred             cCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEE
Q 026794          158 SSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLL  219 (233)
Q Consensus       158 ~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls  219 (233)
                      .|.|..+.+      .+.++++.+|++|+.    +++....++    .+||.+++++.++|.+++++.||
T Consensus         2 ~g~V~~v~~------~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           2 TGKVVSITK------FGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             EEEEEEEEe------eeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            366666653      466777788999995    333222112    57999999999999999998875

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.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.52  E-value=0.0086  Score=55.17  Aligned_cols=61  Identities=21%  Similarity=0.345  Sum_probs=51.3

Q ss_pred             CCCCCEEEEE----e-e-eEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCC---eEEEE
Q 026794           56 VNVEDIFVGR----D-Y-GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS---RITLS  126 (233)
Q Consensus        56 ~~~G~vv~g~----~-~-G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~---ri~LS  126 (233)
                      -++|++++|+    + . ++||+|+      +.+|++|.++..      |.+.|++||.++|-|.+++...+   +|.||
T Consensus       136 ~~~Geiv~g~V~r~~~~~~i~vdlg------~~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilS  203 (374)
T PRK12328        136 KKVGKIVFGTVVRVDNEENTFIEID------EIRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELS  203 (374)
T ss_pred             HhcCcEEEEEEEEEecCCCEEEEcC------CeEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEE
Confidence            4789999999    3 2 4899996      799999999864      57789999999999999998665   77888


Q ss_pred             Ee
Q 026794          127 IK  128 (233)
Q Consensus       127 ~k  128 (233)
                      +.
T Consensus       204 Rt  205 (374)
T PRK12328        204 RT  205 (374)
T ss_pred             cC
Confidence            74

>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]

Probab=96.32  E-value=0.0033  Score=64.30  Aligned_cols=72  Identities=24%  Similarity=0.275  Sum_probs=60.0

Q ss_pred             cCCCCCCEEEEE------eeeE--EEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794           54 SRVNVEDIFVGR------DYGA--FIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (233)
Q Consensus        54 ~~~~~G~vv~g~------~~G~--fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~L  125 (233)
                      +.+.+|.+|.++      .+|.  =|.++     .|++|+||.+++|...+.+|...+++||+|.+||+++|.++=-+.|
T Consensus       981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld-----~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~L 1055 (1299)
T KOG1856|consen  981 ETFYEGAIVPVTVTKVTHRRGICVRVRLD-----CGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVEL 1055 (1299)
T ss_pred             hHhccCceEEEeeeEEEecccceeEEEec-----CCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhh
Confidence            357788888866      3332  35565     5999999999999999999999999999999999999998888888


Q ss_pred             EEecc
Q 026794          126 SIKQL  130 (233)
Q Consensus       126 S~k~~  130 (233)
                      |+|..
T Consensus      1056 s~r~s 1060 (1299)
T KOG1856|consen 1056 SCRTS 1060 (1299)
T ss_pred             hhhhH
Confidence            88753

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.30  E-value=0.00086  Score=63.70  Aligned_cols=122  Identities=8%  Similarity=0.034  Sum_probs=79.7

Q ss_pred             EEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhh-----HHhhhhcC--CCCeeeecCCcc
Q 026794           84 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLL-----ETLEKVIP--QDGSVISDSSSM  156 (233)
Q Consensus        84 Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~-----~~~~~~~~--~g~~~~~~~~~~  156 (233)
                      +.++.++..     .....+++||.+.+.|...+. .+....+.|+....-|.     ...+. |+  .|.+        
T Consensus        73 ~eI~L~eAk-----~~~~~~~vGD~ie~~I~~~~f-gRia~q~aKq~i~Qkire~ere~i~~e-yk~~~GeI--------  137 (470)
T PRK09202         73 KEISLEEAR-----KIDPDAEVGDYIEEEIESVDF-GRIAAQTAKQVIVQKIREAERERVYEE-YKDRVGEI--------  137 (470)
T ss_pred             ceeeHHHHh-----hhCccccCCCeEEEEEccccC-ChHHHHHHHHHHHHHHHHHHHHHHHHH-HHhhcCCE--------
Confidence            555555542     122337899999999998873 22333334455444454     33333 43  6776        


Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEEeeccccc--cccccCceEEEEeecCCCCC--EEEEEEcccceee
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGFE--KRVVSQDLQLWLSNAPPSGK--KFTLLARAGRCKR  227 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~~~~~~~~--~~~vg~~~~v~i~~~d~~~~--ki~Ls~r~~~~vq  227 (233)
                      ++|+|.++...      +.++++ .|++|+.+..+...  .-.+||.++++|.+++.+.+  +|.||-+.-.-+.
T Consensus       138 V~G~V~ri~~~------giiVDL-ggvea~LP~sE~ip~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~p~~l~  205 (470)
T PRK09202        138 ITGVVKRVERG------NIIVDL-GRAEAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLK  205 (470)
T ss_pred             EEEEEEEEecC------CEEEEE-CCeEEEecHHHcCCCccCCCCCEEEEEEEEEecCCCCCeEEEEeCcHHHHH
Confidence            77999988743      566766 58999965444331  11689999999999999877  8999987665544

>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=95.93  E-value=0.0081  Score=41.77  Aligned_cols=53  Identities=6%  Similarity=0.121  Sum_probs=39.6

Q ss_pred             cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecc--ccccc----cccCceEEEEeecCCCCC
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQ--GFEKR----VVSQDLQLWLSNAPPSGK  214 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~--~~~~~----~vg~~~~v~i~~~d~~~~  214 (233)
                      .+.|+|+++.+      .++++++.+|++|+.    ++++  ..+.+    .+||.++++|.+++.++.
T Consensus         3 iV~g~V~~i~~------~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~   65 (70)
T cd05702           3 LVKAKVKSVKP------TQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT   65 (70)
T ss_pred             EEEEEEEEEEC------CcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence            46789988874      467788899999995    4443  23333    679999999999887765

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.

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

Probab=95.52  E-value=0.02  Score=41.03  Aligned_cols=63  Identities=5%  Similarity=-0.118  Sum_probs=45.1

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                      |..+.|+|+.+.+.      ++++++..+.+|+.    ++....++.    .+||.+.++|.+++.+ +++.||.+..
T Consensus         7 GdiV~G~V~~v~~~------~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~~   77 (82)
T cd04454           7 GDIVIGIVTEVNSR------FWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADN   77 (82)
T ss_pred             CCEEEEEEEEEcCC------EEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECCC
Confidence            33477999988743      56677777888884    332222211    6899999999999987 8899999863

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=95.40  E-value=0.01  Score=59.07  Aligned_cols=58  Identities=12%  Similarity=0.072  Sum_probs=46.0

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEE
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTL  218 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~L  218 (233)
                      |..+.|+|+++.      ++|+|+++.+|++|+.    +++.++.++    .+||.+.|++.++|. ++|++|
T Consensus       619 G~i~~G~V~~I~------~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L  684 (684)
T TIGR03591       619 GKIYEGKVVRIM------DFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL  684 (684)
T ss_pred             CcEEEEEEEEEe------CCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence            334779999987      4588898899999994    677666544    579999999999997 677765

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).

>PF09876 DUF2103: Predicted metal-binding protein (DUF2103); InterPro: IPR018664 This family of various putative metal binding prokaryotic proteins has no known function

Probab=95.35  E-value=0.069  Score=40.50  Aligned_cols=59  Identities=24%  Similarity=0.314  Sum_probs=43.4

Q ss_pred             hhhhhcccCCeeEEEeeccccccccccCceEEEEeecCCCCCEEEEEEcccceeeeeEec
Q 026794          173 IFEELLQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRCKRYNFHI  232 (233)
Q Consensus       173 ~~~~l~~~~gv~gl~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~vq~~~~~  232 (233)
                      +...|...++|..+++++-..........+.+|++.-+ ..+-+.|.+|.|..+||+|=|
T Consensus        25 ~L~~la~~~~Vk~IiPG~I~~~~~~~~~gl~lkvt~~~-~~Gn~Kllar~G~SvQEvfVV   83 (103)
T PF09876_consen   25 WLEKLAKHPGVKKIIPGVISRSGGRSSGGLRLKVTRPT-RGGNFKLLARSGSSVQEVFVV   83 (103)
T ss_pred             HHHHHhcCCCCCEEecccEEcCCCCCCCCeEEEEEEec-CCCcEEEEEecCCeeEEEEEE
Confidence            45666777899988877765443343456999998644 444499999999999999954

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=95.17  E-value=0.087  Score=35.93  Aligned_cols=48  Identities=33%  Similarity=0.385  Sum_probs=30.3

Q ss_pred             eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      ++|+|++-+     .+-+-|+|.+++..        .+++||.|.|-|-. |. .+|+..++|
T Consensus        14 ~~g~fL~~~-----~~~~vlLp~~e~~~--------~~~~Gd~v~VFvY~-D~-~~rl~AT~k   61 (61)
T PF13509_consen   14 EFGYFLDDG-----EGKEVLLPKSEVPE--------PLKVGDEVEVFVYL-DK-EGRLVATTK   61 (61)
T ss_dssp             SSEEEEEET-----T-EEEEEEGGG--------------TTSEEEEEEEE--T-TS-EEEE--
T ss_pred             CCEEEEECC-----CCCEEEechHHcCC--------CCCCCCEEEEEEEE-CC-CCCEEEecC
Confidence            899999976     26899999999852        37899999987654 53 567777764

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.05  E-value=0.09  Score=49.50  Aligned_cols=67  Identities=9%  Similarity=0.041  Sum_probs=50.7

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCC---CeEEEEE
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK---SRITLSI  127 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~---~ri~LS~  127 (233)
                      -++|++++|+     +.+++|++...-|..+++|++|.++.      -|.+.|++||.++|-|.++....   -+|.||.
T Consensus       150 ~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eq------ip~E~y~~Gdrika~i~~V~~~~~kGpqIilSR  223 (449)
T PRK12329        150 DLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQ------LPNDNYRANATFKVFLKEVSEGPRRGPQLFVSR  223 (449)
T ss_pred             HhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHc------CCCCcCCCCCEEEEEEEEeecCCCCCCEEEEEc
Confidence            4789999999     55799998410010148999999886      45678999999999999998752   3678876


Q ss_pred             e
Q 026794          128 K  128 (233)
Q Consensus       128 k  128 (233)
                      -
T Consensus       224 t  224 (449)
T PRK12329        224 A  224 (449)
T ss_pred             C
Confidence            4

>PRK11712 ribonuclease G; Provisional

Probab=94.96  E-value=0.12  Score=49.61  Aligned_cols=62  Identities=24%  Similarity=0.492  Sum_probs=46.5

Q ss_pred             hhccCCCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEccccCcc------------cccCcccccCCCCEEEE
Q 026794           51 KYSSRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRV  111 (233)
Q Consensus        51 ~~~~~~~~G~vv~g~-------~~G~fV~l~~~~~~~gv~Glv~~sels~~------------~~~~~~~~~~~Gd~V~v  111 (233)
                      .......+|.+|.|+       =.+|||+|+     .+-.||+|++++...            ...++.+.+++||.|-|
T Consensus        31 ~~~~~~~vGnIY~G~V~~v~pg~~AAFVdIG-----~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLV  105 (489)
T PRK11712         31 REAKRGIVGNIYKGRVSRVLPGMQAAFVDIG-----LDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMV  105 (489)
T ss_pred             cCCcccccccEEEEEEeecCCCCceeEEeeC-----CCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEE
Confidence            334455799999999       346999998     488999999998321            11234566999999999


Q ss_pred             EEEEEe
Q 026794          112 KVIKID  117 (233)
Q Consensus       112 kVi~vd  117 (233)
                      +|..--
T Consensus       106 QV~Ke~  111 (489)
T PRK11712        106 QVVKDP  111 (489)
T ss_pred             EEEeCC
Confidence            998853

>PRK10811 rne ribonuclease E; Reviewed

Probab=94.81  E-value=0.078  Score=54.15  Aligned_cols=57  Identities=26%  Similarity=0.486  Sum_probs=45.3

Q ss_pred             CCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEccccCccccc---------CcccccCCCCEEEEEEEEEe
Q 026794           56 VNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---------DIRDILNEGDEVRVKVIKID  117 (233)
Q Consensus        56 ~~~G~vv~g~-------~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~---------~~~~~~~~Gd~V~vkVi~vd  117 (233)
                      ..+|+||.|+       =.++||+|+     .|..||+|++++...++.         +..+.++.||.|-|.|..-.
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDIG-----~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa  108 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDYG-----AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEE  108 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEec-----CCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecc
Confidence            4589999999       457999998     388999999999654332         23456899999999999854

>TIGR01953 NusA transcription termination factor NusA

Probab=94.81  E-value=0.0056  Score=55.93  Aligned_cols=115  Identities=10%  Similarity=0.097  Sum_probs=72.7

Q ss_pred             CcccccCCCCEEEEEEEEEeCCCCeEEEEEecc-----ccChhhHHhhhhc-CCCCeeeecCCccccCCeeeeccCCChh
Q 026794           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQL-----EEDPLLETLEKVI-PQDGSVISDSSSMSSSNSNTIEPLPGLG  171 (233)
Q Consensus        98 ~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~-----~~dp~~~~~~~~~-~~g~~~~~~~~~~~~g~v~~v~~~~g~~  171 (233)
                      .....+++||.+.+.+...+. .+....+.|+.     ....++...+.+. ..|.+        ++|+|.++.+.    
T Consensus        79 ~~d~~~~vGD~I~~~I~~~~f-gR~aaq~aKqvi~Qkire~ere~i~~ey~~k~Gei--------V~G~V~~v~~~----  145 (341)
T TIGR01953        79 EIDPDVQIGDEVKKEIPPENF-GRIAAQTAKQVILQKIREAERERVYDEFSSKEGEI--------ISGTVKRVNRR----  145 (341)
T ss_pred             hhccccccCCEEEEEecccCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCE--------EEEEEEEEecC----
Confidence            344558899999998865543 22333334442     2333444444432 35666        78999988753    


Q ss_pred             hhhhhhcccCCeeEEEeeccccc--cccccCceEEEEeecCCC--CCEEEEEEcccceee
Q 026794          172 AIFEELLQEDGIDDVRITRQGFE--KRVVSQDLQLWLSNAPPS--GKKFTLLARAGRCKR  227 (233)
Q Consensus       172 ~~~~~l~~~~gv~gl~~~~~~~~--~~~vg~~~~v~i~~~d~~--~~ki~Ls~r~~~~vq  227 (233)
                      + +.++++ .|++|+.+.+....  .-.+||.+++++.+++..  ...+.||.+..+-+.
T Consensus       146 g-~v~Vdi-G~~ea~LP~~E~ip~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~~~v~  203 (341)
T TIGR01953       146 G-NLYVEL-GKTEGILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFVK  203 (341)
T ss_pred             C-cEEEEE-CCeEEEecHHHcCCCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcHHHHH
Confidence            2 135666 48999965554432  226899999999999854  457999988766554

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.

>PHA02945 interferon resistance protein; Provisional

Probab=94.72  E-value=0.048  Score=40.08  Aligned_cols=62  Identities=5%  Similarity=-0.083  Sum_probs=42.4

Q ss_pred             ccCCeeeeccCCChhhhhhhhccc--CCeeEEE-ee-----ccccccc--cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQE--DGIDDVR-IT-----RQGFEKR--VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~--~gv~gl~-~~-----~~~~~~~--~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      +-|+|.. .      ++++++.+.  +|.+|+. +|     ...++.+  .+||.+.+++..+|+.++.|-||.|+-.+
T Consensus        15 vigtV~~-~------d~ga~v~L~EY~g~eg~i~~seveva~~wvK~rd~l~GqkvV~KVirVd~~kg~IDlSlK~V~~   86 (88)
T PHA02945         15 LKGKVYE-N------GYALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKLVGKTVKVKVIRVDYTKGYIDVNYKRMCR   86 (88)
T ss_pred             EEEEEEe-c------CceEEEEecccCCcEEEEEeehhhhccceEeeeeEecCCEEEEEEEEECCCCCEEEeEeeEccc
Confidence            4577665 5      445555444  3788873 23     1122222  57999999999999999999999986543

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

Probab=94.41  E-value=0.043  Score=40.84  Aligned_cols=60  Identities=12%  Similarity=0.030  Sum_probs=41.9

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecccccc-------------c--cccCceEEEEeecCCCC----
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEK-------------R--VVSQDLQLWLSNAPPSG----  213 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~-------------~--~vg~~~~v~i~~~d~~~----  213 (233)
                      +.|.|..+.++      +.|+++. +++|+.    ++++....             .  .+||.++|++.++|.+.    
T Consensus         3 v~g~V~~i~~~------GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~   75 (99)
T cd04460           3 VEGEVVEVVDF------GAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPR   75 (99)
T ss_pred             EEEEEEEEEec------cEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCC
Confidence            45777777744      6666666 588884    33333321             1  67999999999999874    


Q ss_pred             -CEEEEEEccc
Q 026794          214 -KKFTLLARAG  223 (233)
Q Consensus       214 -~ki~Ls~r~~  223 (233)
                       .++.||++..
T Consensus        76 ~~~i~ls~k~~   86 (99)
T cd04460          76 ESKIGLTMRQP   86 (99)
T ss_pred             CceEEEEEecC
Confidence             5899999754

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.

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

Probab=93.85  E-value=0.046  Score=52.66  Aligned_cols=66  Identities=15%  Similarity=0.091  Sum_probs=53.9

Q ss_pred             CCccccCCeeeeccCCChhhhhhhhcccCCeeEE----Eeeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          153 SSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDV----RITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       153 ~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl----~~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      .|++.+++++.+.      ++|+++++.+|..||    +++...+.+|    .|||+++||..+.|+..+ +.||.|+.-
T Consensus       668 ~g~vy~~tIt~~r------d~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~-~~ls~ralL  740 (760)
T KOG1067|consen  668 FGGVYTATITEIR------DTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGG-IMLSSRALL  740 (760)
T ss_pred             eeeEEEEEEeeec------ccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecCccc-eeehhhhhc
Confidence            5666777777766      568889999999998    4788778888    589999999999999888 888888754


Q ss_pred             e
Q 026794          225 C  225 (233)
Q Consensus       225 ~  225 (233)
                      +
T Consensus       741 p  741 (760)
T KOG1067|consen  741 P  741 (760)
T ss_pred             C
Confidence            3

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

Probab=93.72  E-value=0.11  Score=35.70  Aligned_cols=59  Identities=3%  Similarity=0.041  Sum_probs=39.8

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEEeecccc--ccccccCceEEEEeecCCCC--CEEEEE
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVRITRQGF--EKRVVSQDLQLWLSNAPPSG--KKFTLL  219 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~~~~~~~--~~~~vg~~~~v~i~~~d~~~--~ki~Ls  219 (233)
                      |..++|+|..+.+.      ++++++. +++|+.+.....  +.-.+||.+++++.+++.++  .+|.||
T Consensus         4 g~iV~G~V~~~~~~------~~~vdig-~~eg~lp~~e~~~~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS   66 (67)
T cd04455           4 GEIVTGIVKRVDRG------NVIVDLG-KVEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKGPQIILS   66 (67)
T ss_pred             CCEEEEEEEEEcCC------CEEEEcC-CeEEEeeHHHCCCCCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence            34478999888753      5667775 488985433322  11268999999999998654  456665

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.

>TIGR02063 RNase_R ribonuclease R

Probab=93.62  E-value=0.083  Score=52.78  Aligned_cols=61  Identities=10%  Similarity=0.048  Sum_probs=45.4

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccC-CeeEEE----eecccc-----------c---c-ccccCceEEEEeecCCCC
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR----ITRQGF-----------E---K-RVVSQDLQLWLSNAPPSG  213 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~-gv~gl~----~~~~~~-----------~---~-~~vg~~~~v~i~~~d~~~  213 (233)
                      |...+|.|+.++++      |.|+++++ |++|+.    ++.+..           +   . -.+||.++|++.++|.++
T Consensus       628 G~~~~g~V~~v~~f------GifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~  701 (709)
T TIGR02063       628 GEEFEGVISGVTSF------GLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDT  701 (709)
T ss_pred             CcEEEEEEEEEEeC------CEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEeccc
Confidence            44578999988855      66777788 899994    332211           1   1 157999999999999999


Q ss_pred             CEEEEEE
Q 026794          214 KKFTLLA  220 (233)
Q Consensus       214 ~ki~Ls~  220 (233)
                      ++|.++.
T Consensus       702 ~~I~~~l  708 (709)
T TIGR02063       702 GKIDFEL  708 (709)
T ss_pred             CeEEEEE
Confidence            9999874

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.

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

Probab=92.90  E-value=0.076  Score=46.52  Aligned_cols=63  Identities=6%  Similarity=-0.056  Sum_probs=46.9

Q ss_pred             ccCCeeeeccCCChhhhhhhhcc--cCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQ--EDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~--~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      +-|+|..+.++      |+++.|  =+|++|+.    +++..+.+-    .+||.+-+++..+|++++.|-||+|.-++
T Consensus        15 Vv~tV~~V~~~------GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~   87 (269)
T COG1093          15 VVGTVKQVADY------GAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTE   87 (269)
T ss_pred             EEEEEEEeecc------ccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence            55888888754      666644  46899994    444334332    47999999999999999999999987554

>PRK11642 exoribonuclease R; Provisional

Probab=92.52  E-value=0.16  Score=51.51  Aligned_cols=61  Identities=8%  Similarity=0.110  Sum_probs=45.2

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCC-eeEEE----eecc--ccc------------c-ccccCceEEEEeecCCCC
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDG-IDDVR----ITRQ--GFE------------K-RVVSQDLQLWLSNAPPSG  213 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~g-v~gl~----~~~~--~~~------------~-~~vg~~~~v~i~~~d~~~  213 (233)
                      |...+|.|+.++++      |.|++++++ |+|+.    ++++  ...            . -.+||.|+|+|.++|+++
T Consensus       644 Ge~f~G~Is~V~~f------GifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~  717 (813)
T PRK11642        644 GNVFKGVISSVTGF------GFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDE  717 (813)
T ss_pred             CcEEEEEEEEeecC------ceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCC
Confidence            44478999888755      666777875 99994    3332  111            1 157999999999999999


Q ss_pred             CEEEEEE
Q 026794          214 KKFTLLA  220 (233)
Q Consensus       214 ~ki~Ls~  220 (233)
                      ++|.++.
T Consensus       718 rkI~f~l  724 (813)
T PRK11642        718 RKIDFSL  724 (813)
T ss_pred             CeEEEEE
Confidence            9999987

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=89.77  E-value=0.15  Score=47.11  Aligned_cols=106  Identities=9%  Similarity=0.057  Sum_probs=62.0

Q ss_pred             ccccCCCCEEEEEEEEEeCCCCeEEEEEeccccCh-----hhHHhhhh-cCCCCeeeecCCccccCCeeeeccCCChhhh
Q 026794          100 RDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP-----LLETLEKV-IPQDGSVISDSSSMSSSNSNTIEPLPGLGAI  173 (233)
Q Consensus       100 ~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp-----~~~~~~~~-~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~  173 (233)
                      ....++||.+...+...+..+.. ..+.|+....-     .+...+.+ -+.|++        ++|+|.+..+.      
T Consensus        84 ~~~~~vGD~i~~~I~~~~fgR~a-aq~akqvI~Qkire~ere~v~~ef~~k~Gei--------V~G~V~~~~~~------  148 (362)
T PRK12327         84 NPAYELGDVIEIEVTPKDFGRIA-AQTAKQVIMQRLREAEREIIYNEFSEREGDI--------VTGVVQRRDNR------  148 (362)
T ss_pred             CccccCCCEEEEecCcCCCChHH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCE--------EEEEEEEEeCC------
Confidence            34478899999988776643322 22222221111     11122222 145666        78999987753      


Q ss_pred             hhhhcccCCeeEEEeeccccccc--cccCceEEEEeecCCCCC--EEEEEEc
Q 026794          174 FEELLQEDGIDDVRITRQGFEKR--VVSQDLQLWLSNAPPSGK--KFTLLAR  221 (233)
Q Consensus       174 ~~~l~~~~gv~gl~~~~~~~~~~--~vg~~~~v~i~~~d~~~~--ki~Ls~r  221 (233)
                      +.++++. |++|+.+.+......  .+||.+++++.+++.+.+  .+.||--
T Consensus       149 ~~~Vdlg-~vEa~LP~~E~ip~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt  199 (362)
T PRK12327        149 FVYVNLG-KIEAVLPPAEQIPGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT  199 (362)
T ss_pred             cEEEEeC-CeEEEecHHHcCCCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence            4456664 699996533332211  579999999999986543  4766654

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

Probab=88.67  E-value=0.67  Score=46.01  Aligned_cols=61  Identities=10%  Similarity=0.122  Sum_probs=44.4

Q ss_pred             CccccCCeeeeccCCChhhhhhhhccc-CCeeEEE----eeccc---------c--c---c-ccccCceEEEEeecCCCC
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVR----ITRQG---------F--E---K-RVVSQDLQLWLSNAPPSG  213 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~-~gv~gl~----~~~~~---------~--~---~-~~vg~~~~v~i~~~d~~~  213 (233)
                      |...+|.|+.+.++      |.|++++ .|++|+.    ++++.         +  +   . -.+||.++|++.++|+++
T Consensus       573 G~~~~g~I~~v~~~------GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~  646 (654)
T TIGR00358       573 GTEFSGEISSVTRF------GMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMET  646 (654)
T ss_pred             CcEEEEEEEeEEcC------cEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEeccc
Confidence            34477999888855      6667777 7899984    43331         0  1   1 158999999999999999


Q ss_pred             CEEEEEE
Q 026794          214 KKFTLLA  220 (233)
Q Consensus       214 ~ki~Ls~  220 (233)
                      ++|.++.
T Consensus       647 ~~I~f~l  653 (654)
T TIGR00358       647 RSIIFEL  653 (654)
T ss_pred             CeEEEEE
Confidence            9998874

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.

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

Probab=88.63  E-value=0.7  Score=38.22  Aligned_cols=59  Identities=15%  Similarity=0.070  Sum_probs=40.3

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEEe----ecccc--------------ccc-cccCceEEEEeecC-----CC
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVRI----TRQGF--------------EKR-VVSQDLQLWLSNAP-----PS  212 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~~----~~~~~--------------~~~-~vg~~~~v~i~~~d-----~~  212 (233)
                      ++|.|+++.++      |.|+++. .++|+..    ..+..              +.. .+||.+.++|.+++     ++
T Consensus        85 v~G~V~~v~~~------GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~  157 (179)
T TIGR00448        85 VEGEVIEIVEF------GAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPE  157 (179)
T ss_pred             EEEEEEEEEee------EEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCC
Confidence            66888888855      5556554 4777742    11111              011 57999999999998     67


Q ss_pred             CCEEEEEEcc
Q 026794          213 GKKFTLLARA  222 (233)
Q Consensus       213 ~~ki~Ls~r~  222 (233)
                      ..++.|++|+
T Consensus       158 ~~~I~lt~k~  167 (179)
T TIGR00448       158 GSKIGLTMRQ  167 (179)
T ss_pred             cceEEEEecc
Confidence            7899999986

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

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

Probab=86.94  E-value=3.3  Score=33.91  Aligned_cols=63  Identities=17%  Similarity=0.180  Sum_probs=43.2

Q ss_pred             hhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc----cccC-------cccccCCCCEEEEEEE
Q 026794           51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQD-------IRDILNEGDEVRVKVI  114 (233)
Q Consensus        51 ~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~----~~~~-------~~~~~~~Gd~V~vkVi  114 (233)
                      ...-+.-.|++++|+     ..|+|++.+      .++.++..-....+    .-+|       -.+..++|..|+++|+
T Consensus        74 av~FkpfKGEVvdgvV~~Vnk~G~F~~~G------Pl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kii  147 (170)
T KOG3298|consen   74 AVTFKPFKGEVVDGVVTKVNKMGVFARSG------PLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKII  147 (170)
T ss_pred             EEEEeecCCcEEEEEEEEEeeeeEEEecc------ceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEE
Confidence            334467789999999     889999997      57777654333322    2222       1225788999999999


Q ss_pred             EEeCC
Q 026794          115 KIDRE  119 (233)
Q Consensus       115 ~vd~e  119 (233)
                      ....+
T Consensus       148 gtr~~  152 (170)
T KOG3298|consen  148 GTRVD  152 (170)
T ss_pred             EEEEe
Confidence            87643

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

Probab=85.09  E-value=4.5  Score=33.57  Aligned_cols=72  Identities=21%  Similarity=0.126  Sum_probs=46.1

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCC---CccEEEEEEccccCcc--cccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWD--LIQDIRDILNEGDEVRVKVIKIDREKSRIT  124 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~---~~gv~Glv~~sels~~--~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~  124 (233)
                      ....|++|.++     ..-+=|+|--.++   -...+|+||..++...  ---++...|++||.|.|+|++.+. .....
T Consensus        65 LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~-~~~y~  143 (193)
T KOG3409|consen   65 LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGD-GSNYL  143 (193)
T ss_pred             CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCC-CCcEE
Confidence            46799999998     1113333321111   0257899999888542  123466679999999999999764 45555


Q ss_pred             EEE
Q 026794          125 LSI  127 (233)
Q Consensus       125 LS~  127 (233)
                      |+.
T Consensus       144 LTt  146 (193)
T KOG3409|consen  144 LTT  146 (193)
T ss_pred             EEE
Confidence            554

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=84.84  E-value=6.3  Score=34.09  Aligned_cols=59  Identities=3%  Similarity=-0.091  Sum_probs=41.7

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecccc----ccc----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGF----EKR----VVSQDLQLWLSNAPPSGKKFTLLARA  222 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~----~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~  222 (233)
                      +-|+|+.+.+.      +.++++.++.+|+.    +++.++    .+.    .+||.+.++|.+++.++. +.||.|.
T Consensus        67 ViG~V~~i~~~------~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~-~~LS~k~  137 (235)
T PRK04163         67 VIGKVTDVTFS------GWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRD-VVLTLKG  137 (235)
T ss_pred             EEEEEEEEeCc------eEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCc-EEEEEcC
Confidence            56888887743      56677787788773    444432    111    569999999999986654 9999875

>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]

Probab=83.22  E-value=1.9  Score=41.41  Aligned_cols=73  Identities=23%  Similarity=0.371  Sum_probs=53.5

Q ss_pred             hhhccCCCCCCEEEEE-------eeeEEEEEccCCCCccEEEEEEccccCcccccCc-----ccccCCCCEEEEEEEEEe
Q 026794           50 NKYSSRVNVEDIFVGR-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI-----RDILNEGDEVRVKVIKID  117 (233)
Q Consensus        50 ~~~~~~~~~G~vv~g~-------~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~-----~~~~~~Gd~V~vkVi~vd  117 (233)
                      +.-.....+|.+|.|+       =-.+||+++.     .-.||+|.+++.+ +...+     ...++.||.+-|.|+.-.
T Consensus        29 e~~~~~~~~gniy~grv~~i~p~~~aafvdig~-----~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~  102 (487)
T COG1530          29 ERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIGL-----ERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEP  102 (487)
T ss_pred             ecCCcEeeecCceEEEecccCccchhheeeccC-----CccceEEecccch-hhhhcccccceeeecCCceEEEEEEeec
Confidence            3445566789999999       2358999983     6789999999998 54433     457999999999999876


Q ss_pred             CCCCeEEEEEe
Q 026794          118 REKSRITLSIK  128 (233)
Q Consensus       118 ~e~~ri~LS~k  128 (233)
                      ..+.--.||..
T Consensus       103 ~G~Kga~lT~~  113 (487)
T COG1530         103 RGTKGARLTTD  113 (487)
T ss_pred             CccccccceeE
Confidence            54443344443

>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=81.94  E-value=1.4  Score=31.23  Aligned_cols=42  Identities=10%  Similarity=0.099  Sum_probs=30.4

Q ss_pred             CCCCCCCCCchhHhhhcccCCCCEE-EEEEEEEeCCCCEEEEEec
Q 026794            2 SPSHSCKEPQKSIHEIAKGLTGSII-SVKVIQANEEMKKLVFSEK   45 (233)
Q Consensus         2 ~~~~~~~~p~~~~~~~~~~~vG~~v-~~~Vi~id~~~~~i~lS~k   45 (233)
                      +.+||+.++++.......-.+||++ ++.|+  |...+.+.+|.|
T Consensus        30 ~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL--~~~~r~i~lt~K   72 (72)
T cd05699          30 PTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             EccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence            4578877666555433444599999 88888  888888888865

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.

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

Probab=80.57  E-value=2.8  Score=34.66  Aligned_cols=59  Identities=14%  Similarity=0.085  Sum_probs=39.0

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccc-------------cc--cccCceEEEEeecCCCCC---
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFE-------------KR--VVSQDLQLWLSNAPPSGK---  214 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~-------------~~--~vg~~~~v~i~~~d~~~~---  214 (233)
                      +.|.|+.+.+.      |.++++. .++|+.    +..++..             ..  .+||.+.++|.+++.++.   
T Consensus        85 v~g~V~~v~~~------Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~  157 (187)
T PRK08563         85 VEGEVVEVVEF------GAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPR  157 (187)
T ss_pred             EEEEEEEEEcc------EEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCC
Confidence            56888888754      5555555 377773    2222111             01  569999999999987653   


Q ss_pred             --EEEEEEcc
Q 026794          215 --KFTLLARA  222 (233)
Q Consensus       215 --ki~Ls~r~  222 (233)
                        ++.|+++.
T Consensus       158 ~~~I~ls~~~  167 (187)
T PRK08563        158 GSKIGLTMRQ  167 (187)
T ss_pred             CCEEEEEecC
Confidence              89999884

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	233
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		6e-06
1yz6_A	274	Crystal Structure Of Intact Alpha Subunit Of Aif2 F		7e-06
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		2e-05
3bzc_A	785	Crystal Structure Of The Tex Protein From Pseudomon		3e-05
2oce_A	780	Crystal Structure Of Tex Family Protein Pa5201 From		3e-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 = 60.5 bits (145), 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 = 47.4 bits (111), Expect = 6e-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 = 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: 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 = 46.2 bits (108), Expect = 2e-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|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas Aeruginosa, Crystal Form I Length = 785

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-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|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From Pseudomonas Aeruginosa Length = 780

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-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|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures Length = 76

Iteration: 1
 Score = 43.5 bits (101), 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	233
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	3e-22
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	5e-22
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	1e-21
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	2e-04
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	2e-21
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	7e-06
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	2e-19
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	6e-19
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	1e-18
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	1e-17
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	8e-17
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	1e-15
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	2e-15
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	2e-15
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	4e-15
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	9e-13
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	5e-12
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	2e-07
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	2e-07
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	3e-07
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	5e-07
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	2e-06
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	5e-05
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	5e-05
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	6e-04

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Length = 130

 Score = 87.5 bits (217), Expect = 3e-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 = 5e-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 = 1e-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 = 2e-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 = 7e-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 = 2e-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 = 82.7 bits (204), Expect = 6e-19
 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 = 81.2 bits (200), Expect = 1e-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 = 1e-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 = 8e-17
 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 = 74.5 bits (184), 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

>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

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 74.1 bits (183), 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

>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 = 4e-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 = 66.1 bits (162), 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 = 5e-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

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Length = 1030

 Score = 50.3 bits (120), Expect = 2e-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

>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 = 48.4 bits (115), 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

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Length = 1219

 Score = 49.9 bits (119), Expect = 3e-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 = 47.6 bits (113), Expect = 5e-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 = 46.9 bits (111), 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 = 41.5 bits (97), Expect = 5e-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 = 40.8 bits (95), Expect = 5e-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 = 38.4 bits (89), Expect = 6e-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	233
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.89
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.83
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.77
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.75
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.74
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.69
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.68
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.68
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.68
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.67
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.66
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.62
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.61
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.54
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.51
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.44
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.42
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	99.37
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.35
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.28
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.23
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	99.17
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	99.15
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.15
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	99.13
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	99.12
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.12
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	99.11
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.98
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.91
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.88
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	98.87
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.86
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.85
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.81
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.44
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	98.4
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	98.39
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	98.37
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	98.31
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	98.3
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	98.29
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.23
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	98.22
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	98.19
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.18
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.18
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.16
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	98.11
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	98.06
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.04
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	98.03
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	97.9
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	97.87
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.86
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	97.84
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.7
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.55
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	97.54
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.52
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	97.51
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.4
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	97.4
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	97.35
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	96.72
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	96.43
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	96.4
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	96.21
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	96.11
2r7d_A	469	Ribonuclease II family protein; structural genomic	95.66
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	95.51
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	93.65
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	92.98
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	92.55
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	92.18
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	92.11
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	91.71
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	91.57
1jjg_A	102	M156R; beta barrel, S1 motif, OB fold, MYXV156R, N	91.16
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	87.95
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	87.84
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	85.6
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	82.11

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

Probab=99.89  E-value=9.3e-23  Score=179.50  Aligned_cols=171  Identities=13%  Similarity=0.095  Sum_probs=136.3

Q ss_pred             CCCCEEEEEEEEEeCCCCEEEEEechhhHhhhccCCCCCCEEEEE------eeeEEEEEccCCCCccEEEEEEccccCcc
Q 026794           21 LTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR------DYGAFIHLRFPDGLYHLTGLVHVSEVSWD   94 (233)
Q Consensus        21 ~vG~~v~~~Vi~id~~~~~i~lS~k~~~~~~~~~~~~~G~vv~g~------~~G~fV~l~~~~~~~gv~Glv~~sels~~   94 (233)
                      .+||+|+|.|+ .|. .+++++|.+.       ..+++|+++.|+      +|||||+++.    ++.+||||+||++|.
T Consensus        41 ~vGdevev~v~-~d~-~~r~iat~~~-------p~~~~G~~~~g~V~~v~~~~GaFVdiG~----~~~d~lvp~sel~~~  107 (285)
T 3go5_A           41 TVGDTVKGFAY-TDM-KQKLRLTTLE-------VTATQDQFGWGRVTEVRKDLGVFVDTGL----PDKEIVVSLDILPEL  107 (285)
T ss_dssp             CTTSEEEEEEE-ECT-TSCEEEECSC-------CCSCSSSCEEEEEEEEETTTEEEEECSC----TTCCEEEEGGGSCSS
T ss_pred             ccCCEEEEEEE-ECC-CCCEEEeccc-------ccccCCCEEEEEEEEEccCceEEEEECC----CCcEEEEEHHHCCcc
Confidence            69999999987 565 4566677543       247899999998      3899999961    158999999999996


Q ss_pred             cccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecc-ccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhhh
Q 026794           95 LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL-EEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAI  173 (233)
Q Consensus        95 ~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~-~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~  173 (233)
                      +.    ..+++||.+.|. +.+|+ ++||.+|+|+. ..+||....+ .++.|+.        ++|+|.++++      +
T Consensus       108 ~~----~~~~~Gd~v~v~-l~iD~-~~Ri~ls~k~~~~~~~~~~~~~-~~~~G~~--------V~g~V~~i~~------~  166 (285)
T 3go5_A          108 KE----LWPKKGDQLYIR-LEVDK-KDRIWGLLAYQEDFQRLARPAY-NNMQNQN--------WPAIVYRLKL------S  166 (285)
T ss_dssp             GG----GSCCTTCEEEEE-EEECT-TSCEEEEECCHHHHHHHCCCCC-SCCTTCE--------EEEEEEEEET------T
T ss_pred             cc----cccCCCCEEEEE-EEECC-CCcEEEEehhhhhcchhhhhhh-hCCCCCE--------EEEEEEEEeC------C
Confidence            53    346899999766 69998 79999999986 5789965444 4677887        7799999885      5


Q ss_pred             hhhh-cccCCeeEEEeeccccccccccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          174 FEEL-LQEDGIDDVRITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       174 ~~~l-~~~~gv~gl~~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      |+|+ .+++|+.||.--.+..+...+||+++++|.+++++++||+||.|+...
T Consensus       167 G~fV~~i~~g~~Glih~SEl~~~l~~Gd~v~~~V~~id~~d~kI~LSlk~~~~  219 (285)
T 3go5_A          167 GTFVYLPENNMLGFIHPSERYAEPRLGQVLDARVIGFREVDRTLNLSLKPRSF  219 (285)
T ss_dssp             EEEEEETTTTEEEEECGGGCSSCCCTTCEEEEEEEEEETTTTEEEEECSCCCC
T ss_pred             cEEEEEeCCCeEEEEEHHHccccCCCCCEEEEEEEEEECCCCeEEEEeChhhh
Confidence            7888 889999999633333334578999999999999999999999997644

>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=99.83  E-value=5e-22  Score=164.26  Aligned_cols=112  Identities=21%  Similarity=0.375  Sum_probs=84.7

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~  130 (233)
                      +++|+++.|+     +||+||+|.+.   .+++||||+|+++|+++.++++.|++||.|+|+|+++|.++++|+||+|++
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     99999999421   279999999999999999999999999999999999999999999999999


Q ss_pred             ccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEE
Q 026794          131 EEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDV  186 (233)
Q Consensus       131 ~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl  186 (233)
                      .++||....++ ++.|+.        ++|++..+++     .|+  +++++|++||
T Consensus        90 ~~~p~~~~~~~-~~~g~~--------v~g~v~~i~~-----~~g--v~l~~giegl  129 (182)
T 1kl9_A           90 SPEEAIKCEDK-FTKSKT--------VYSILRHVAE-----VLE--YTKDEQLESL  129 (182)
T ss_dssp             CHHHHHHHHHH-HHHHHH--------HHHHHHHHHH-----HTT--CCSHHHHHHH
T ss_pred             CcChHHHHHHh-ccCCCE--------EEEEEEEchh-----hcC--CcccCChhhe
Confidence            99999766654 566666        6788887775     145  5668899988

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

Probab=99.77  E-value=2.7e-19  Score=137.39  Aligned_cols=88  Identities=36%  Similarity=0.627  Sum_probs=80.0

Q ss_pred             hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc-cccCcccccCCCCEEEEEEEEEeCCCC
Q 026794           48 VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKS  121 (233)
Q Consensus        48 ~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~-~~~~~~~~~~~Gd~V~vkVi~vd~e~~  121 (233)
                      +|+.+...+++|+++.|+     +||+||+|+     ++++||||+|+++|+ +..++.+.|++||.|+|+|+++|.+++
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            488888899999999999     999999997     389999999999984 788999999999999999999999999


Q ss_pred             eEEEEEeccccChhhHHhh
Q 026794          122 RITLSIKQLEEDPLLETLE  140 (233)
Q Consensus       122 ri~LS~k~~~~dp~~~~~~  140 (233)
                      +|.||+|++.+|||+++.+
T Consensus        95 rI~lslk~~~~~p~~~~~~  113 (115)
T 2khi_A           95 RISLGLKQCKANPWQQFAE  113 (115)
T ss_dssp             EEEECCCCCCSSCCCCCCC
T ss_pred             EEEEEEEecCcCHHHHHHh
Confidence            9999999999999975443

>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=99.75  E-value=2.1e-19  Score=147.71  Aligned_cols=97  Identities=23%  Similarity=0.388  Sum_probs=77.7

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccc
Q 026794           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  131 (233)
Q Consensus        57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~  131 (233)
                      ++|+++.|+     +||+||+|.++   .+++||||+|+++|+++.++++.|++||.|+|+|+++|.++++|.||+|++.
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            499999999     99999999411   2799999999999999999999999999999999999999999999999999


Q ss_pred             cChhhHHhhhhcCCCCeeeecCCccccCCeeeec
Q 026794          132 EDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE  165 (233)
Q Consensus       132 ~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~  165 (233)
                      ++||....++ ++.|+.        +.|+|..++
T Consensus        91 ~~~~~~~~~~-~~~g~~--------v~g~V~~i~  115 (175)
T 2a19_A           91 SEDIIKCEEK-YQKSKT--------VHSILRYCA  115 (175)
T ss_dssp             HHHHHHHHHH-HHHHHH--------HHHHHHHHH
T ss_pred             cChHHHHHHh-ccCCCc--------ceEEEEEch
Confidence            9999876665 566666        568777776

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

Probab=99.74  E-value=9.4e-18  Score=147.59  Aligned_cols=108  Identities=13%  Similarity=0.122  Sum_probs=95.2

Q ss_pred             cCCCCEEEEEEEEEeCCCCEEEEEechh----hHhhhccCCCCCCEEEEE-----eeeEEE-EEccCCCCccEEEEEEcc
Q 026794           20 GLTGSIISVKVIQANEEMKKLVFSEKDA----VWNKYSSRVNVEDIFVGR-----DYGAFI-HLRFPDGLYHLTGLVHVS   89 (233)
Q Consensus        20 ~~vG~~v~~~Vi~id~~~~~i~lS~k~~----~~~~~~~~~~~G~vv~g~-----~~G~fV-~l~~~~~~~gv~Glv~~s   89 (233)
                      ..+||++.++ +.+|+ ++|+++|+|++    +|+.....+++|++++|+     +||+|| .++     .+++||||+|
T Consensus       112 ~~~Gd~v~v~-l~iD~-~~Ri~ls~k~~~~~~~~~~~~~~~~~G~~V~g~V~~i~~~G~fV~~i~-----~g~~Glih~S  184 (285)
T 3go5_A          112 PKKGDQLYIR-LEVDK-KDRIWGLLAYQEDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYLPE-----NNMLGFIHPS  184 (285)
T ss_dssp             CCTTCEEEEE-EEECT-TSCEEEEECCHHHHHHHCCCCCSCCTTCEEEEEEEEEETTEEEEEETT-----TTEEEEECGG
T ss_pred             cCCCCEEEEE-EEECC-CCcEEEEehhhhhcchhhhhhhhCCCCCEEEEEEEEEeCCcEEEEEeC-----CCeEEEEEHH
Confidence            3699999766 79998 78999999754    488888999999999999     999999 997     3899999999


Q ss_pred             ccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhh
Q 026794           90 EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKV  142 (233)
Q Consensus        90 els~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~  142 (233)
                      |++.        .+++||.|+|+|+++|++++||+||+|++..++|++.++..
T Consensus       185 El~~--------~l~~Gd~v~~~V~~id~~d~kI~LSlk~~~~~~~~~~a~~i  229 (285)
T 3go5_A          185 ERYA--------EPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQMI  229 (285)
T ss_dssp             GCSS--------CCCTTCEEEEEEEEEETTTTEEEEECSCCCCCCCCHHHHHH
T ss_pred             Hccc--------cCCCCCEEEEEEEEEECCCCeEEEEeChhhhhccchHHHHH
Confidence            9973        58999999999999999899999999999999987766654

>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=99.69  E-value=1.1e-17  Score=129.31  Aligned_cols=87  Identities=28%  Similarity=0.389  Sum_probs=78.1

Q ss_pred             hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCC--
Q 026794           48 VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--  120 (233)
Q Consensus        48 ~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~--  120 (233)
                      .|+.+...+++|++|.|+     +||+||+|.+    .+.+||||+|+++|.++.++.+.|++||.|+|+|+++|.++  
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            477778889999999999     9999999962    23699999999999999999999999999999999999764  


Q ss_pred             CeEEEEEeccccChhhHH
Q 026794          121 SRITLSIKQLEEDPLLET  138 (233)
Q Consensus       121 ~ri~LS~k~~~~dp~~~~  138 (233)
                      ++|.||+|++.++||++.
T Consensus        88 ~~i~LSlk~~~~~~~~~~  105 (119)
T 2cqo_A           88 IKVSLSMKVVNQGTGKDL  105 (119)
T ss_dssp             EEEEEESTTBCSSSCCBS
T ss_pred             ceEEEEEeecccCCcccc
Confidence            799999999999999653

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

Probab=99.68  E-value=7.4e-17  Score=126.41  Aligned_cols=78  Identities=41%  Similarity=0.742  Sum_probs=74.0

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        54 ~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      ..+++|++|.|+     +||+||+|.+     +++||||+|+++|.++.++.+.|++||.|+|+|+++|.++++|.||+|
T Consensus         3 ~~~~vG~iv~G~V~~i~~~G~FV~l~~-----~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk   77 (130)
T 2k4k_A            3 AKFEVGSVYTGKVTGLQAYGAFVALDE-----ETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIR   77 (130)
T ss_dssp             CCCCTTCEEEEEEEEEETTEEEEEEET-----TEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESH
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEECC-----CcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence            568999999998     9999999973     899999999999999999999999999999999999999999999999


Q ss_pred             ccccChhh
Q 026794          129 QLEEDPLL  136 (233)
Q Consensus       129 ~~~~dp~~  136 (233)
                      ++.++||.
T Consensus        78 ~~~~~p~~   85 (130)
T 2k4k_A           78 ATQAAPEK   85 (130)
T ss_dssp             HHHHSCCC
T ss_pred             ecccCccc
Confidence            99999985

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

Probab=99.68  E-value=6.8e-17  Score=118.48  Aligned_cols=77  Identities=32%  Similarity=0.439  Sum_probs=69.3

Q ss_pred             ccCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEEcc-ccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           53 SSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        53 ~~~~~~G~vv~g~----~~G~fV~l~~~~~~~gv~Glv~~s-els~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      +...++|+++.|+    +||+||+|.+.   ++++||+|+| +++|+++.++++.+ +||.|+|+|+++|.+++||.||+
T Consensus         6 y~~~~vG~~~~G~V~v~~fG~FVel~~~---~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lsl   81 (88)
T 1luz_A            6 YSLPNAGDVIKGRVYEKDYALYIYLFDY---PHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNY   81 (88)
T ss_dssp             SCCCCTTCEEEEEEEEETTEEEEEETTC---TTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEE
T ss_pred             ecCCCCCCEEEEEEEEEccEEEEEECCC---CCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEE
Confidence            3457899999998    99999999631   1699999999 99999999999999 99999999999999999999999


Q ss_pred             eccccC
Q 026794          128 KQLEED  133 (233)
Q Consensus       128 k~~~~d  133 (233)
                      |++.+|
T Consensus        82 k~~~~~   87 (88)
T 1luz_A           82 KRMCRH   87 (88)
T ss_dssp             EEECSC
T ss_pred             eecCCC
Confidence            998765

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

Probab=99.68  E-value=6.1e-17  Score=123.03  Aligned_cols=86  Identities=28%  Similarity=0.412  Sum_probs=75.4

Q ss_pred             EEechh---hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEE
Q 026794           42 FSEKDA---VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKV  113 (233)
Q Consensus        42 lS~k~~---~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkV  113 (233)
                      -|.|++   +|+.+...+++|+++.|+     +||+||+|+     .+++||||+|++++.++.++.+.|++||.|+|+|
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   599999999999999999     999999997     3899999999999999999999999999999999


Q ss_pred             EEEeCCCCeEEEEEecccc
Q 026794          114 IKIDREKSRITLSIKQLEE  132 (233)
Q Consensus       114 i~vd~e~~ri~LS~k~~~~  132 (233)
                      +++|.++++|.||+|++.+
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            9999988999999998754

>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=1e-17  Score=148.66  Aligned_cols=99  Identities=26%  Similarity=0.441  Sum_probs=86.7

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~  130 (233)
                      +++|+++.|+     +||+||+|.+++   +++||||+|+++|+++.++.+.|++||.|.|+|+++|+++++|.||+|++
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            4699999999     999999996211   79999999999999999999999999999999999999999999999999


Q ss_pred             ccChhhHHhhhhcCCCCeeeecCCccccCCeeeecc
Q 026794          131 EEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEP  166 (233)
Q Consensus       131 ~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~  166 (233)
                      .++||....++ ++.|+.        +.|.|+++.+
T Consensus        88 ~~~p~~~~~~~-~~~G~~--------v~G~V~~v~~  114 (308)
T 1q8k_A           88 SPEEAIKCEDK-FTKSKT--------VYSILRHVAE  114 (308)
T ss_dssp             CHHHHHHHHHH-HHHHHH--------HHHHHHHHHH
T ss_pred             ccChHHHHHHH-ccCCCe--------eEEEEEEccc
Confidence            99999877665 555665        5688877765

>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=99.66  E-value=1.6e-16  Score=119.70  Aligned_cols=81  Identities=26%  Similarity=0.553  Sum_probs=71.7

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEcccc-CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV-SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sel-s~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      ...+++|+++.|+     +||+||+|.+.+  ++++||||+|++ ++.++.++.+.|++||.|+|+|+++|.  +||.||
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            4568999999998     999999997311  169999999999 677889999999999999999999996  699999


Q ss_pred             EeccccChhhH
Q 026794          127 IKQLEEDPLLE  137 (233)
Q Consensus       127 ~k~~~~dp~~~  137 (233)
                      +|++.++||.+
T Consensus        83 lk~~~~~~~~~   93 (103)
T 2eqs_A           83 MKDVDQETGED   93 (103)
T ss_dssp             STTBCTTTCCB
T ss_pred             EeecccCCchh
Confidence            99999999963

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

Probab=99.62  E-value=2.3e-15  Score=108.14  Aligned_cols=70  Identities=31%  Similarity=0.491  Sum_probs=63.2

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .+++|+++.|+     +||+||+|+     .+++||||+|+++|.++    +.|++||.|+|+|+++|.+++||.||+|+
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            47899999998     999999998     38999999999999876    78999999999999999989999999998


Q ss_pred             cccC
Q 026794          130 LEED  133 (233)
Q Consensus       130 ~~~d  133 (233)
                      +.+.
T Consensus        73 ~~~~   76 (80)
T 2k52_A           73 LEHH   76 (80)
T ss_dssp             CC--
T ss_pred             cccc
Confidence            8653

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

Probab=99.61  E-value=1.5e-15  Score=132.92  Aligned_cols=98  Identities=27%  Similarity=0.436  Sum_probs=83.7

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecc
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  130 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~  130 (233)
                      +++|+++.|+     +||+||+|.+++   |++||||+|+++|+++.++.+.|++||.|.|+|+++|.++++|.||+|++
T Consensus         9 p~~Gdiv~G~V~~I~~fGaFV~L~e~~---gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~   85 (275)
T 3aev_A            9 PEEGEFVVATVKRIHNYGAFLELDEYP---GKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRV   85 (275)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTST---TCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESTTC
T ss_pred             CCCCCEEEEEEEEEECcEEEEEECCCC---CeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence            4589999999     999999996211   79999999999999999999999999999999999999999999999999


Q ss_pred             ccChhhHHhhhhcCCCCeeeecCCccccCCeeeec
Q 026794          131 EEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIE  165 (233)
Q Consensus       131 ~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~  165 (233)
                      .++||....++ ++.|+.        +.|.+..++
T Consensus        86 ~~~~~~~~~~~-~~~g~~--------v~g~v~~v~  111 (275)
T 3aev_A           86 TQQQRKAKLQE-FKRAQK--------AENLLRLAA  111 (275)
T ss_dssp             CHHHHHHHHHH-HHHHHH--------HHHHHHHHH
T ss_pred             CcchhHHHHHh-ccCCCe--------EEEEEEEch
Confidence            99999866655 455554        445555554

>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=99.54  E-value=2.5e-15  Score=130.96  Aligned_cols=86  Identities=30%  Similarity=0.476  Sum_probs=77.3

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        54 ~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      ..+++|+++.|+     +||+||+|.+++   +++||||+|+++|+++.++.+.|++||.|.|+|+++|.++++|.||+|
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            356899999999     999999995211   799999999999999999999999999999999999999999999999


Q ss_pred             ccccChhhHHhhhh
Q 026794          129 QLEEDPLLETLEKV  142 (233)
Q Consensus       129 ~~~~dp~~~~~~~~  142 (233)
                      ++.++||.+..+++
T Consensus        84 ~~~~~~~~~~~~~~   97 (266)
T 3cw2_C           84 KVTDDERRKKNLQW   97 (266)
T ss_dssp             TSCTTHHHHHHHHH
T ss_pred             ecchhhHHHHHHhc
Confidence            99999997766553

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

Probab=99.51  E-value=1.2e-15  Score=148.41  Aligned_cols=124  Identities=26%  Similarity=0.411  Sum_probs=4.6

Q ss_pred             CCCchhHhhhcccCCCCEEE--EE-----------EEEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-
Q 026794            8 KEPQKSIHEIAKGLTGSIIS--VK-----------VIQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-   65 (233)
Q Consensus         8 ~~p~~~~~~~~~~~vG~~v~--~~-----------Vi~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~vv~g~-   65 (233)
                      ..|+....+...+.+|+.|-  .+           -|+++ +.+.+.++....        .++.+...+++|++|.|+ 
T Consensus       567 ~ap~~~~~~i~~~ki~~vig~gg~~i~~i~~~tg~~idi~-ddG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V  645 (726)
T 4aid_A          567 FAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKVDIN-DDGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKV  645 (726)
T ss_dssp             SCCC--------------------------------------------CCSCHHHHHHHHHC------------------
T ss_pred             cCCeEEEEeCCHHHHHhhcCCCchhHHHHHHHHCCceeEE-CCceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEEEEE
Confidence            45777777666666666553  11           15565 345665554421        256677889999999999 


Q ss_pred             ----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHH
Q 026794           66 ----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET  138 (233)
Q Consensus        66 ----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~  138 (233)
                          +||+||+|.     ++++||||+|+++|+++.++.+.|++||.|+|||+++|. ++||.||+|++.++||++.
T Consensus       646 ~~I~~fGaFVel~-----~g~eGLvHiSels~~rv~~~~d~~kvGD~V~VkVi~iD~-~grI~LS~K~~~~~~G~~~  716 (726)
T 4aid_A          646 VKVVDFGAFVNFF-----GAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDD-RGKTKLSMKVVDQETGEDL  716 (726)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             EEEeccEEEEEEC-----CCcEEEEEHHHcCcccccCccccCCCCCEEEEEEEEECC-CCcEEEEEeecccCcchhh
Confidence                999999998     489999999999999999999999999999999999997 8999999999999999654

>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=99.44  E-value=1.5e-15  Score=148.57  Aligned_cols=124  Identities=21%  Similarity=0.390  Sum_probs=43.1

Q ss_pred             CCCchhHhhhcccCCCCEEE--EEE-----------EEEeCCCCEEEEEechhh--------Hhhhc--cCCCCCCEEEE
Q 026794            8 KEPQKSIHEIAKGLTGSIIS--VKV-----------IQANEEMKKLVFSEKDAV--------WNKYS--SRVNVEDIFVG   64 (233)
Q Consensus         8 ~~p~~~~~~~~~~~vG~~v~--~~V-----------i~id~~~~~i~lS~k~~~--------~~~~~--~~~~~G~vv~g   64 (233)
                      ..|.....+.+.+.+|+.|.  .++           ++++. .+.+.+|.....        .+.+.  ..+++|++|+|
T Consensus       595 ~ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~IdI~~-dG~v~Is~~~~~~~~~a~~~i~~i~~p~~~~vG~i~~G  673 (757)
T 1e3p_A          595 NAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIED-DGTIYIGAADGPAAEAARATINGIANPTSPEVGERILG  673 (757)
T ss_dssp             TSCBCCCC------------------CTTCCCCCSCC---------CCCBSSHHHHCC---------------------C
T ss_pred             cCceeEEEEEChHHeehcccccceeeehhhHhhCCEEEecC-CceEEEecCCHHHHHHHHHHHHHhcchhhcccccEEEE
Confidence            45665555566666666553  122           55663 577888876431        23344  67899999999


Q ss_pred             E-----eeeEEEEEccCCCCccEEEEEEcccc----CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChh
Q 026794           65 R-----DYGAFIHLRFPDGLYHLTGLVHVSEV----SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPL  135 (233)
Q Consensus        65 ~-----~~G~fV~l~~~~~~~gv~Glv~~sel----s~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~  135 (233)
                      +     +||+||+|.     +|++||||+|++    +|+|+.++.+.|++||.|+|+|+++|. ++||+||+|++.++||
T Consensus       674 ~V~~i~~fGaFV~l~-----~g~eGLvHiSel~~~~s~~rv~~~~~~~~vGd~V~VkVi~vd~-~grI~LS~k~~~~~pw  747 (757)
T 1e3p_A          674 SVVKTTTFGAFVSLL-----PGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDS-RGKLSLIPVIEGEEAA  747 (757)
T ss_dssp             BEEECC-CSCEECCC--------CCCCC-------------------CCSSCBCCCCCCCCCS-SCC-------------
T ss_pred             EEEEccccEEEEEEc-----CCcEEEEEhHHhccccCCCcccCcccccCCCCEEEEEEEEECC-CCCEEEEEecCCCCch
Confidence            8     999999997     489999999999    999999999999999999999999998 9999999999999999


Q ss_pred             hHH
Q 026794          136 LET  138 (233)
Q Consensus       136 ~~~  138 (233)
                      ...
T Consensus       748 ~~~  750 (757)
T 1e3p_A          748 SDE  750 (757)
T ss_dssp             ---
T ss_pred             hhh
Confidence            653

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

Probab=99.42  E-value=1.3e-14  Score=141.45  Aligned_cols=101  Identities=30%  Similarity=0.541  Sum_probs=0.0

Q ss_pred             EEEeCCCCEEEEEechh--------hHhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc
Q 026794           31 IQANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ   97 (233)
Q Consensus        31 i~id~~~~~i~lS~k~~--------~~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~   97 (233)
                      ++++. .+.+.+|....        .++.+...+++|++|+|+     +||+||+|.     +|.+||||+|+++|+|+.
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            45553 46666665432        245667889999999999     999999997     489999999999999999


Q ss_pred             CcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHH
Q 026794           98 DIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET  138 (233)
Q Consensus        98 ~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~  138 (233)
                      ++.+.|++||.|+|||+++|. ++||+||+|++.++||.+.
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 9999999999999999653

>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=99.37  E-value=2.4e-13  Score=111.68  Aligned_cols=82  Identities=28%  Similarity=0.596  Sum_probs=68.4

Q ss_pred             HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc-----------cCcccccCCCCEEEEE
Q 026794           49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVK  112 (233)
Q Consensus        49 ~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~-----------~~~~~~~~~Gd~V~vk  112 (233)
                      ++....++.+|++++|+     +||+||+++      +.+||+|+|+++++++           ++..+.|++||.|+||
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            45566789999999999     999999996      6899999999999877           4677889999999999


Q ss_pred             EEEEeCC----CCeEEEEEec--cccChhh
Q 026794          113 VIKIDRE----KSRITLSIKQ--LEEDPLL  136 (233)
Q Consensus       113 Vi~vd~e----~~ri~LS~k~--~~~dp~~  136 (233)
                      |+++|.+    ..||.||+|+  +-+.+|-
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            9999864    4589999998  4445564

>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=99.35  E-value=7e-13  Score=109.47  Aligned_cols=81  Identities=25%  Similarity=0.474  Sum_probs=69.2

Q ss_pred             hhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc-----------CcccccCCCCEEEEEE
Q 026794           50 NKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKV  113 (233)
Q Consensus        50 ~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~-----------~~~~~~~~Gd~V~vkV  113 (233)
                      +.....+.+|+++.|+     +||+||+|.      +.+||+|+|+++++++.           ++.+.|++||.|+|+|
T Consensus        73 ~~i~~~~~~Gev~~G~V~~v~~~G~fV~l~------~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV  146 (187)
T 1go3_E           73 ETLVYIPEMYELIEGEVVDVVEFGSFVRLG------PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARI  146 (187)
T ss_dssp             EEEEECCCTTCEEEEEEEEEETTEEEEECS------SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEE
T ss_pred             EEEEEccCCCCEEEEEEEEEeCcEEEEEEc------CccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEE
Confidence            3445678999999999     999999996      59999999999998875           7889999999999999


Q ss_pred             EEEeCCCC-----eEEEEEecccc--Chhh
Q 026794          114 IKIDREKS-----RITLSIKQLEE--DPLL  136 (233)
Q Consensus       114 i~vd~e~~-----ri~LS~k~~~~--dp~~  136 (233)
                      +++|.+++     +|.||+|+...  .+|-
T Consensus       147 ~~vd~~~~~p~~~~I~lS~k~~~LG~~~w~  176 (187)
T 1go3_E          147 VAISLKAERKRGSKIALTMRQPYLGKLEWI  176 (187)
T ss_dssp             EEEECCC-----CEEEEECCSTTCEEHHHH
T ss_pred             EEEEcccCCCCccEEEEEEcCCCCCcHHHH
Confidence            99998755     99999998544  4453

>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=99.28  E-value=3.9e-12  Score=97.80  Aligned_cols=77  Identities=13%  Similarity=0.187  Sum_probs=64.0

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEcccc-CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEV-SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sel-s~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      ...+++|++++|+     +||+||+|+.    .+..||+|.++. +|.++.++.+.|++||.|+|+|+++|.++++|.||
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            4678999999999     9999999971    156777776664 35556688999999999999999999999999999


Q ss_pred             EeccccC
Q 026794          127 IKQLEED  133 (233)
Q Consensus       127 ~k~~~~d  133 (233)
                      +|+....
T Consensus        92 lk~~~l~   98 (119)
T 1wi5_A           92 VGHSEVS   98 (119)
T ss_dssp             CCCCCSC
T ss_pred             Echhhcc
Confidence            9976443

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

Probab=99.23  E-value=8.6e-12  Score=127.07  Aligned_cols=73  Identities=15%  Similarity=0.094  Sum_probs=68.7

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccc-ccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~-~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      .+.+++|+++.|+     +||+||+|+     .|++||||+|+++|++ +.++.+.|++||.|+|+|+++|.++++|.||
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            4789999999999     999999997     4899999999999998 8999999999999999999999999999999


Q ss_pred             Eecc
Q 026794          127 IKQL  130 (233)
Q Consensus       127 ~k~~  130 (233)
                      +|+.
T Consensus       972 lk~~  975 (1219)
T 3psi_A          972 LLDH  975 (1219)
T ss_dssp             CCHH
T ss_pred             ecHH
Confidence            9864

>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=99.17  E-value=7.6e-12  Score=122.84  Aligned_cols=74  Identities=30%  Similarity=0.585  Sum_probs=68.3

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      ...+++|+++.|+     +||+||+|+     .+++||||+|+++|.++.++.+.|++||.|+|+|+++|.++++|.||+
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            4568899999888     999999997     479999999999999999999999999999999999999999999999


Q ss_pred             eccc
Q 026794          128 KQLE  131 (233)
Q Consensus       128 k~~~  131 (233)
                      |...
T Consensus       724 k~~~  727 (785)
T 3bzc_A          724 RMSD  727 (785)
T ss_dssp             SSCC
T ss_pred             ecCC
Confidence            9654

>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=99.15  E-value=4.5e-11  Score=97.39  Aligned_cols=114  Identities=14%  Similarity=0.153  Sum_probs=72.7

Q ss_pred             CCCCCCCC-CchhHhhhcccCCCCEEE--EE---EEEEe--C-CCCEEEEEech----hhHhhhccCCCCCCEEEEE---
Q 026794            2 SPSHSCKE-PQKSIHEIAKGLTGSIIS--VK---VIQAN--E-EMKKLVFSEKD----AVWNKYSSRVNVEDIFVGR---   65 (233)
Q Consensus         2 ~~~~~~~~-p~~~~~~~~~~~vG~~v~--~~---Vi~id--~-~~~~i~lS~k~----~~~~~~~~~~~~G~vv~g~---   65 (233)
                      +|++++.+ |+....+...+++|+.+.  .+   +++++  . ..+.+.-.-..    ...+....+..+|++++|+   
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            46666533 555555556667776663  22   23333  2 13444422111    1133445678899999999   


Q ss_pred             --eeeEEEEEccCCCCccEEEEEEccccCcccccCc----------ccccCCCCEEEEEEEEEeCCCC
Q 026794           66 --DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI----------RDILNEGDEVRVKVIKIDREKS  121 (233)
Q Consensus        66 --~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~----------~~~~~~Gd~V~vkVi~vd~e~~  121 (233)
                        +||+||+++     + .+||+|+|++++.+..++          ++.|++||.|+|||+++|.+++
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              999999997     4 999999999986543222          2679999999999999998764

>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=99.15  E-value=5.8e-11  Score=99.88  Aligned_cols=77  Identities=19%  Similarity=0.205  Sum_probs=66.7

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCC---CccEEEEEEccccCccccc--CcccccCCCCEEEEEEEEEeCCCCeE
Q 026794           54 SRVNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRI  123 (233)
Q Consensus        54 ~~~~~G~vv~g~-----~~G~fV~l~~~~~---~~gv~Glv~~sels~~~~~--~~~~~~~~Gd~V~vkVi~vd~e~~ri  123 (233)
                      ..+++|++|.|+     ++|+||+|.+.++   ..+.+|+||+||+++.+..  ++++.|++||.|+|+|++++.+++++
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     9999999963211   0257899999999999988  99999999999999999999877899


Q ss_pred             EEEEecc
Q 026794          124 TLSIKQL  130 (233)
Q Consensus       124 ~LS~k~~  130 (233)
                      .||+|+.
T Consensus       157 ~LS~k~~  163 (209)
T 2nn6_I          157 LLTTAEN  163 (209)
T ss_dssp             EEECCSS
T ss_pred             EEEEecC
Confidence            9999975

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

Probab=99.13  E-value=4.8e-12  Score=127.19  Aligned_cols=74  Identities=15%  Similarity=0.104  Sum_probs=0.0

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccc-ccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~-~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      .+.+++|+++.|+     +||+||+|+     .|++||||+|++++++ +.++.+.|++||.|+|+|+++|.+++||.||
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            3788999999999     999999997     4899999999999998 8999999999999999999999999999999


Q ss_pred             Eeccc
Q 026794          127 IKQLE  131 (233)
Q Consensus       127 ~k~~~  131 (233)
                      +|+..
T Consensus       975 lk~~d  979 (1030)
T 3psf_A          975 LLDHD  979 (1030)
T ss_dssp             -----
T ss_pred             echHH
Confidence            99743

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

Probab=99.12  E-value=1.3e-10  Score=95.51  Aligned_cols=70  Identities=27%  Similarity=0.393  Sum_probs=60.7

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCC-----CccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDG-----LYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT  124 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~-----~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~  124 (233)
                      .++ |++|.|+     ++|+||+|...++     ..+.+|+||+|++++.++.++++.|++||.|+|+|++     +++.
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            457 9999999     9999999973100     0168999999999999999999999999999999998     7899


Q ss_pred             EEEecc
Q 026794          125 LSIKQL  130 (233)
Q Consensus       125 LS~k~~  130 (233)
                      ||+|+.
T Consensus       129 LS~k~~  134 (179)
T 3m7n_A          129 LSTKEE  134 (179)
T ss_dssp             EECCST
T ss_pred             EEEecC
Confidence            999875

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

Probab=99.12  E-value=3.4e-11  Score=91.09  Aligned_cols=88  Identities=9%  Similarity=0.119  Sum_probs=62.3

Q ss_pred             EEEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc---
Q 026794          124 TLSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR---  196 (233)
Q Consensus       124 ~LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~---  196 (233)
                      +-|+|++.+|||+.... .++.|++        ++|+|.++.++      |+|+++.+|++|+.    +++.+++.+   
T Consensus        11 ~~~iKq~~~~p~~~~~~-~~~~G~i--------v~G~V~~v~~~------G~fV~l~~~~~Gll~~sel~~~~~~~~~~~   75 (109)
T 2khj_A           11 SSGLVPRGSHMFNNWVA-LNKKGAI--------VTGKVTAVDAK------GATVELADGVEGYLRASEASRDRVEDATLV   75 (109)
T ss_dssp             ----------CHHHHTT-TCCSSSE--------EEEEEEEECSS------CEEEECSTTCBCCBCTTCCCSSSSSSGGGS
T ss_pred             ccchhhcccCHHHHHhh-cCCCCCE--------EEEEEEEEECC------eEEEEECCCCEEEEEHHHcCcccccChhhc
Confidence            46899999999976655 4677887        67999999854      77888899999994    555554433   


Q ss_pred             -cccCceEEEEeecCCCCCEEEEEEccccee
Q 026794          197 -VVSQDLQLWLSNAPPSGKKFTLLARAGRCK  226 (233)
Q Consensus       197 -~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~v  226 (233)
                       .+||.++|+|.++|.+++++.||.|+..+-
T Consensus        76 ~~vGd~V~v~V~~vd~~~~ki~LS~k~~~~~  106 (109)
T 2khj_A           76 LSVGDEVEAKFTGVDRKNRAISLSVRAKDEA  106 (109)
T ss_dssp             CCTTCEEEEEEEEEETTTTEEEEETTSSSSC
T ss_pred             cCCCCEEEEEEEEEECCCCEEEEEEeecChh
Confidence             589999999999999999999999986543

>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=99.11  E-value=3.1e-11  Score=101.95  Aligned_cols=127  Identities=15%  Similarity=0.107  Sum_probs=87.5

Q ss_pred             CCCCCCC-CCchhHhhhcccCCCCEEE--E-EEEEEeCC-----CCEEEEEech-----hhHhhhccCCCCCCEEEEE--
Q 026794            2 SPSHSCK-EPQKSIHEIAKGLTGSIIS--V-KVIQANEE-----MKKLVFSEKD-----AVWNKYSSRVNVEDIFVGR--   65 (233)
Q Consensus         2 ~~~~~~~-~p~~~~~~~~~~~vG~~v~--~-~Vi~id~~-----~~~i~lS~k~-----~~~~~~~~~~~~G~vv~g~--   65 (233)
                      +|+++.. -|+....+...+++|+.+.  . .|..+|-+     .+.+.-. ..     ..........++|++++|+  
T Consensus        14 pp~~~~~~~p~~i~~~I~~~~ig~vIg~~G~vI~~~dI~~~di~dG~I~~g-dg~~~~~v~~~~i~~~p~vGev~~G~V~   92 (215)
T 2b8k_G           14 HPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPT-DGSAEFNVKYRAVVFKPFKGEVVDGTVV   92 (215)
T ss_dssp             CGGGCSSSHHHHHHHHHHHSSTTCEETTTEEEEEECCSTTCBCCCEEECSS-SCCEEEEEECCEEEECCCTTEEEEEEEE
T ss_pred             CHHHHChhHhHHHHhcCCHHHCCeEcCCCCEEEEEEEeeecccccceEeCC-CHHHHHHHHhhhheeccCCCCEEEEEEE
Confidence            4556643 3555556667778888875  3 33334444     3444311 11     1133445677999999999  


Q ss_pred             ---eeeEEEEEccCCCCccEEEEEEccccCcccccCcc----------cccCCCCEEEEEEEEEeCCCC---eEEEEEec
Q 026794           66 ---DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR----------DILNEGDEVRVKVIKIDREKS---RITLSIKQ  129 (233)
Q Consensus        66 ---~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~----------~~~~~Gd~V~vkVi~vd~e~~---ri~LS~k~  129 (233)
                         +||+||+|+     + .+||||+|+|++.+..++.          +.|++||.|+|+|+++|.+.+   +|. |+|+
T Consensus        93 ~vt~fG~FVelg-----~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~~i~~Ig-Smk~  165 (215)
T 2b8k_G           93 SCSQHGFEVQVG-----P-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIG-SIKE  165 (215)
T ss_dssp             EEETTEEEEECT-----T-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETTEEEEEE-ECCS
T ss_pred             EEecceEEEEec-----C-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcCCCccEEEE-EcCC
Confidence               999999997     4 8999999999865443332          669999999999999998764   777 9988


Q ss_pred             cccChhh
Q 026794          130 LEEDPLL  136 (233)
Q Consensus       130 ~~~dp~~  136 (233)
                      ...-||.
T Consensus       166 ~~LG~~~  172 (215)
T 2b8k_G          166 DYLGAIS  172 (215)
T ss_dssp             TTCEEC-
T ss_pred             CCCCCcc
Confidence            7666664

>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=98.98  E-value=8e-10  Score=89.94  Aligned_cols=71  Identities=15%  Similarity=0.262  Sum_probs=56.7

Q ss_pred             hccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCc------------ccccCCCCEEEEEEE
Q 026794           52 YSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI------------RDILNEGDEVRVKVI  114 (233)
Q Consensus        52 ~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~------------~~~~~~Gd~V~vkVi  114 (233)
                      ...+..+|++++|+     +||+||+|+      ..+||+|+|++++.+..++            .+.|++||.|+|||+
T Consensus        75 ~~~~~~~Gev~~G~V~~v~~fG~fV~l~------~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~  148 (172)
T 2c35_B           75 IVFRPFKGEVVDAVVTQVNKVGLFTEIG------PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIV  148 (172)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEEET------TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEE
T ss_pred             EEeeCCCCCEEEEEEEEEeCCEEEEEEC------CEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEE
Confidence            35567899999999     999999996      5779999999986533222            457999999999999


Q ss_pred             EEeCCCC---eEEEEEec
Q 026794          115 KIDREKS---RITLSIKQ  129 (233)
Q Consensus       115 ~vd~e~~---ri~LS~k~  129 (233)
                      ++|.+++   ++. |+|+
T Consensus       149 ~vd~~~~~~~~ig-sm~~  165 (172)
T 2c35_B          149 GTRVDKNDIFAIG-SLMD  165 (172)
T ss_dssp             EEEEETTEEEEEE-ECCS
T ss_pred             EEEcCCCCcEEEE-EecC
Confidence            9998765   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=98.91  E-value=1.1e-09  Score=98.12  Aligned_cols=107  Identities=14%  Similarity=0.098  Sum_probs=79.0

Q ss_pred             hcccCCCCEEEEEEEEEeCCCCEEEEEechhh--------HhhhccCCC--CCCEEEEE-----eeeEEEEEccCCCCcc
Q 026794           17 IAKGLTGSIISVKVIQANEEMKKLVFSEKDAV--------WNKYSSRVN--VEDIFVGR-----DYGAFIHLRFPDGLYH   81 (233)
Q Consensus        17 ~~~~~vG~~v~~~Vi~id~~~~~i~lS~k~~~--------~~~~~~~~~--~G~vv~g~-----~~G~fV~l~~~~~~~g   81 (233)
                      +++..+|+.+.+.|...|.. ++...+.|+..        .+.+++.|+  .|++++|+     ++|+||+++      +
T Consensus        84 d~~~~vGd~ie~~I~~~dfg-R~aa~~aKqvi~qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~v~VDlG------k  156 (344)
T 1hh2_P           84 DPLAEVGSIVKKELNVKNFG-RIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIG------K  156 (344)
T ss_dssp             CTTCCTTCEEEEECCCCCSS-SCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEET------T
T ss_pred             CccccCCCEEEEEEccccCc-cHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCcEEEEeC------C
Confidence            35668999999999887753 33444444432        223456665  89999999     889999996      7


Q ss_pred             EEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhh
Q 026794           82 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLL  136 (233)
Q Consensus        82 v~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~  136 (233)
                      .+|++|.+|++      |.+.|++||+|+|.|++++.+++...+++-...++...
T Consensus       157 ~EgiLp~sE~i------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p~~lk  205 (344)
T 1hh2_P          157 LETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVI  205 (344)
T ss_dssp             EEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESSSHHHHH
T ss_pred             eEEEEeHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEeeccHHHH
Confidence            99999999996      56789999999999999997665444444444444443

>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=98.88  E-value=2.1e-09  Score=92.78  Aligned_cols=71  Identities=25%  Similarity=0.359  Sum_probs=63.6

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc---cCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI---QDIRDILNEGDEVRVKVIKIDREKSRITL  125 (233)
Q Consensus        54 ~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~---~~~~~~~~~Gd~V~vkVi~vd~e~~ri~L  125 (233)
                      ..+++|++|.|+     ++|+||+|+     .+.+|+||+|++++.+.   .++++.|++||.|.|+|++++. .+++.|
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            356999999999     899999997     37899999999998887   8899999999999999999996 579999


Q ss_pred             EEecc
Q 026794          126 SIKQL  130 (233)
Q Consensus       126 S~k~~  130 (233)
                      |+|+.
T Consensus       144 S~r~~  148 (251)
T 2je6_I          144 SVKGK  148 (251)
T ss_dssp             ECCST
T ss_pred             EEccc
Confidence            98753

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

Probab=98.87  E-value=9.2e-10  Score=83.99  Aligned_cols=85  Identities=8%  Similarity=0.034  Sum_probs=57.9

Q ss_pred             EEEeccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecc-ccccc---
Q 026794          125 LSIKQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQ-GFEKR---  196 (233)
Q Consensus       125 LS~k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~-~~~~~---  196 (233)
                      -|+|++..+||+... ..++.|++        +.|+|+.+++      +|+|+++++|++|+.    ++++ +.+++   
T Consensus        11 ~~~k~~~~~p~~~~~-~~~~~G~~--------~~G~V~~v~~------~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~   75 (115)
T 2khi_A           11 SSGLVPRGSHWVAIA-KRYPEGTK--------LTGRVTNLTD------YGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKV   75 (115)
T ss_dssp             ----------CCCSS-CSSCSSCE--------EEEEEEEEET------TEEEEECSTTCEEEEETTSSSCSSTTCSSTTT
T ss_pred             cchhhcccCCHHHHh-hcCCCCCE--------EEEEEEEEEC------CEEEEEECCCCEEEEEHHHCCccccccCcccE
Confidence            489999999997543 34677887        6799999885      477888899999995    4442 22222   


Q ss_pred             -cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          197 -VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       197 -~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                       .+||.++|+|.++|.+++||.||.|+..
T Consensus        76 ~~vGd~V~vkV~~vd~~~~rI~lslk~~~  104 (115)
T 2khi_A           76 VNVGDVVEVMVLDIDEERRRISLGLKQCK  104 (115)
T ss_dssp             CCTTCEEEEEEEEEETTTTEEEECCCCCC
T ss_pred             ECCCCEEEEEEEEEECCCCEEEEEEEecC
Confidence             5799999999999999999999998653

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

Probab=98.86  E-value=1e-09  Score=89.54  Aligned_cols=68  Identities=18%  Similarity=0.258  Sum_probs=56.9

Q ss_pred             HhhhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCc----------ccccCCCCEEEEEE
Q 026794           49 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI----------RDILNEGDEVRVKV  113 (233)
Q Consensus        49 ~~~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~----------~~~~~~Gd~V~vkV  113 (233)
                      .+.+..+..+|++++|+     +||+||+++      .++||+|+|++++.+..++          .+.|++||.|+|||
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            44556788999999999     999999996      5789999999986654443          56899999999999


Q ss_pred             EEEeCCCCe
Q 026794          114 IKIDREKSR  122 (233)
Q Consensus       114 i~vd~e~~r  122 (233)
                      +++|.+.++
T Consensus       149 ~~vd~~~~~  157 (172)
T 3h0g_G          149 VGTRTDATE  157 (172)
T ss_dssp             EEEEESSSC
T ss_pred             EEEECCCCC
Confidence            999987744

>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=98.85  E-value=2.3e-09  Score=91.64  Aligned_cols=71  Identities=17%  Similarity=0.325  Sum_probs=62.0

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc----cccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 026794           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQDIRDILNEGDEVRVKVIKIDREKSRIT  124 (233)
Q Consensus        54 ~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~----~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~  124 (233)
                      ..+++|++|.|+     ++|+||+|+     .+.+|++|+|+++.+    +..++++.|++||.|.|+|++++. .+++.
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            357999999999     899999997     378999999999873    457889999999999999999996 56899


Q ss_pred             EEEecc
Q 026794          125 LSIKQL  130 (233)
Q Consensus       125 LS~k~~  130 (233)
                      ||+|+.
T Consensus       136 LS~k~~  141 (235)
T 2z0s_A          136 LTVQGE  141 (235)
T ss_dssp             EECCSS
T ss_pred             EEEecc
Confidence            998753

>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=98.81  E-value=9.5e-09  Score=87.45  Aligned_cols=70  Identities=26%  Similarity=0.356  Sum_probs=62.7

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc-cccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~-~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      .+++||+|.|+     ++|+||+|+     .+.+|++|+|+++.. +..++++.|++||.|.|+|++++. .+++.||+|
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            47999999999     899999997     368999999999974 678899999999999999999996 579999987


Q ss_pred             cc
Q 026794          129 QL  130 (233)
Q Consensus       129 ~~  130 (233)
                      +.
T Consensus       128 ~~  129 (229)
T 2ba0_A          128 DR  129 (229)
T ss_dssp             SS
T ss_pred             cc
Confidence            63

>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=98.44  E-value=3.1e-07  Score=88.75  Aligned_cols=70  Identities=11%  Similarity=0.081  Sum_probs=57.9

Q ss_pred             CCCCCC--EEEEE-----eeeEEEEEccCCCCccEEEEEEccccCc--ccc--c--------CcccccCCCCEEEEEEEE
Q 026794           55 RVNVED--IFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI--Q--------DIRDILNEGDEVRVKVIK  115 (233)
Q Consensus        55 ~~~~G~--vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~--~~~--~--------~~~~~~~~Gd~V~vkVi~  115 (233)
                      .-++|+  +++|+     +||+||+|.+    +|++||||+|++++  +++  .        +....|++||.|+|+|++
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  88887     9999999953    48999999999973  331  1        345679999999999999


Q ss_pred             EeCCCCeEEEEEe
Q 026794          116 IDREKSRITLSIK  128 (233)
Q Consensus       116 vd~e~~ri~LS~k  128 (233)
                      +|.++++|.|++-
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

>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=98.40  E-value=1.3e-07  Score=77.22  Aligned_cols=70  Identities=14%  Similarity=0.073  Sum_probs=52.1

Q ss_pred             hhcC-CCCeeeecCCccccCCeeeeccCCChhhhhhhhccc--CCeeEEE----eeccccccc----cccCceEEEEeec
Q 026794          141 KVIP-QDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE--DGIDDVR----ITRQGFEKR----VVSQDLQLWLSNA  209 (233)
Q Consensus       141 ~~~~-~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~--~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~  209 (233)
                      ..++ .|++        +.|+|++++      +||+|+++.  +|++||.    +++.++.++    .+||.++|+|.++
T Consensus        10 ~~~p~~G~i--------v~G~V~~i~------~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~v   75 (175)
T 2a19_A           10 NKYPEIDDI--------VMVNVQQIA------EMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRV   75 (175)
T ss_dssp             SSSCCTTCE--------EEEEEEEEE------TTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEE
T ss_pred             hcCCCCCCE--------EEEEEEEEe------cceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEE
Confidence            3444 6777        679999888      458888885  8999994    777777665    5799999999999


Q ss_pred             CCCCCEEEEEEcccc
Q 026794          210 PPSGKKFTLLARAGR  224 (233)
Q Consensus       210 d~~~~ki~Ls~r~~~  224 (233)
                      |++++||+||+|+..
T Consensus        76 d~~~~~I~LSlk~~~   90 (175)
T 2a19_A           76 DKEKGYIDLSKRRVS   90 (175)
T ss_dssp             ETTTTEEEEESTTCC
T ss_pred             ECCCCeEEEEEEecC
Confidence            999999999998754

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

Probab=98.39  E-value=4.1e-07  Score=64.62  Aligned_cols=62  Identities=8%  Similarity=0.036  Sum_probs=50.3

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccccccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKRVVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      ++|+|.++++      +|+|+++++|++|+.    +++.+++.-.+||.++++|.++|.+++|++||.++..
T Consensus         9 v~G~V~~v~~------~G~fV~l~~~~~Gllh~sel~~~~~~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~~~   74 (80)
T 2k52_A            9 YKGVVTRIEK------YGAFINLNEQVRGLLRPRDMISLRLENLNVGDEIIVQAIDVRPEKREIDFKYIPLE   74 (80)
T ss_dssp             EEEEEEEEET------TEEEEEEETTEEEEECGGGCSSCCGGGCCTTCEEEEEEEEEETTTTEEEEEECSCC
T ss_pred             EEEEEEEEeC------CEEEEEECCCCEEEEEHHHCCcccceeeCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence            7799999885      478888899999995    4443332236899999999999999999999998754

>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=98.37  E-value=2.1e-07  Score=76.43  Aligned_cols=67  Identities=9%  Similarity=0.047  Sum_probs=50.5

Q ss_pred             CCCCeeeecCCccccCCeeeeccCCChhhhhhhhcc--cCCeeEEE----eeccccccc----cccCceEEEEeecCCCC
Q 026794          144 PQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ--EDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSG  213 (233)
Q Consensus       144 ~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~--~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~  213 (233)
                      +.|++        +.|+|+++++      ||+|+++  .+|++||.    +++.++.++    .+||.++|+|.++|.++
T Consensus        14 ~~G~i--------v~G~V~~I~~------fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~   79 (182)
T 1kl9_A           14 EVEDV--------VMVNVRSIAE------MGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEK   79 (182)
T ss_dssp             CTTCE--------EEEEEEEECS------SEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTT
T ss_pred             CCCCE--------EEEEEEEEec------cEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCC
Confidence            56776        7799999885      5888888  58999994    777777665    58999999999999999


Q ss_pred             CEEEEEEcccc
Q 026794          214 KKFTLLARAGR  224 (233)
Q Consensus       214 ~ki~Ls~r~~~  224 (233)
                      +||+||+|+..
T Consensus        80 ~rI~LSlk~~~   90 (182)
T 1kl9_A           80 GYIDLSKRRVS   90 (182)
T ss_dssp             TEEEEESTTCC
T ss_pred             CEEEEEEeecC
Confidence            99999998754

>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=98.31  E-value=2.2e-08  Score=98.14  Aligned_cols=106  Identities=16%  Similarity=0.133  Sum_probs=47.5

Q ss_pred             eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHHhhhhcCC
Q 026794           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ  145 (233)
Q Consensus        66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~~~~~~~~  145 (233)
                      ++|+||+++       -+|.+|+|..+|...+...+.                    +    +.+ .+|+      .+++
T Consensus       626 ~~G~~IdI~-------~dG~v~Is~~~~~~~~~a~~~--------------------i----~~i-~~p~------~~~v  667 (757)
T 1e3p_A          626 DTGAEITIE-------DDGTIYIGAADGPAAEAARAT--------------------I----NGI-ANPT------SPEV  667 (757)
T ss_dssp             CCCSCC---------------CCCBSSHHHHCC-----------------------------------------------
T ss_pred             hhCCEEEec-------CCceEEEecCCHHHHHHHHHH--------------------H----HHh-cchh------hccc
Confidence            899999996       379999999988654332111                    1    111 1342      2456


Q ss_pred             CCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEE----Ee----eccccccc----cccCceEEEEeecCCCC
Q 026794          146 DGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDV----RI----TRQGFEKR----VVSQDLQLWLSNAPPSG  213 (233)
Q Consensus       146 g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl----~~----~~~~~~~~----~vg~~~~v~i~~~d~~~  213 (233)
                      |++        ++|+|+++++      ||+|+++.+|++||    ++    ++++++++    .+||.++|+|.++|. +
T Consensus       668 G~i--------~~G~V~~i~~------fGaFV~l~~g~eGLvHiSel~~~~s~~rv~~~~~~~~vGd~V~VkVi~vd~-~  732 (757)
T 1e3p_A          668 GER--------ILGSVVKTTT------FGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDS-R  732 (757)
T ss_dssp             -------------CBEEECC-------CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCS-S
T ss_pred             ccE--------EEEEEEEccc------cEEEEEEcCCcEEEEEhHHhccccCCCcccCcccccCCCCEEEEEEEEECC-C
Confidence            776        7799999884      58889889999999    37    77777665    589999999999998 9


Q ss_pred             CEEEEEEcccc
Q 026794          214 KKFTLLARAGR  224 (233)
Q Consensus       214 ~ki~Ls~r~~~  224 (233)
                      +||+||.|+..
T Consensus       733 grI~LS~k~~~  743 (757)
T 1e3p_A          733 GKLSLIPVIEG  743 (757)
T ss_dssp             CC---------
T ss_pred             CCEEEEEecCC
Confidence            99999998654

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

Probab=98.30  E-value=2.6e-07  Score=67.17  Aligned_cols=62  Identities=2%  Similarity=-0.105  Sum_probs=48.6

Q ss_pred             ccCCeeeeccCCChhhhhhhhccc--CCeeEEE-ee----ccccccc---cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQE--DGIDDVR-IT----RQGFEKR---VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~--~gv~gl~-~~----~~~~~~~---~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      ..|+|+ +++|      |+|++++  +|++||. +|    +++++.+   .+||.++|++.++|.+++||+||.|+..+
T Consensus        15 ~~G~V~-v~~f------G~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~kI~lslk~~~~   86 (88)
T 1luz_A           15 IKGRVY-EKDY------ALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKLVGKTVKVKVIRVDYTKGYIDVNYKRMCR   86 (88)
T ss_dssp             EEEEEE-EETT------EEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEEEECS
T ss_pred             EEEEEE-EEcc------EEEEEECCCCCeEEEEEeeHHhCcccccCHhHEeCCCEEEEEEEEEECCCCEEEEEEeecCC
Confidence            779999 8854      7778777  4899995 44    4443332   48999999999999999999999997544

>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=98.29  E-value=2.9e-07  Score=70.56  Aligned_cols=81  Identities=7%  Similarity=-0.038  Sum_probs=61.1

Q ss_pred             ccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccC-CeeEEE----eeccccccc----ccc
Q 026794          129 QLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR----ITRQGFEKR----VVS  199 (233)
Q Consensus       129 ~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~-gv~gl~----~~~~~~~~~----~vg  199 (233)
                      .+.+++|+. +...+..|++        +.|+|+++++      ||+|+++.+ +++||.    +++.+++++    .+|
T Consensus         7 ~~~~~~~~~-~~~~~~vG~i--------v~G~V~~I~~------fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~G   71 (119)
T 2cqo_A            7 GMNSGRPET-MENLPALYTI--------FQGEVAMVTD------YGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVG   71 (119)
T ss_dssp             CSCCCCCCC-SCCSCCTTCE--------EEEEEEEEET------TEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTT
T ss_pred             cccccchhh-hhcccCCCCE--------EEEEEEEEeC------ceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCC
Confidence            457888864 4444677777        6799999985      478888854 369995    666655443    589


Q ss_pred             CceEEEEeecCCCC--CEEEEEEcccc
Q 026794          200 QDLQLWLSNAPPSG--KKFTLLARAGR  224 (233)
Q Consensus       200 ~~~~v~i~~~d~~~--~ki~Ls~r~~~  224 (233)
                      |.+.|+|.++|.++  +||+||+|...
T Consensus        72 d~V~VkV~~vd~~~~~~~i~LSlk~~~   98 (119)
T 2cqo_A           72 DKVWVKLIGREMKNDRIKVSLSMKVVN   98 (119)
T ss_dssp             CEEEEEEEEEEECSSCEEEEEESTTBC
T ss_pred             CEEEEEEEEEeccccCceEEEEEeecc
Confidence            99999999999864  79999998754

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

Probab=98.23  E-value=1.9e-06  Score=71.80  Aligned_cols=62  Identities=11%  Similarity=0.212  Sum_probs=52.7

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc-------------------cCcccccCCCCE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDE  108 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~-------------------~~~~~~~~~Gd~  108 (233)
                      .-+..+|++++|+     ++|+||+|+      .++|++|.+++.+++.                   ++....|++||.
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            4567899999999     999999995      6899999999987654                   445667999999


Q ss_pred             EEEEEEEEeCCC
Q 026794          109 VRVKVIKIDREK  120 (233)
Q Consensus       109 V~vkVi~vd~e~  120 (233)
                      |++||.+++...
T Consensus       150 VrvrV~~v~~~~  161 (203)
T 3ayh_B          150 IRFQIESEDFVD  161 (203)
T ss_dssp             EEEEEEEEEECC
T ss_pred             EEEEEEEEEccc
Confidence            999999998643

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

Probab=98.22  E-value=7.4e-07  Score=69.23  Aligned_cols=61  Identities=11%  Similarity=0.088  Sum_probs=50.1

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                      +.|+|+.+++      +|+|+++.+|++|+.    +++.++..+    .+||.++|+|.++|.++++|.||.|+.
T Consensus        11 v~G~V~~i~~------~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk~~   79 (130)
T 2k4k_A           11 YTGKVTGLQA------YGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIRAT   79 (130)
T ss_dssp             EEEEEEEEET------TEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESHHH
T ss_pred             EEEEEEEEeC------CeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence            6799999885      478888899999995    455444333    589999999999999999999999864

>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=98.19  E-value=3.2e-06  Score=76.11  Aligned_cols=85  Identities=9%  Similarity=0.150  Sum_probs=61.2

Q ss_pred             hhhccCCC--CCCEEEEE--e-------eeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeC
Q 026794           50 NKYSSRVN--VEDIFVGR--D-------YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDR  118 (233)
Q Consensus        50 ~~~~~~~~--~G~vv~g~--~-------~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~  118 (233)
                      +..+..|+  +|++++|+  .       +++||+|++.+  .+.+|++|.+|+.      |.+.|++||.|+|.|++++.
T Consensus       120 ~~i~~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~--~k~EgiLP~~Eqi------P~E~~~~GDrVkvyV~~V~~  191 (366)
T 1k0r_A          120 ERTYGEFSTREGEIVAGVIQRDSRANARGLVVVRIGTET--KASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTR  191 (366)
T ss_dssp             -------CCCTTCEEEEEEECCHHHHHTTCEEEEECCSS--SCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEEC
T ss_pred             HHHHHHHHhcCCCEEEEEEEEccccccCCeEEEEeCCCc--cceEEEEcHHHcC------CCccCCCCCEEEEEEEEEec
Confidence            34555665  99999999  2       58999997200  1499999999986      46889999999999999998


Q ss_pred             CCCeEEEEEeccccChhhHHhhhh
Q 026794          119 EKSRITLSIKQLEEDPLLETLEKV  142 (233)
Q Consensus       119 e~~ri~LS~k~~~~dp~~~~~~~~  142 (233)
                      +++...+.+..+.++.....++.-
T Consensus       192 ~~kgpqI~LSRT~p~lv~~Lfe~E  215 (366)
T 1k0r_A          192 GAREPLITLSRTHPNLVRKLFSLE  215 (366)
T ss_dssp             CSSSCEEEEESSCHHHHHHHHHHH
T ss_pred             CCCccEEEEEeCChHHHHHHHHhc
Confidence            876667777777776665555543

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

Probab=98.18  E-value=2e-06  Score=64.00  Aligned_cols=70  Identities=23%  Similarity=0.283  Sum_probs=49.1

Q ss_pred             CCCEEEEEEEEEeCCCCEEEEE-----------echhhHhhh-ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEE
Q 026794           22 TGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKY-SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTG   84 (233)
Q Consensus        22 vG~~v~~~Vi~id~~~~~i~lS-----------~k~~~~~~~-~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~G   84 (233)
                      .++.++.+|..+|.+++-=.+.           ..+..+..+ ...+++|+++++.     +||+||+|.     .+++|
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            5777888888887654422222           222223322 2689999999998     899999997     38999


Q ss_pred             EEEccccCcccc
Q 026794           85 LVHVSEVSWDLI   96 (233)
Q Consensus        85 lv~~sels~~~~   96 (233)
                      |||+|+++|.++
T Consensus        88 lvhis~i~~~~~   99 (101)
T 2bh8_A           88 LVHLSDISWAQA   99 (101)
T ss_dssp             EEEEEEEEECCC
T ss_pred             EEEHHHCccCcC
Confidence            999999999875

>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=98.18  E-value=2.1e-06  Score=80.75  Aligned_cols=75  Identities=23%  Similarity=0.396  Sum_probs=61.2

Q ss_pred             hhhccCCCCCCEEEEE-----ee--eEEEEEccCCCCccEEEEEEccccCcccc---------cCcccccCCCCEEEEEE
Q 026794           50 NKYSSRVNVEDIFVGR-----DY--GAFIHLRFPDGLYHLTGLVHVSEVSWDLI---------QDIRDILNEGDEVRVKV  113 (233)
Q Consensus        50 ~~~~~~~~~G~vv~g~-----~~--G~fV~l~~~~~~~gv~Glv~~sels~~~~---------~~~~~~~~~Gd~V~vkV  113 (233)
                      +.......+|++|.|+     ++  ||||+++     +|..||+|+|+++|.++         .++.+.+++||.|.|+|
T Consensus        37 E~~~~~~~vGnIY~GkV~rv~p~~~aAFVdiG-----~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV  111 (517)
T 2bx2_L           37 ESPGHEQKKANIYKGKITRIEPSLEAAFVDYG-----AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQI  111 (517)
T ss_dssp             ECSSSCCCTTCEEEEEEEEEETTTTEEEEESS-----SSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEE
T ss_pred             ecCCCcCCCCCEEEEEEEEeccCCceEEEEeC-----CCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEE
Confidence            3344567899999999     77  9999998     48899999999998874         34678899999999999


Q ss_pred             EEEeCCCCeEEEEEec
Q 026794          114 IKIDREKSRITLSIKQ  129 (233)
Q Consensus       114 i~vd~e~~ri~LS~k~  129 (233)
                      ++....++...||..-
T Consensus       112 ~Ke~~g~KGa~lTt~i  127 (517)
T 2bx2_L          112 DKEERGNKGAALTTFI  127 (517)
T ss_dssp             EECCCTTCCCEEESSC
T ss_pred             EeeccccCCceEEeeE
Confidence            9988776666666543

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

Probab=98.16  E-value=2.5e-07  Score=90.34  Aligned_cols=66  Identities=12%  Similarity=0.117  Sum_probs=0.0

Q ss_pred             cCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEE----Eeeccccccc----cccCceEEEEeecCCCCC
Q 026794          143 IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDV----RITRQGFEKR----VVSQDLQLWLSNAPPSGK  214 (233)
Q Consensus       143 ~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl----~~~~~~~~~~----~vg~~~~v~i~~~d~~~~  214 (233)
                      +++|++        ++|+|+++.      +||+|+++.+|++||    ++++++++++    .+||.++|++.++|. ++
T Consensus       625 ~~vG~i--------~~G~V~~i~------~fGaFVel~~g~eGLvHiSel~~~~v~~~~~~~~vGd~V~VkVi~vd~-~g  689 (723)
T 3cdi_A          625 IEVGRV--------YTGKVTRIV------DFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QG  689 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhcCcE--------EEEEEEEEe------cceEEEEeCCCceEEEEHHHcCCccccCcccccCCCCEEEEEEEEECC-CC
Confidence            455666        679998887      568889889999998    3777777655    589999999999998 89


Q ss_pred             EEEEEEccc
Q 026794          215 KFTLLARAG  223 (233)
Q Consensus       215 ki~Ls~r~~  223 (233)
                      ||+||+|+.
T Consensus       690 rI~LS~k~~  698 (723)
T 3cdi_A          690 RIRLSIKEA  698 (723)
T ss_dssp             ---------
T ss_pred             cEEEEEEec
Confidence            999999865

>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=98.11  E-value=2.3e-06  Score=84.12  Aligned_cols=65  Identities=17%  Similarity=0.199  Sum_probs=47.1

Q ss_pred             CEEEEE-----eeeEEEEEccCCCCccEEEEEEccccC--cccc-----------cC----cccccCCCCEEEEEEEEEe
Q 026794           60 DIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS--WDLI-----------QD----IRDILNEGDEVRVKVIKID  117 (233)
Q Consensus        60 ~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels--~~~~-----------~~----~~~~~~~Gd~V~vkVi~vd  117 (233)
                      ++++|+     +||+||.|..    .|++||||+|+++  .+++           .+    ....|++||.|+|+|+.+|
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     9999999973    4899999999996  4431           12    2578999999999999999


Q ss_pred             CC---CCeEEEEEe
Q 026794          118 RE---KSRITLSIK  128 (233)
Q Consensus       118 ~e---~~ri~LS~k  128 (233)
                      .+   ++||.||+|
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

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

Probab=98.06  E-value=4.6e-06  Score=70.30  Aligned_cols=116  Identities=9%  Similarity=0.136  Sum_probs=72.6

Q ss_pred             CCCCCCCCCCchhHhhhccc-CCCCEEE-----EEEEEEeC-CCCEEEEE----echhhHhhhccCCCCCCEEEEE----
Q 026794            1 MSPSHSCKEPQKSIHEIAKG-LTGSIIS-----VKVIQANE-EMKKLVFS----EKDAVWNKYSSRVNVEDIFVGR----   65 (233)
Q Consensus         1 ~~~~~~~~~p~~~~~~~~~~-~vG~~v~-----~~Vi~id~-~~~~i~lS----~k~~~~~~~~~~~~~G~vv~g~----   65 (233)
                      |+|+++.++....+.+.++. +.|+.+.     ..|.++.. ..++|.-.    .-........-+..+|++++|+    
T Consensus        13 I~P~~f~~~l~~~i~~~L~~kyegkv~~~~Gl~I~v~di~~i~eG~I~~GdG~~~~~V~fk~~~f~p~vGEv~~G~Is~V   92 (218)
T 2ckz_B           13 IPPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVVFKPFLGEIVTGWISKC   92 (218)
T ss_dssp             ECGGGTTSCHHHHHHHHHHHHHTTEEETTTEEEEEEEEEEEECCCEECSSSSCEEEEEEEEEEEECCCTTCEEEEEEEEE
T ss_pred             ECHHHcCchHHHHHHHHHHHHhcCcCcCCccEEEEEEEeeeccCcEEeCCCCCEEEEEEEEEEEecCCCCCEEEEEEEEE
Confidence            35666655555545444433 4455432     33344432 23333210    0001122335567899999999    


Q ss_pred             -eeeEEEEEccCCCCccEEEEEEccccCcccc--------------cCcccccCCCCEEEEEEEEEeCCCC
Q 026794           66 -DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI--------------QDIRDILNEGDEVRVKVIKIDREKS  121 (233)
Q Consensus        66 -~~G~fV~l~~~~~~~gv~Glv~~sels~~~~--------------~~~~~~~~~Gd~V~vkVi~vd~e~~  121 (233)
                       +||+||+|.+     .++|++|++++..++.              ++....|++||.|++||.++|...+
T Consensus        93 t~fGifVeL~g-----~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~~~~  158 (218)
T 2ckz_B           93 TAEGIKVSLLG-----IFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVDV  158 (218)
T ss_dssp             ETTEEEEECTT-----SCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEECCC
T ss_pred             ccCcEEEEccC-----ccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEcccC
Confidence             9999999953     5899999999976653              3345669999999999999997554

>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=98.04  E-value=2.9e-06  Score=64.71  Aligned_cols=68  Identities=12%  Similarity=0.021  Sum_probs=52.8

Q ss_pred             cCCCCeeeecCCccccCCeeeeccCCChhhhhhhhccc-CCeeEEEeeccc-----cccc----cccCceEEEEeecCCC
Q 026794          143 IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE-DGIDDVRITRQG-----FEKR----VVSQDLQLWLSNAPPS  212 (233)
Q Consensus       143 ~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~-~gv~gl~~~~~~-----~~~~----~vg~~~~v~i~~~d~~  212 (233)
                      ++.|++        +.|+|.++++|      |+|+++. +++.+++++...     ..++    .+||.++|+|.++|.+
T Consensus        19 l~~G~i--------~~G~V~~v~~f------G~fV~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~   84 (119)
T 1wi5_A           19 LKPGML--------LTGTVSSLEDH------GYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGN   84 (119)
T ss_dssp             CCTTCE--------EEEEEEEECSS------EEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTT
T ss_pred             CCCCCE--------EEEEEEEEeCc------eEEEEECCCCeEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCC
Confidence            567777        67999998854      7777777 688888765532     1122    5899999999999999


Q ss_pred             CCEEEEEEcccc
Q 026794          213 GKKFTLLARAGR  224 (233)
Q Consensus       213 ~~ki~Ls~r~~~  224 (233)
                      ++|+.|+.+...
T Consensus        85 ~~~i~Lslk~~~   96 (119)
T 1wi5_A           85 GGVVSLSVGHSE   96 (119)
T ss_dssp             SCEEEEECCCCC
T ss_pred             CCEEEEEEchhh
Confidence            999999998654

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

Probab=98.03  E-value=3.7e-06  Score=84.59  Aligned_cols=66  Identities=18%  Similarity=0.214  Sum_probs=54.8

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccC--cccc-----------cC----cccccCCCCEEEEEEEEE
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS--WDLI-----------QD----IRDILNEGDEVRVKVIKI  116 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels--~~~~-----------~~----~~~~~~~Gd~V~vkVi~v  116 (233)
                      |++++|+     +||+||.|..    .|++|+||+|+++  .+++           .+    ....|++||.|+|+|..+
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     9999999973    4899999999997  4431           12    357899999999999999


Q ss_pred             eCC---CCeEEEEEe
Q 026794          117 DRE---KSRITLSIK  128 (233)
Q Consensus       117 d~e---~~ri~LS~k  128 (233)
                      |.+   ++||.||+|
T Consensus       963 d~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          963 MDPITSKRKAELLLK  977 (977)
T ss_dssp             CCSSSCCCCCCEEEC
T ss_pred             cCcccCCCceEEEeC
Confidence            874   489999987

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

Probab=97.90  E-value=7.6e-06  Score=71.29  Aligned_cols=67  Identities=10%  Similarity=-0.001  Sum_probs=55.2

Q ss_pred             CCCCeeeecCCccccCCeeeeccCCChhhhhhhhccc--CCeeEEE----eeccccccc----cccCceEEEEeecCCCC
Q 026794          144 PQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE--DGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSG  213 (233)
Q Consensus       144 ~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~--~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~  213 (233)
                      +.|++        +.|+|+++.+      +|+|+++.  +|++|+.    +++.++.++    .+||.+.|+|.++|+++
T Consensus        10 ~~Gdi--------v~G~V~~I~~------fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~   75 (275)
T 3aev_A           10 EEGEF--------VVATVKRIHN------YGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRK   75 (275)
T ss_dssp             CTTCE--------EEEEEEEEET------TEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTT
T ss_pred             CCCCE--------EEEEEEEEEC------cEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCC
Confidence            36777        6799999884      57888888  6999995    666666544    58999999999999999


Q ss_pred             CEEEEEEcccc
Q 026794          214 KKFTLLARAGR  224 (233)
Q Consensus       214 ~ki~Ls~r~~~  224 (233)
                      ++++||+|+..
T Consensus        76 ~~I~LSlk~~~   86 (275)
T 3aev_A           76 GHIDLSLRRVT   86 (275)
T ss_dssp             TEEEEESTTCC
T ss_pred             CEEEEEEeecC
Confidence            99999999754

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

Probab=97.87  E-value=8.4e-06  Score=72.06  Aligned_cols=62  Identities=10%  Similarity=0.056  Sum_probs=52.5

Q ss_pred             ccCCeeeeccCCChhhhhhhhccc--CCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQE--DGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~--~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      +.|+|+++++      +|+|+++.  +|++|+.    ++|.+++++    .+||.+.|+|.++|+++++|+||.|...
T Consensus        17 v~G~V~~I~~------fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~~   88 (308)
T 1q8k_A           17 VMVNVRSIQE------MGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRVS   88 (308)
T ss_dssp             EEEEEEEEET------TEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSSCC
T ss_pred             EEEEEEEEeC------cEEEEEECCCCCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEecc
Confidence            7799999985      47888888  7999995    777766555    5799999999999999999999998753

>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=97.86  E-value=6.9e-06  Score=72.59  Aligned_cols=69  Identities=22%  Similarity=0.278  Sum_probs=56.2

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc----cc------cCcccccCCCCEEEEEEEEEeCC
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LI------QDIRDILNEGDEVRVKVIKIDRE  119 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~----~~------~~~~~~~~~Gd~V~vkVi~vd~e  119 (233)
                      .+++|++|.|+     ++++||+|..     ...|++|+|++++.    +.      .+.++.|++||.|.|+|++++. 
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 IGEVGDIVVGRITEVQQKRWKVETNS-----RLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-  165 (308)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECSS-----SSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEECC-----CcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCC-
Confidence            57999999998     8999999972     56899999999753    22      2456789999999999999995 


Q ss_pred             CCeEEEEEec
Q 026794          120 KSRITLSIKQ  129 (233)
Q Consensus       120 ~~ri~LS~k~  129 (233)
                      .+++.||+|+
T Consensus       166 ~~~i~LStr~  175 (308)
T 2nn6_H          166 DGAVSLHTRS  175 (308)
T ss_dssp             TTEEEEECCS
T ss_pred             CCCEEEEecC
Confidence            7889999885

>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=97.84  E-value=1.5e-05  Score=59.24  Aligned_cols=66  Identities=8%  Similarity=-0.048  Sum_probs=50.2

Q ss_pred             cCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccC---CeeEEE----e-eccccccc----cccCceEEEEeecC
Q 026794          143 IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQED---GIDDVR----I-TRQGFEKR----VVSQDLQLWLSNAP  210 (233)
Q Consensus       143 ~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~---gv~gl~----~-~~~~~~~~----~vg~~~~v~i~~~d  210 (233)
                      ++.|++        +.|+|+++++|      |+|+++.+   |++|+.    + ++.+++++    .+||.++|++.++|
T Consensus        10 ~~vG~i--------~~G~V~~v~~f------G~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd   75 (103)
T 2eqs_A           10 PTIGDI--------YNGKVTSIMQF------GCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFT   75 (103)
T ss_dssp             CCTTCE--------EEEEEEEECSS------CEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEE
T ss_pred             CCCCCE--------EEEEEEEEecc------EEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEE
Confidence            456776        67999998854      77888886   999995    4 33333333    58999999999998


Q ss_pred             CCCCEEEEEEcccc
Q 026794          211 PSGKKFTLLARAGR  224 (233)
Q Consensus       211 ~~~~ki~Ls~r~~~  224 (233)
                      .  +||+||+|...
T Consensus        76 ~--~~i~LSlk~~~   87 (103)
T 2eqs_A           76 G--TKTSLSMKDVD   87 (103)
T ss_dssp             T--TEEEEESTTBC
T ss_pred             C--CeeEEEEeecc
Confidence            7  59999998754

>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=97.70  E-value=6.3e-05  Score=61.24  Aligned_cols=67  Identities=15%  Similarity=0.147  Sum_probs=56.5

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCc-cEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLY-HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~-gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      .+++||+|.|+     .++++|+|.     + ...|++|++++. ...++.+..|++||.|.|+|.+++. .+.+.||..
T Consensus         4 ~P~~gDvViG~V~~v~~~~~~VdI~-----~~~~~a~L~~s~~~-g~~k~~r~~l~~GDlV~ArV~~~~~-~~~~~Ltc~   76 (175)
T 2ja9_A            4 IPSVNDFVIGVIIGTFSDSYKVSLQ-----NFSSSVSLSYMAFP-NASKKNRPTLQVGDLVYARVCTAEK-ELEAEIECF   76 (175)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESS-----TTSCCEEEETTSST-TCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEESS
T ss_pred             cCCCcCEEEEEEEEEECcEEEEEEC-----CCCccEEEEHHHCC-chhhhhhccCCCCCEEEEEEEEecC-CCceEEEec
Confidence            46899999998     789999997     4 589999999886 3356788889999999999999996 567888843

>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=97.55  E-value=0.00032  Score=60.02  Aligned_cols=66  Identities=18%  Similarity=0.235  Sum_probs=53.4

Q ss_pred             CCCCCEEEEE-e--------eeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCC--CeEE
Q 026794           56 VNVEDIFVGR-D--------YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRIT  124 (233)
Q Consensus        56 ~~~G~vv~g~-~--------~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~--~ri~  124 (233)
                      -++|++++|+ .        ..+||+|+..+  .+.+|++|.+|+.      |.+.|++||.|+|.|++++.+.  .+|.
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            3689999998 2        36999996100  1499999999985      5788999999999999999764  6899


Q ss_pred             EEEec
Q 026794          125 LSIKQ  129 (233)
Q Consensus       125 LS~k~  129 (233)
                      ||...
T Consensus        77 LSRt~   81 (251)
T 2asb_A           77 LSRTH   81 (251)
T ss_dssp             EESSC
T ss_pred             EEecc
Confidence            99865

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

Probab=97.54  E-value=3.7e-05  Score=78.74  Aligned_cols=64  Identities=3%  Similarity=-0.187  Sum_probs=53.4

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccc-cccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQG-FEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~-~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                      |..++|+|+++++      ||+|++++.|++|+.    +++.+ +.++    .+||.|+|+|.++|.+++||+||+|..
T Consensus       903 G~iv~G~V~~V~~------fGaFV~L~~gveGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~  975 (1219)
T 3psi_A          903 GSIIPVRVERFWH------NDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDH  975 (1219)
T ss_dssp             TCEEEEEEEEECS------SCEEEECTTSCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEECCHH
T ss_pred             CCEEEEEEEEEec------ceEEEEeCCCceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEecHH
Confidence            3337899999985      578888899999995    77776 4544    589999999999999999999999854

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

Probab=97.52  E-value=1.3e-05  Score=78.12  Aligned_cols=65  Identities=11%  Similarity=-0.028  Sum_probs=0.0

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEE----Eeeccccccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDV----RITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl----~~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      |..+.|+|+++.      +||+|+++.+|++||    ++++++++++    .+||.++|+|.++|. ++||+||+|+..+
T Consensus       638 G~v~~G~V~~I~------~fGaFVel~~g~eGLvHiSels~~rv~~~~d~~kvGD~V~VkVi~iD~-~grI~LS~K~~~~  710 (726)
T 4aid_A          638 GKIYDGKVVKVV------DFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDD-RGKTKLSMKVVDQ  710 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CcEEEEEEEEEe------ccEEEEEECCCcEEEEEHHHcCcccccCccccCCCCCEEEEEEEEECC-CCcEEEEEeeccc
Confidence            333789998887      568889889999998    4788777665    589999999999998 7999999997643

>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=97.51  E-value=2.8e-05  Score=67.40  Aligned_cols=62  Identities=2%  Similarity=-0.054  Sum_probs=51.4

Q ss_pred             ccCCeeeeccCCChhhhhhhhccc--CCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQE--DGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~--~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      +.|+|.++.+      +|+|+++.  +|++|+.    ++++++.++    .+||.+.|+|.++|.++++++||.|...
T Consensus        15 v~G~V~~I~~------~GaFV~l~e~~~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~~~   86 (266)
T 3cw2_C           15 LIATVKQVFD------YGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKKVT   86 (266)
T ss_dssp             EEEEEEECCS------SSBEEEETTTTSEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEESTTSC
T ss_pred             EEEEEEEEec------cEEEEEEcCCCCeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEEecc
Confidence            7799999885      47888887  8999994    666665544    5799999999999999999999998754

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

Probab=97.40  E-value=0.00017  Score=53.32  Aligned_cols=77  Identities=18%  Similarity=0.082  Sum_probs=48.9

Q ss_pred             CCCCCEEEEE--------eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           56 VNVEDIFVGR--------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        56 ~~~G~vv~g~--------~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      .+.++.++|+        .|| |+.-++    .+.+.|+|+|++++..+                               
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            3456677887        588 887652    26899999999987642                               


Q ss_pred             eccccChhhHHhhhhcCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecccc
Q 026794          128 KQLEEDPLLETLEKVIPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGF  193 (233)
Q Consensus       128 k~~~~dp~~~~~~~~~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~  193 (233)
                                 ..+.++.|+.        +++.+..++      ++|+|+++++|++||.    ++|.++
T Consensus        55 -----------~~~~l~~Ge~--------V~g~V~~i~------~fG~fv~l~~~~eGlvhis~i~~~~~   99 (101)
T 2bh8_A           55 -----------VRGNPQQGDR--------VEGKIKSIT------DFGIFIGLDGGIDGLVHLSDISWAQA   99 (101)
T ss_dssp             -----------CCCCCCTTCE--------EEEEEEECC------SEEEEECTTSCEEEEEEEEEEEECCC
T ss_pred             -----------cccCCCCCCE--------EEEEEEEeC------CcEEEEEcCCCceEEEEHHHCccCcC
Confidence                       0112344555        556776665      4577888888999994    565543

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

Probab=97.40  E-value=2.3e-05  Score=79.08  Aligned_cols=65  Identities=3%  Similarity=-0.184  Sum_probs=0.0

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccc-cccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQG-FEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~-~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      |..+.|+|++++      +||+|++++.|++|+.    +++.+ +.++    .+||.|+|+|.++|.+++||+||+|...
T Consensus       906 G~iv~G~V~~V~------~fGaFV~L~~gveGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~d  979 (1030)
T 3psf_A          906 GSIIPVRVERFW------HNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDHD  979 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCEEEEEEEEEc------cCeEEEEeCCCcEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEechHH
Confidence            444889998887      5688888899999983    77766 4444    5899999999999999999999998643

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

Probab=97.35  E-value=7e-05  Score=73.70  Aligned_cols=65  Identities=5%  Similarity=-0.053  Sum_probs=53.9

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      |..+.|+|+++++      ||+|+++..|++|+.    +++.++.++    .+||.|+|+|.++|.++++|+||+|...
T Consensus       655 G~iv~G~V~~V~~------fGaFV~l~~~~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~LSlk~~~  727 (785)
T 3bzc_A          655 GMVLEGVVTNVTN------FGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMSD  727 (785)
T ss_dssp             TCBCCCEEEEEET------TEEEEECSSSSEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEECCSSCC
T ss_pred             CCEEEEEEEEEec------CCeEEEeCCCcEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEEEecCC
Confidence            4458899999985      578888899999995    666666554    5899999999999999999999998643

>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=96.72  E-value=0.0012  Score=53.69  Aligned_cols=60  Identities=8%  Similarity=0.034  Sum_probs=44.5

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccc-----------cc----cccCceEEEEeecCCCCC---
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFE-----------KR----VVSQDLQLWLSNAPPSGK---  214 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~-----------~~----~vg~~~~v~i~~~d~~~~---  214 (233)
                      ++|+|+++.++      |+|+++.+ ++|+.    ++++++.           ++    .+||.+.|++.++|.+++   
T Consensus        85 ~~G~V~~v~~~------G~fV~l~~-~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~p~  157 (187)
T 1go3_E           85 IEGEVVDVVEF------GSFVRLGP-LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKR  157 (187)
T ss_dssp             EEEEEEEEETT------EEEEECSS-SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC----
T ss_pred             EEEEEEEEeCc------EEEEEEcC-ccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccCCCC
Confidence            67999999855      67777765 99994    3333332           22    579999999999998765   


Q ss_pred             --EEEEEEccc
Q 026794          215 --KFTLLARAG  223 (233)
Q Consensus       215 --ki~Ls~r~~  223 (233)
                        ++.||++..
T Consensus       158 ~~~I~lS~k~~  168 (187)
T 1go3_E          158 GSKIALTMRQP  168 (187)
T ss_dssp             -CEEEEECCST
T ss_pred             ccEEEEEEcCC
Confidence              999999863

>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=96.43  E-value=0.0001  Score=65.96  Aligned_cols=109  Identities=9%  Similarity=0.065  Sum_probs=69.5

Q ss_pred             cccCCCCEEEEEEEEEeCCCCeEEEEEeccccChhhHH-----hhhh-cCCCCeeeecCCccccCCeeeeccCCChhhhh
Q 026794          101 DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET-----LEKV-IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIF  174 (233)
Q Consensus       101 ~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~~~~dp~~~~-----~~~~-~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~  174 (233)
                      ..+.+||.+.+.|...|.. +....+.|+....-+.+.     .+.+ ...|++        ++|+|.++.+.      +
T Consensus        85 ~~~~vGd~ie~~I~~~dfg-R~aa~~aKqvi~qkireaere~i~~e~~~~~GeI--------V~G~V~ri~~~------~  149 (344)
T 1hh2_P           85 PLAEVGSIVKKELNVKNFG-RIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTV--------TTAEVIRVMGE------W  149 (344)
T ss_dssp             TTCCTTCEEEEECCCCCSS-SCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCE--------EEEEEEEECSS------E
T ss_pred             ccccCCCEEEEEEccccCc-cHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCE--------EEEEEEEEecC------c
Confidence            4478999999999888753 333334455433233222     1111 113444        88999998753      5


Q ss_pred             hhhcccCCeeEEEeeccccc--cccccCceEEEEeecCCCCC--EEEEEEcccce
Q 026794          175 EELLQEDGIDDVRITRQGFE--KRVVSQDLQLWLSNAPPSGK--KFTLLARAGRC  225 (233)
Q Consensus       175 ~~l~~~~gv~gl~~~~~~~~--~~~vg~~~~v~i~~~d~~~~--ki~Ls~r~~~~  225 (233)
                      +++++. +++|+.+......  .-.+||.+++++.+++.+++  ++.||-+....
T Consensus       150 v~VDlG-k~EgiLp~sE~ip~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p~~  203 (344)
T 1hh2_P          150 ADIRIG-KLETRLPKKEWIPGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEF  203 (344)
T ss_dssp             EEEEET-TEEEEEEGGGSCTTCCCCTTCEEEEEEEEEEEETTEEEEEEESSSHHH
T ss_pred             EEEEeC-CeEEEEeHHHcCCCcCCCCCCEEEEEEEEEEcCCCCcEEEEEeeccHH
Confidence            677776 8999964443321  11679999999999987654  68888765443

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

Probab=96.40  E-value=0.0024  Score=53.25  Aligned_cols=68  Identities=4%  Similarity=0.017  Sum_probs=49.5

Q ss_pred             cCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcc--------cCCeeEEE----eeccccc--cc----cccCceEE
Q 026794          143 IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQ--------EDGIDDVR----ITRQGFE--KR----VVSQDLQL  204 (233)
Q Consensus       143 ~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~--------~~gv~gl~----~~~~~~~--~~----~vg~~~~v  204 (233)
                      .++|++        +.|+|+.+.++      ++|+++        ..+++|+.    +++.+.+  +.    .+||.+.+
T Consensus        79 p~vGDv--------V~G~V~~v~~~------~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~a  144 (209)
T 2nn6_I           79 PDVGAI--------VTCKVSSINSR------FAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLA  144 (209)
T ss_dssp             CCTTCE--------EEEEEEEECSS------EEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEE
T ss_pred             CCCCCE--------EEEEEEEEECc------eEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEE
Confidence            466777        77999999865      555553        35777773    4444443  22    57999999


Q ss_pred             EEeecCCCCCEEEEEEcccc
Q 026794          205 WLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       205 ~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      +|.+++.++++|+||.|+.+
T Consensus       145 kVisi~~~~~~i~LS~k~~~  164 (209)
T 2nn6_I          145 KVISLGDAQSNYLLTTAENE  164 (209)
T ss_dssp             EEEEEETTTTEEEEECCSSS
T ss_pred             EEEEEeCCCCeEEEEEecCC
Confidence            99999887789999998754

>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=96.21  E-value=0.0036  Score=50.59  Aligned_cols=59  Identities=10%  Similarity=0.074  Sum_probs=42.0

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccc-----------cc----cccCceEEEEeecCCC----C
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFE-----------KR----VVSQDLQLWLSNAPPS----G  213 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~-----------~~----~vg~~~~v~i~~~d~~----~  213 (233)
                      ++|+|++++++      |+|+++. +++|+.    +++++..           +.    .+||.++|+|.+++.+    .
T Consensus        85 ~~G~V~~v~~~------G~fv~l~-~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~~~~~  157 (180)
T 4ayb_E           85 VEGEVLQVDNY------GVFVNLG-PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTGRL  157 (180)
T ss_dssp             EEEEEEEEETT------EEEEECS-SSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC------
T ss_pred             EEEEEeeeccc------eEEEEEC-CccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCCCCccc
Confidence            67999999855      6677765 589984    4444331           11    5799999999999864    4


Q ss_pred             CEEEEEEcc
Q 026794          214 KKFTLLARA  222 (233)
Q Consensus       214 ~ki~Ls~r~  222 (233)
                      .||+||+|.
T Consensus       158 ~rI~ls~k~  166 (180)
T 4ayb_E          158 PRIALTMRQ  166 (180)
T ss_dssp             -CEEEECCS
T ss_pred             CcEEEEcCC
Confidence            589999985

>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=96.11  E-value=0.0052  Score=53.67  Aligned_cols=68  Identities=7%  Similarity=-0.038  Sum_probs=55.6

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .+++||+|-|+     ...+.|+|.     ....|++|.+++. ...+..+..|++||.|.|+|++++. .+.+.||...
T Consensus       124 iP~vGDiVIG~Vt~v~~~~~~VdI~-----s~~~a~L~~~~f~-Gatk~~r~~f~~GDlV~ArV~s~~~-~~~~eLsc~~  196 (289)
T 2nn6_G          124 VPVKGDHVIGIVTAKSGDIFKVDVG-----GSEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVCID  196 (289)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECS-----SSSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCT-TSCCEEECSB
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEEC-----CCceeEEehhhcC-cchhhhhhhcCCCCEEEEEEEEcCC-CCceEEEecc
Confidence            46999999999     566899997     3578999999876 3346788899999999999999985 5568888744

>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=95.66  E-value=0.021  Score=53.08  Aligned_cols=60  Identities=13%  Similarity=0.279  Sum_probs=48.2

Q ss_pred             CCCCCEEEEEeeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           56 VNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        56 ~~~G~vv~g~~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      -..|+.++|    +||++.      +.+|++|++++..+  ......|++||.|+|+|.++|..+++|.+..
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 AQPERVWDA----VVVDRR------GAQATLLIPDLAFD--VQVNTPAAPGTALQVQFADIDLPQMRVRARS  460 (469)
T ss_dssp             TCTTCCEEE----EEEEEE------TTEEEEEEGGGTEE--EEEECCCCTTCEEEEEEEEEETTTTEEEEEE
T ss_pred             hCCCCEEEE----EEEEEe------CcEEEEEECCCCeE--EecCCcCCCCCEEEEEEEEEccCCCEEEEEE
Confidence            367888764    678886      45899999999875  2234569999999999999999999998865

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

Probab=95.51  E-value=0.0046  Score=50.16  Aligned_cols=57  Identities=4%  Similarity=-0.091  Sum_probs=42.8

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccC----------CeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEE
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQED----------GIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTL  218 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~----------gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~L  218 (233)
                      +.|+|+++.++      ++|+++.+          +++|+.    +++.++++.    .+||.+.++|.+     ++|+|
T Consensus        61 V~G~V~~V~~~------ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~-----~~i~L  129 (179)
T 3m7n_A           61 VLGRVVDLRNS------IALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG-----DNLRL  129 (179)
T ss_dssp             EEEEEEEECSS------EEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE-----TTTEE
T ss_pred             EEEEEEEEeCC------cEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC-----CeEEE
Confidence            67999998854      67777776          899984    444444333    579999999976     78999


Q ss_pred             EEcccc
Q 026794          219 LARAGR  224 (233)
Q Consensus       219 s~r~~~  224 (233)
                      |.|+.+
T Consensus       130 S~k~~~  135 (179)
T 3m7n_A          130 STKEEE  135 (179)
T ss_dssp             ECCSTT
T ss_pred             EEecCC
Confidence            998743

>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=93.65  E-value=0.037  Score=46.20  Aligned_cols=57  Identities=2%  Similarity=-0.084  Sum_probs=40.5

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccc----ccc--------c--cccCceEEEEeecCCCCC---E
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQG----FEK--------R--VVSQDLQLWLSNAPPSGK---K  215 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~----~~~--------~--~vg~~~~v~i~~~d~~~~---k  215 (233)
                      ++|+|+++++      ||+|+++.+ ++||.    ++...    .+.        .  .+||.++|+|.++|.+.+   +
T Consensus        87 ~~G~V~~vt~------fG~FVelg~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~~i~~  159 (215)
T 2b8k_G           87 VDGTVVSCSQ------HGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHA  159 (215)
T ss_dssp             EEEEEEEEET------TEEEEECTT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETTEEEE
T ss_pred             EEEEEEEEec------ceEEEEecC-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcCCCccEE
Confidence            7799999985      477788887 99994    33211    111        1  469999999999998875   4


Q ss_pred             EEEEEc
Q 026794          216 FTLLAR  221 (233)
Q Consensus       216 i~Ls~r  221 (233)
                      +. |++
T Consensus       160 Ig-Smk  164 (215)
T 2b8k_G          160 IG-SIK  164 (215)
T ss_dssp             EE-ECC
T ss_pred             EE-EcC
Confidence            54 554

>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=92.98  E-value=0.091  Score=44.23  Aligned_cols=60  Identities=7%  Similarity=-0.094  Sum_probs=43.9

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecccccc-------c-cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEK-------R-VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~-------~-~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                      +.|+|+.+.+      .++++++..+.+|+.    ++..+.+.       - .+||.+.++|.+++.+ +++.||.|+.
T Consensus        70 V~G~V~~v~~------~~~~V~I~~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~-~~i~LS~k~~  141 (235)
T 2z0s_A           70 VIGLIQSVGI------MNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKT-RSPLLTVQGE  141 (235)
T ss_dssp             EEEEEEEECS------SEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTT-SCEEEECCSS
T ss_pred             EEEEEEEEeC------CeEEEEeCCCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECCC-CcEEEEEecc
Confidence            7799998875      477888888899984    22211111       1 5799999999999854 5799999854

>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=92.55  E-value=0.087  Score=42.04  Aligned_cols=54  Identities=2%  Similarity=-0.059  Sum_probs=38.4

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecc-c---ccc--------c--cccCceEEEEeecCCCCCEEE
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQ-G---FEK--------R--VVSQDLQLWLSNAPPSGKKFT  217 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~-~---~~~--------~--~vg~~~~v~i~~~d~~~~ki~  217 (233)
                      ++|+|+++++      ||+|+++.+ ++||.    ++.. +   .++        .  .+||.++|++.++|.+.+.+.
T Consensus        87 ~~G~V~~v~~------fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~~~  158 (171)
T 1y14_B           87 VDGTVVSCSQ------HGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIH  158 (171)
T ss_dssp             EEEEEEEEET------TEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTEEE
T ss_pred             EEEEEEEEec------CEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEEcCCCCcE
Confidence            6799999985      577888888 99994    3221 1   111        1  469999999999998876443

>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=92.18  E-value=0.084  Score=42.10  Aligned_cols=51  Identities=4%  Similarity=-0.075  Sum_probs=36.0

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecc----cccc---------c---cccCceEEEEeecCCCCC
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQ----GFEK---------R---VVSQDLQLWLSNAPPSGK  214 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~----~~~~---------~---~vg~~~~v~i~~~d~~~~  214 (233)
                      ++|+|++++++      |+|+++. .++|+.    ++..    ..++         .   .+||.++|++.++|.+.+
T Consensus        85 ~~G~V~~v~~f------G~fV~l~-~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  155 (172)
T 2c35_B           85 VDAVVTQVNKV------GLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKN  155 (172)
T ss_dssp             EEEEEEEEETT------EEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETT
T ss_pred             EEEEEEEEeCC------EEEEEEC-CEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCCC
Confidence            67999999855      7777775 577884    2211    1221         1   479999999999998876

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

Probab=92.11  E-value=0.1  Score=41.76  Aligned_cols=53  Identities=4%  Similarity=-0.029  Sum_probs=36.7

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccc----------ccc---c-cccCceEEEEeecCCCCCEE
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQG----------FEK---R-VVSQDLQLWLSNAPPSGKKF  216 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~----------~~~---~-~vg~~~~v~i~~~d~~~~ki  216 (233)
                      ++|+|++++++      |+|+++. .++|+.    +++..          +++   . .+||.++|++.+++.+.+++
T Consensus        88 ~~G~V~~v~~f------G~FV~l~-~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~~~~~~  158 (172)
T 3h0g_G           88 VDAIVTTVNKM------GFFANIG-PLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDATEI  158 (172)
T ss_dssp             EECCCCEEETT------EEECCBT-TBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEESSSCE
T ss_pred             EEEEEEEEEcc------eEEEEeC-CeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEECCCCCc
Confidence            67999998855      6667665 477874    33221          111   1 57999999999999988544

>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=91.71  E-value=0.13  Score=43.77  Aligned_cols=66  Identities=8%  Similarity=-0.119  Sum_probs=48.6

Q ss_pred             cCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccc---cc----cccCceEEEEeecCC
Q 026794          143 IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFE---KR----VVSQDLQLWLSNAPP  211 (233)
Q Consensus       143 ~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~---~~----~vg~~~~v~i~~~d~  211 (233)
                      .+.|++        +.|+|+.+.+      +++|+++..+.+|+.    +...+.+   +.    .+||.+.++|.+++.
T Consensus        72 p~~GDi--------V~G~V~~v~~------~ga~VdI~~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~  137 (251)
T 2je6_I           72 PKINDI--------VIGLVEDVEI------YGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR  137 (251)
T ss_dssp             CCTTCE--------EEEEEEEECS------SEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET
T ss_pred             CCCCCE--------EEEEEEEEeC------ceEEEEcCCCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECC
Confidence            356777        6799999875      478888888899984    2322221   11    579999999999985


Q ss_pred             CCCEEEEEEccc
Q 026794          212 SGKKFTLLARAG  223 (233)
Q Consensus       212 ~~~ki~Ls~r~~  223 (233)
                      + +++.||.|..
T Consensus       138 ~-~~i~LS~r~~  148 (251)
T 2je6_I          138 S-IDPVLSVKGK  148 (251)
T ss_dssp             T-EEEEEECCST
T ss_pred             C-CcEEEEEccc
Confidence            4 6899999864

>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=91.57  E-value=0.15  Score=49.16  Aligned_cols=59  Identities=5%  Similarity=-0.033  Sum_probs=43.2

Q ss_pred             cccCCeeeeccCCChhhhhhhhcc-cCCeeEEE----eec--cc--c---------c--c-ccccCceEEEEeecCCCCC
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQ-EDGIDDVR----ITR--QG--F---------E--K-RVVSQDLQLWLSNAPPSGK  214 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~-~~gv~gl~----~~~--~~--~---------~--~-~~vg~~~~v~i~~~d~~~~  214 (233)
                      ..+|.|+.++++      |.|+++ +.|++|+.    ++.  +.  .         .  . -.+||.|+|+|.++|++.+
T Consensus       563 ~f~g~V~~V~~~------G~fV~L~~~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~vd~~~~  636 (644)
T 2id0_A          563 RFAAEIVDISRG------GMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETR  636 (644)
T ss_dssp             CEEEEEEEEETT------EEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTT
T ss_pred             eEEEEEEEEeCC------ceEEEEcCCcEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEEEEEeCCCC
Confidence            367899888854      667777 57899995    221  11  1         1  1 1579999999999999999


Q ss_pred             EEEEEE
Q 026794          215 KFTLLA  220 (233)
Q Consensus       215 ki~Ls~  220 (233)
                      +|.++.
T Consensus       637 ~I~~~l  642 (644)
T 2id0_A          637 SIIARP  642 (644)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            999875

>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=91.16  E-value=0.4  Score=34.51  Aligned_cols=62  Identities=13%  Similarity=0.136  Sum_probs=45.5

Q ss_pred             ccCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEEcc-ccCcccccCcccccCCCCEEEEEEEEEeC
Q 026794           53 SSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDR  118 (233)
Q Consensus        53 ~~~~~~G~vv~g~----~~G~fV~l~~~~~~~gv~Glv~~s-els~~~~~~~~~~~~~Gd~V~vkVi~vd~  118 (233)
                      .-.+-+|++.+|.    ++-++|.|.+++   |.+|++--. .+..++..++++.+ +|.+|+++|+.+|.
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            4568899999999    666789998643   788887322 22334555566655 79999999999985

>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=87.95  E-value=0.66  Score=38.80  Aligned_cols=65  Identities=9%  Similarity=-0.080  Sum_probs=47.0

Q ss_pred             CCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecc-cccc--c--cccCceEEEEeecCCCCC
Q 026794          144 PQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQ-GFEK--R--VVSQDLQLWLSNAPPSGK  214 (233)
Q Consensus       144 ~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~-~~~~--~--~vg~~~~v~i~~~d~~~~  214 (233)
                      +.|++        +.|+|+.+.++      ++++++....+|+.    +++. ...+  +  .+||.+.++|.+++.+ +
T Consensus        56 ~~GDi--------V~G~V~~v~~~------~a~V~I~~~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~~-~  120 (229)
T 2ba0_A           56 SVGDV--------VIGIIREVAAN------GWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPK-M  120 (229)
T ss_dssp             CTTCE--------EEEEEEEECSS------EEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTT-C
T ss_pred             CCCCE--------EEEEEEEEeCC------eEEEEeCCCeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECCC-C
Confidence            56776        67999988754      77888888888884    2211 0100  1  5799999999999864 6


Q ss_pred             EEEEEEccc
Q 026794          215 KFTLLARAG  223 (233)
Q Consensus       215 ki~Ls~r~~  223 (233)
                      ++.||.|..
T Consensus       121 ~i~LS~r~~  129 (229)
T 2ba0_A          121 KVTLTMKDR  129 (229)
T ss_dssp             CEEEECCSS
T ss_pred             cEEEEEccc
Confidence            899999864

>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=87.84  E-value=0.25  Score=48.40  Aligned_cols=59  Identities=14%  Similarity=0.137  Sum_probs=36.6

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccC-CeeEEE----ee--ccc---------c--cc------c--cccCceEEEEeecC
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQED-GIDDVR----IT--RQG---------F--EK------R--VVSQDLQLWLSNAP  210 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~-gv~gl~----~~--~~~---------~--~~------~--~vg~~~~v~i~~~d  210 (233)
                      .+|.|+.+.+      +|.|+++.+ |++|+.    ++  .+.         +  +.      .  .+||.|+|+|.++|
T Consensus       673 ~~g~V~~V~~------~G~fV~l~~~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV~~vd  746 (760)
T 2vnu_D          673 ETGYVIKVFN------NGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVM  746 (760)
T ss_dssp             EEEEEEEEET------TEEEEEETTTTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC---
T ss_pred             EEEEEEEEEC------CeEEEEEeCCCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCCEEEEEEEEEE
Confidence            5688888774      466777788 999995    32  211         0  11      1  57999999999999


Q ss_pred             CC---CCEEEEEEc
Q 026794          211 PS---GKKFTLLAR  221 (233)
Q Consensus       211 ~~---~~ki~Ls~r  221 (233)
                      .+   ++||.|+.|
T Consensus       747 ~~~~~~~kI~lslk  760 (760)
T 2vnu_D          747 DPITSKRKAELLLK  760 (760)
T ss_dssp             -----CCEEEC---
T ss_pred             CccccCCcEEEEeC
Confidence            88   689999875

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

Probab=85.60  E-value=0.39  Score=48.37  Aligned_cols=59  Identities=14%  Similarity=0.136  Sum_probs=42.1

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccC-CeeEEE----ee--ccc---------c--cc------c--cccCceEEEEeecC
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQED-GIDDVR----IT--RQG---------F--EK------R--VVSQDLQLWLSNAP  210 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~-gv~gl~----~~--~~~---------~--~~------~--~vg~~~~v~i~~~d  210 (233)
                      .+|.|+.+.++      |.|+++.+ |++|+.    ++  .+.         +  +.      .  .+||.|+|+|.+++
T Consensus       890 ~~g~V~~V~~~------G~fV~L~~~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~VkV~~vd  963 (977)
T 2wp8_J          890 ETGYVIKVFNN------GIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVM  963 (977)
T ss_dssp             EEEEEEEECSS------EEEEECTTTCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEEECCCC
T ss_pred             EEEEEEEEcCC------eEEEEEcCCCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCCEEEEEEEEEc
Confidence            56888888754      66677788 999995    32  111         0  11      2  57999999999988


Q ss_pred             CC---CCEEEEEEc
Q 026794          211 PS---GKKFTLLAR  221 (233)
Q Consensus       211 ~~---~~ki~Ls~r  221 (233)
                      .+   ++||+|++|
T Consensus       964 ~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          964 DPITSKRKAELLLK  977 (977)
T ss_dssp             CSSSCCCCCCEEEC
T ss_pred             CcccCCCceEEEeC
Confidence            74   478999875

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

Probab=82.11  E-value=6.6  Score=32.22  Aligned_cols=66  Identities=11%  Similarity=0.059  Sum_probs=43.2

Q ss_pred             hhccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcc------------cccCCCCEEEEEE
Q 026794           51 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR------------DILNEGDEVRVKV  113 (233)
Q Consensus        51 ~~~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~------------~~~~~Gd~V~vkV  113 (233)
                      .+.-++..|++++|+     +.|+.+-+.|     -...+||...|..++.-++.            +--++|+.|+.+|
T Consensus       122 ~iVFrPf~GevL~G~V~~~s~~~Ig~~~~G-----~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV  196 (214)
T 2rf4_A          122 LYVWQPQVGDVLEGYIFIQSASHIGLLIHD-----AFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTV  196 (214)
T ss_dssp             EEEECCCTTCEEEEEECCCCSSCEEEEETT-----TEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEE
T ss_pred             EEEEecCCCCEEEEEEEEECCCcEEEEEeC-----CEEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEE
Confidence            345578999999999     5455443332     46789999988533211111            1123699999999


Q ss_pred             EEEeCCCC
Q 026794          114 IKIDREKS  121 (233)
Q Consensus       114 i~vd~e~~  121 (233)
                      .+++...+
T Consensus       197 ~~~~~~~~  204 (214)
T 2rf4_A          197 RNVHTTGR  204 (214)
T ss_dssp             EEEECCSS
T ss_pred             EEEEecCC
Confidence            99986443

---

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	233
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	2e-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	9e-11
d1wi5a_	119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	4e-09
d1y14b1	91	b.40.4.5 (B:81-171) C-terminal domain of RNA polym	2e-08
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	4e-08
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	5e-08
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	5e-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	9e-06
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	0.001
d2ix0a3	87	b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Esche	0.002
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	0.002
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 = 2e-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 = 56.9 bits (137), 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 = 56.1 bits (135), 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 = 9e-11
 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 = 50.9 bits (121), Expect = 4e-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 = 48.3 bits (115), Expect = 2e-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

>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 = 47.2 bits (112), 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

>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 = 46.9 bits (111), Expect = 5e-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

>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 = 47.3 bits (112), Expect = 5e-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 = 46.1 bits (109), 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 = 41.0 bits (96), Expect = 9e-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 = 35.2 bits (81), Expect = 0.001
 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

>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 = 34.4 bits (79), Expect = 0.002
 Identities = 6/67 (8%), Positives = 16/67 (23%), Gaps = 14/67 (20%)

Query: 71  IHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVIKIDR 118
           + +R  D        +    +               +      +    D + V + ++  
Sbjct: 19  MRVRLVDN--GAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRM 76

Query: 119 EKSRITL 125
           E   I  
Sbjct: 77  ETRSIIA 83

>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 = 34.4 bits (79), Expect = 0.002
 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

>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	233
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.74
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.72
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.7
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.7
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.64
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.59
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.49
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.48
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.47
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.27
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.19
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	99.13
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.99
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.85
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	98.75
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.65
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.64
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.61
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	98.51
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.4
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	98.15
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	98.04
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.02
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	97.99
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	97.98
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	97.86
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	97.78
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	97.71
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.42
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	96.73
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	96.62
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	96.35
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	95.8
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	95.48
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	93.95
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	88.27
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	81.13

>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=99.74  E-value=6.2e-19  Score=124.21  Aligned_cols=71  Identities=38%  Similarity=0.710  Sum_probs=66.3

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        54 ~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      +.+++|+++.|+     +||+||+|.     ++++||||+|+++|.++.+|++.|++||.|+|+|+++|+ ++|+.||+|
T Consensus         1 ad~kvG~iv~G~V~~v~~~G~fV~l~-----~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~-~~ri~LS~k   74 (76)
T d1sroa_           1 AEIEVGRVYTGKVTRIVDFGAFVAIG-----GGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIK   74 (76)
T ss_dssp             CCCCTTSEEEEEEEEEETTEEEEECS-----SSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCT-TCCCEEEEC
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEeC-----CCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECC-CCCEEEEEE
Confidence            368999999999     999999998     389999999999999999999999999999999999996 679999999


Q ss_pred             cc
Q 026794          129 QL  130 (233)
Q Consensus       129 ~~  130 (233)
                      ++
T Consensus        75 ~a   76 (76)
T d1sroa_          75 EA   76 (76)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=99.72  E-value=7.3e-18  Score=121.24  Aligned_cols=70  Identities=31%  Similarity=0.507  Sum_probs=53.7

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      ++|+++.|+     +||+||+|...   +|++||||+|+++|.+..++.+.|++||.|+|+|+++|++++||.||+|+
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   27999999999999999999999999999999999999999999999986

>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=99.70  E-value=1.1e-17  Score=122.26  Aligned_cols=76  Identities=30%  Similarity=0.603  Sum_probs=71.9

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  127 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~  127 (233)
                      ++++++|+++.|+     ++|+||+|+     .+++||||.++++|++..++++.|++||.|+|+|+++|.++++|.||+
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     999999997     389999999999999999999999999999999999999999999999


Q ss_pred             eccccCh
Q 026794          128 KQLEEDP  134 (233)
Q Consensus       128 k~~~~dp  134 (233)
                      |+. ++|
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            986 666

>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=99.70  E-value=9.8e-18  Score=119.94  Aligned_cols=72  Identities=35%  Similarity=0.575  Sum_probs=61.3

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .+++|++++|+     +||+||+|...+   |++||||.|+++|.+..++.+.|++||.|+|+|+++|.+++++.||+|+
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            34689999999     999999996312   7999999999999999999999999999999999999999999999986

>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=99.64  E-value=2.1e-16  Score=117.86  Aligned_cols=80  Identities=29%  Similarity=0.512  Sum_probs=69.7

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc-----------cCcccccCCCCEEEEEEEEEeCC
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDRE  119 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~-----------~~~~~~~~~Gd~V~vkVi~vd~e  119 (233)
                      +++|++++|+     +||+||+|+      +++||||+|+|+++++           .++.+.|++||.|+|+|+++|.+
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            4789999999     999999996      6999999999999887           47788999999999999999988


Q ss_pred             CCe-----EEEEEeccccChhhHHhhh
Q 026794          120 KSR-----ITLSIKQLEEDPLLETLEK  141 (233)
Q Consensus       120 ~~r-----i~LS~k~~~~dp~~~~~~~  141 (233)
                      +++     +.||+|+...+||+...++
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     8899999999999765543

>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=99.59  E-value=1.3e-15  Score=108.44  Aligned_cols=74  Identities=26%  Similarity=0.359  Sum_probs=66.6

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccc-ccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~-~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      +++|+++.|+     ++|+||+|+     .+++||+|+|+++|.+ ..++++.|++||.|.|+|+++|+ ++++.||+|+
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            5899999999     999999998     3899999999999875 78999999999999999999996 6799999999


Q ss_pred             cccChh
Q 026794          130 LEEDPL  135 (233)
Q Consensus       130 ~~~dp~  135 (233)
                      ....|+
T Consensus        77 ~~~~k~   82 (83)
T d2ba0a1          77 RICRPI   82 (83)
T ss_dssp             SSCEEE
T ss_pred             CCCCCC
Confidence            866554

>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=99.49  E-value=1.1e-14  Score=110.52  Aligned_cols=78  Identities=13%  Similarity=0.175  Sum_probs=70.2

Q ss_pred             ccCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccc-ccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           53 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        53 ~~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~-~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      .+.+++|+++.|+     ++|+||+|+.    .+++||||++++++.+ ..++.+.|++||.|+|+|+++|.+++++.||
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            4679999999999     9999999941    3799999999999875 7889999999999999999999999999999


Q ss_pred             EeccccCh
Q 026794          127 IKQLEEDP  134 (233)
Q Consensus       127 ~k~~~~dp  134 (233)
                      +|+.....
T Consensus        92 ~k~~~~~~   99 (119)
T d1wi5a_          92 VGHSEVST   99 (119)
T ss_dssp             CCCCCSCC
T ss_pred             ecHHHhhh
Confidence            99876655

>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=99.48  E-value=2.1e-14  Score=102.99  Aligned_cols=70  Identities=26%  Similarity=0.368  Sum_probs=62.7

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc---CcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---DIRDILNEGDEVRVKVIKIDREKSRITLS  126 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~---~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS  126 (233)
                      .+++|+++.|+     +||+||+|+     .+++||||+|+++|+++.   ++++.|++||.|.|+|+++|+ .+++.||
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     379999999999998764   677899999999999999996 6899999


Q ss_pred             Eecc
Q 026794          127 IKQL  130 (233)
Q Consensus       127 ~k~~  130 (233)
                      +|+.
T Consensus        78 ~k~~   81 (87)
T d2je6i1          78 VKGK   81 (87)
T ss_dssp             CCST
T ss_pred             EecC
Confidence            9975

>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=99.47  E-value=2.5e-14  Score=102.79  Aligned_cols=70  Identities=17%  Similarity=0.323  Sum_probs=62.9

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc----CcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----DIRDILNEGDEVRVKVIKIDREKSRITL  125 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~----~~~~~~~~Gd~V~vkVi~vd~e~~ri~L  125 (233)
                      .+++|+++.|+     +||+||+|.     ++.+||||.|+++|.++.    +++++|++||.|.|+|+++|+ .+++.|
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     999999998     479999999999998764    678899999999999999996 579999


Q ss_pred             EEecc
Q 026794          126 SIKQL  130 (233)
Q Consensus       126 S~k~~  130 (233)
                      |+|+.
T Consensus        78 s~k~~   82 (88)
T d2z0sa1          78 TVQGE   82 (88)
T ss_dssp             ECCSS
T ss_pred             EEecC
Confidence            99974

>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=99.27  E-value=4.3e-14  Score=95.26  Aligned_cols=50  Identities=30%  Similarity=0.588  Sum_probs=29.3

Q ss_pred             eeeEEEEEccCCCCccEEEEEEccccCcc----cccCcccccCCCCEEEEEEEEEeCCC
Q 026794           66 DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQDIRDILNEGDEVRVKVIKIDREK  120 (233)
Q Consensus        66 ~~G~fV~l~~~~~~~gv~Glv~~sels~~----~~~~~~~~~~~Gd~V~vkVi~vd~e~  120 (233)
                      +|||||+|.     ++++||||+|++||.    ++.++++.|++||+|+|+|+++|+++
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    68899999999999999999999754

>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=99.19  E-value=3.4e-12  Score=92.76  Aligned_cols=69  Identities=23%  Similarity=0.303  Sum_probs=58.7

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcc----------cccCcccccCCCCEEEEEEEEEeCCC
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----------LIQDIRDILNEGDEVRVKVIKIDREK  120 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~----------~~~~~~~~~~~Gd~V~vkVi~vd~e~  120 (233)
                      +++|++|.|+     ++|+||+|.     .+.+|++|+|+++|.          +..++++.|++||.|.|+|+++|. .
T Consensus         6 P~vGdiV~G~V~~v~~~g~~V~I~-----~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~-d   79 (95)
T d2nn6h1           6 GEVGDIVVGRITEVQQKRWKVETN-----SRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-D   79 (95)
T ss_dssp             CCSSBCCCEEEEEEETTEEEEECS-----SSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-T
T ss_pred             CCCCCEEEEEEEEEecCcEEEEeC-----CCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECC-C
Confidence            5789999998     999999998     378999999999864          234577889999999999999997 6


Q ss_pred             CeEEEEEecc
Q 026794          121 SRITLSIKQL  130 (233)
Q Consensus       121 ~ri~LS~k~~  130 (233)
                      +++.||+|..
T Consensus        80 g~i~Ls~r~~   89 (95)
T d2nn6h1          80 GAVSLHTRSL   89 (95)
T ss_dssp             TEEEEECCSS
T ss_pred             CCEEEEeccc
Confidence            9999999864

>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=99.13  E-value=6.1e-11  Score=84.71  Aligned_cols=63  Identities=11%  Similarity=0.064  Sum_probs=52.3

Q ss_pred             CCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCccccc------------CcccccCCCCEEEEEEEEEeCCCC
Q 026794           59 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ------------DIRDILNEGDEVRVKVIKIDREKS  121 (233)
Q Consensus        59 G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~------------~~~~~~~~Gd~V~vkVi~vd~e~~  121 (233)
                      ++.++|+     +||+||+|.+    .+++||||+|+|++++..            +....|++||+|+|+|+++|++++
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            4556666     9999999963    479999999999997542            234569999999999999999999


Q ss_pred             eEEE
Q 026794          122 RITL  125 (233)
Q Consensus       122 ri~L  125 (233)
                      +|.+
T Consensus        80 ~I~~   83 (87)
T d2ix0a3          80 SIIA   83 (87)
T ss_dssp             EEEE
T ss_pred             eEEE
Confidence            9975

>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=98.99  E-value=8.1e-10  Score=79.05  Aligned_cols=63  Identities=19%  Similarity=0.200  Sum_probs=54.5

Q ss_pred             CCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc----------cCcccccCCCCEEEEEEEEEeCCCC
Q 026794           57 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----------QDIRDILNEGDEVRVKVIKIDREKS  121 (233)
Q Consensus        57 ~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~----------~~~~~~~~~Gd~V~vkVi~vd~e~~  121 (233)
                      -.|++++|+     +||+||+++      .++||||++++++++.          .+....|+.||.|+|||+++|.+++
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     999999996      6899999999998765          2345579999999999999999999


Q ss_pred             eEEE
Q 026794          122 RITL  125 (233)
Q Consensus       122 ri~L  125 (233)
                      +|..
T Consensus        76 ~i~~   79 (91)
T d1y14b1          76 SIHA   79 (91)
T ss_dssp             EEEE
T ss_pred             ccEE
Confidence            9864

>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=98.85  E-value=3.7e-09  Score=76.03  Aligned_cols=72  Identities=15%  Similarity=0.235  Sum_probs=57.5

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccc------------cCcccccCCCCEEEEEEEEEeC
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI------------QDIRDILNEGDEVRVKVIKIDR  118 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~------------~~~~~~~~~Gd~V~vkVi~vd~  118 (233)
                      +-.|++++|+     ++|+||+++      .++||+|.+++.+++.            .+....|+.||.|++||++++.
T Consensus         2 Pf~Gev~~g~V~~v~~~G~fv~lg------~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~   75 (94)
T d2c35b1           2 PFKGEVVDAVVTQVNKVGLFTEIG------PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV   75 (94)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEET------TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEec------CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEec
Confidence            3469999998     999999996      5899999999998852            2334568999999999999999


Q ss_pred             CCCeEEEEEeccccChh
Q 026794          119 EKSRITLSIKQLEEDPL  135 (233)
Q Consensus       119 e~~ri~LS~k~~~~dp~  135 (233)
                      +.++|.. + ....+||
T Consensus        76 ~~~~I~~-i-gt~~~d~   90 (94)
T d2c35b1          76 DKNDIFA-I-GSLMDDY   90 (94)
T ss_dssp             ETTEEEE-E-EECCSTT
T ss_pred             CcCcceE-E-EEccCCC
Confidence            9999864 2 2334454

>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=98.75  E-value=2e-09  Score=74.60  Aligned_cols=60  Identities=12%  Similarity=0.107  Sum_probs=51.7

Q ss_pred             ccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                      +.|+|.++.+      +|+|+++.+|++|+.    ++|.+++++    .+||+++++|.++|+ ++|++||+|+.
T Consensus         9 v~G~V~~v~~------~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~-~~ri~LS~k~a   76 (76)
T d1sroa_           9 YTGKVTRIVD------FGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIKEA   76 (76)
T ss_dssp             EEEEEEEEET------TEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCT-TCCCEEEECCC
T ss_pred             EEEEEEEEeC------cEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECC-CCCEEEEEEcC
Confidence            7799999984      588899999999994    888887776    689999999999996 57899999863

>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=98.65  E-value=1.4e-08  Score=72.26  Aligned_cols=69  Identities=7%  Similarity=-0.067  Sum_probs=60.7

Q ss_pred             CCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           55 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        55 ~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .+++||+|-|+     .+++||+|.     ++..|++|++++++ +.++.++.|++||.|.|+|.++|. .+++.||..+
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     889999998     47899999999964 678889999999999999999996 7889998865


Q ss_pred             c
Q 026794          130 L  130 (233)
Q Consensus       130 ~  130 (233)
                      .
T Consensus        76 ~   76 (88)
T d2nn6g1          76 S   76 (88)
T ss_dssp             T
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=98.64  E-value=9.4e-09  Score=72.60  Aligned_cols=65  Identities=9%  Similarity=0.068  Sum_probs=48.3

Q ss_pred             CCCCeeeecCCccccCCeeeeccCCChhhhhhhhccc--CCeeEEE----eeccccccc----cccCceEEEEeecCCCC
Q 026794          144 PQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQE--DGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSG  213 (233)
Q Consensus       144 ~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~--~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~  213 (233)
                      ++|++        +.|+|+++.++      |+|+++.  +|++|+.    +++.+.+++    .+||+++++|.++|+++
T Consensus        12 ~~G~i--------v~G~V~~i~~~------G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd~~~   77 (86)
T d1kl9a2          12 EVEDV--------VMVNVRSIAEM------GAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEK   77 (86)
T ss_dssp             CTTCE--------EEEEEEEECSS------EEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTT
T ss_pred             CCCCE--------EEEEEEEEeCC------eEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEEECCC
Confidence            46777        77999999854      6777666  6899995    777777666    58999999999999999


Q ss_pred             CEEEEEEcc
Q 026794          214 KKFTLLARA  222 (233)
Q Consensus       214 ~ki~Ls~r~  222 (233)
                      +|+.||.|+
T Consensus        78 ~ki~LS~Kq   86 (86)
T d1kl9a2          78 GYIDLSKRR   86 (86)
T ss_dssp             TEEEEESTT
T ss_pred             CEEEEEeeC
Confidence            999999985

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

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

Probab=98.61  E-value=1e-08  Score=71.97  Aligned_cols=63  Identities=2%  Similarity=-0.015  Sum_probs=48.5

Q ss_pred             CccccCCeeeeccCCChhhhhhhhccc--CCeeEEE----eeccccccc----cccCceEEEEeecCCCCCEEEEEEcc
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQE--DGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGKKFTLLARA  222 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~--~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~  222 (233)
                      |..++|+|.+++++      |+|+++.  +|++|+.    +++.+.+++    .+||+++++|.++|++++|+.||.|+
T Consensus        12 G~iv~G~V~~v~~~------G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2          12 GEILIATVKQVFDY------GSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             TCCCEEEEEEEETT------EEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             CCEEEEEEEEEECC------EEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEEcC
Confidence            33488999999854      7777766  5899995    777776665    58999999999999999999999984

>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=98.51  E-value=4.1e-08  Score=70.41  Aligned_cols=67  Identities=4%  Similarity=-0.062  Sum_probs=56.6

Q ss_pred             cCCCCeeeecCCccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc----cccCceEEEEeecCCCCC
Q 026794          143 IPQDGSVISDSSSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR----VVSQDLQLWLSNAPPSGK  214 (233)
Q Consensus       143 ~~~g~~~~~~~~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~----~vg~~~~v~i~~~d~~~~  214 (233)
                      +++|++        +.|.|.++.      ++|+++++.+|++|+.    +++.+.+++    .+||.++++|.++|.+++
T Consensus        16 ~k~G~i--------v~g~V~~v~------~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~   81 (94)
T d3bzka4          16 LKPGMV--------LEGVVTNVT------NFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRN   81 (94)
T ss_dssp             CCTTCE--------EEEEEEEEE------TTEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTT
T ss_pred             CCCCCE--------EEEEEEEEE------CcEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCC
Confidence            566776        779999987      4588888899999995    677666666    589999999999999999


Q ss_pred             EEEEEEccc
Q 026794          215 KFTLLARAG  223 (233)
Q Consensus       215 ki~Ls~r~~  223 (233)
                      |+.||+|+.
T Consensus        82 ~i~LS~K~~   90 (94)
T d3bzka4          82 RVGLSMRMS   90 (94)
T ss_dssp             EEEEESCTT
T ss_pred             EEEEEEecc
Confidence            999999964

>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=98.40  E-value=1.9e-07  Score=66.46  Aligned_cols=68  Identities=15%  Similarity=0.125  Sum_probs=60.6

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  129 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k~  129 (233)
                      .++||+|-|+     .+++||+|.     ....|++|.++......++.+..|++||.|.|+|.++|. .+.+.||++.
T Consensus         5 P~~gD~ViG~V~~~~~~~~~vdI~-----~~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~-~~~~~Lsc~~   77 (90)
T d2ja9a1           5 PSVNDFVIGVIIGTFSDSYKVSLQ-----NFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEK-ELEAEIECFD   77 (90)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEESS-----TTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEESSC
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEcC-----CcchhhhhhhhccCccccccCCccCCCCEEEEEEEEECC-CCCEEEEEec
Confidence            5899999999     889999997     367899999988888888999999999999999999996 7789998754

>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=98.15  E-value=2.9e-06  Score=63.69  Aligned_cols=74  Identities=20%  Similarity=0.232  Sum_probs=58.8

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCC---CccEEEEEEccccCc--ccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDG---LYHLTGLVHVSEVSW--DLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~---~~gv~Glv~~sels~--~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~L  125 (233)
                      +++|++|.|+     ...++|+|...++   ...+.|++|.+++..  ....++.+.|++||.|+|+|+++...+..+.|
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            5789999998     7789999964332   125679999999843  34557899999999999999999876667888


Q ss_pred             EEec
Q 026794          126 SIKQ  129 (233)
Q Consensus       126 S~k~  129 (233)
                      |.++
T Consensus        85 st~~   88 (125)
T d2nn6i1          85 TTAE   88 (125)
T ss_dssp             ECCS
T ss_pred             EecC
Confidence            8865

>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=98.04  E-value=2.4e-06  Score=59.28  Aligned_cols=63  Identities=10%  Similarity=-0.070  Sum_probs=49.0

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccc-cccc----cccCceEEEEeecCCCCCEEEEEEccc
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQG-FEKR----VVSQDLQLWLSNAPPSGKKFTLLARAG  223 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~-~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~  223 (233)
                      |..+.|+|.++.++      ++|+++.++++|+.    +++.. ..++    .+||.+.++|.++|. ++|+.||+|.-
T Consensus         6 Gd~V~G~V~~v~~~------g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~LS~k~~   77 (83)
T d2ba0a1           6 GDVVIGIIREVAAN------GWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMKDR   77 (83)
T ss_dssp             TCEEEEEEEEECSS------EEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECCSS
T ss_pred             CCEEEEEEEEEECC------EEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEEEEECC-CCCEEEEecCC
Confidence            33478999999854      78888899999995    45443 3333    589999999999995 57899999864

>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=98.02  E-value=1.6e-05  Score=53.87  Aligned_cols=59  Identities=19%  Similarity=0.157  Sum_probs=48.9

Q ss_pred             CCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCCC--eEEEE
Q 026794           56 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS--RITLS  126 (233)
Q Consensus        56 ~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~--ri~LS  126 (233)
                      -++|++++|+     +..++|+|+      +.+|++|.+|..      |.+.|++||.|+|-|.+++.+.+  +|.||
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     667899997      799999999964      67889999999999999986543  45555

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

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.99  E-value=2.1e-06  Score=63.80  Aligned_cols=63  Identities=13%  Similarity=0.026  Sum_probs=50.6

Q ss_pred             ccCCeeeeccCCChhhhhhhhccc-CCeeEEE----eeccc-cccc----cccCceEEEEeecCCCCCEEEEEEcccce
Q 026794          157 SSSNSNTIEPLPGLGAIFEELLQE-DGIDDVR----ITRQG-FEKR----VVSQDLQLWLSNAPPSGKKFTLLARAGRC  225 (233)
Q Consensus       157 ~~g~v~~v~~~~g~~~~~~~l~~~-~gv~gl~----~~~~~-~~~~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~~  225 (233)
                      ++|+|.++++      +|+|+++. ++++|+.    +++.. .+.|    .+||.++|+|.++|.++++++||.|+.+.
T Consensus        25 v~G~V~~i~~------~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~k~~~~   97 (119)
T d1wi5a_          25 LTGTVSSLED------HGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV   97 (119)
T ss_dssp             EEEEEEEECS------SEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCCCS
T ss_pred             EEEEEEEEec------cEEEEEEeccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEEecHHHh
Confidence            7899999885      47788884 8999996    45432 2223    58999999999999999999999997654

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

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

Probab=97.98  E-value=2.1e-06  Score=60.14  Aligned_cols=62  Identities=6%  Similarity=-0.112  Sum_probs=49.5

Q ss_pred             cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecccccc---c----cccCceEEEEeecCCCCCEEEEEEcccc
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEK---R----VVSQDLQLWLSNAPPSGKKFTLLARAGR  224 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~---~----~vg~~~~v~i~~~d~~~~ki~Ls~r~~~  224 (233)
                      .+.|+|.++.+      +|+|+++.++++|+.    ++|+++..   +    .+||.+.++|.++|. ++++.||+|...
T Consensus        10 iv~G~V~~i~~------~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~-~~~i~LS~k~~~   82 (87)
T d2je6i1          10 IVIGLVEDVEI------YGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVLSVKGKD   82 (87)
T ss_dssp             EEEEEEEEECS------SEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEEECCSTT
T ss_pred             EEEEEEEEEEC------CEEEEEeCCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECC-CCCEEEEEecCC
Confidence            37899999984      488888999999995    66655432   1    579999999999995 578999998654

>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=97.86  E-value=6.1e-06  Score=60.01  Aligned_cols=61  Identities=7%  Similarity=0.041  Sum_probs=45.3

Q ss_pred             cccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccc-----------cc----cccCceEEEEeecCCCCCE-
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFE-----------KR----VVSQDLQLWLSNAPPSGKK-  215 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~-----------~~----~vg~~~~v~i~~~d~~~~k-  215 (233)
                      +++|.|+++.++      |+|+++. +++|+.    ++++++.           .+    .+||.++|+|.++|.++++ 
T Consensus         6 i~~g~V~~v~~~------G~FVel~-~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~~~~~   78 (106)
T d1go3e1           6 LIEGEVVDVVEF------GSFVRLG-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERK   78 (106)
T ss_dssp             EEEEEEEEEETT------EEEEECS-SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC---
T ss_pred             EEEEEEEEEeee------EEEEEee-CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchhhccc
Confidence            377999998855      6677775 799995    6665542           22    6899999999999998876 


Q ss_pred             ----EEEEEccc
Q 026794          216 ----FTLLARAG  223 (233)
Q Consensus       216 ----i~Ls~r~~  223 (233)
                          +.|++|+.
T Consensus        79 ~~~~i~ls~K~~   90 (106)
T d1go3e1          79 RGSKIALTMRQP   90 (106)
T ss_dssp             --CEEEEECCST
T ss_pred             cCceeecccccC
Confidence                77887754

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

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

Probab=97.78  E-value=9.2e-06  Score=56.85  Aligned_cols=64  Identities=6%  Similarity=-0.086  Sum_probs=49.6

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccccc--------cccCceEEEEeecCCCCCEEEEEEc
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFEKR--------VVSQDLQLWLSNAPPSGKKFTLLAR  221 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~~~--------~vg~~~~v~i~~~d~~~~ki~Ls~r  221 (233)
                      |..+.|+|.++.+      +++|+++.++++|+.    +++.+.+.+        .+||.+.++|.++|. ++++.||+|
T Consensus         8 GdvV~G~V~~v~~------~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~Ls~k   80 (88)
T d2z0sa1           8 GDVVIGLIQSVGI------MNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPLLTVQ   80 (88)
T ss_dssp             TCCEEEEEEEECS------SEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEEEECC
T ss_pred             CCEEEEEEEEEEC------CeEEEEeCCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECC-CCCEEEEEe
Confidence            3347799999885      478888899999994    666554321        479999999999995 568999998


Q ss_pred             ccc
Q 026794          222 AGR  224 (233)
Q Consensus       222 ~~~  224 (233)
                      .-.
T Consensus        81 ~~~   83 (88)
T d2z0sa1          81 GEG   83 (88)
T ss_dssp             SSS
T ss_pred             cCC
Confidence            643

>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=97.71  E-value=1.9e-06  Score=56.81  Aligned_cols=49  Identities=16%  Similarity=0.134  Sum_probs=29.8

Q ss_pred             CCeeeeccCCChhhhhhhhcccCCeeEE----Eeecc----ccccc----cccCceEEEEeecCCCC
Q 026794          159 SNSNTIEPLPGLGAIFEELLQEDGIDDV----RITRQ----GFEKR----VVSQDLQLWLSNAPPSG  213 (233)
Q Consensus       159 g~v~~v~~~~g~~~~~~~l~~~~gv~gl----~~~~~----~~~~~----~vg~~~~v~i~~~d~~~  213 (233)
                      |+|.+++      +||+|+++.+|++||    ++++.    +++++    .+||+++|+|.++|+++
T Consensus         1 G~V~~i~------~fG~FV~l~~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           1 GSVVKTT------TFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             CBEEECC-------CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCSSC
T ss_pred             CEEEEEE------eceEEEEecCCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCCC
Confidence            6777777      558899999999999    36643    44455    58999999999999654

>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=97.42  E-value=0.00035  Score=47.47  Aligned_cols=62  Identities=19%  Similarity=0.255  Sum_probs=47.4

Q ss_pred             CCCCEEEEE----ee-----eEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEE
Q 026794           57 NVEDIFVGR----DY-----GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITL  125 (233)
Q Consensus        57 ~~G~vv~g~----~~-----G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~--~ri~L  125 (233)
                      ++|++++|+    +.     -++|+|+...  .+++|++|.+|.      -|.+.|++||.|+|-|.+++...  -+|.|
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  269999999986      46788999999999999998644  24444


Q ss_pred             E
Q 026794          126 S  126 (233)
Q Consensus       126 S  126 (233)
                      |
T Consensus        75 S   75 (76)
T d2asba1          75 S   75 (76)
T ss_dssp             E
T ss_pred             e
Confidence            4

>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=96.73  E-value=0.0005  Score=48.43  Aligned_cols=64  Identities=9%  Similarity=0.033  Sum_probs=46.5

Q ss_pred             CccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccccc----------cc----cccCceEEEEeecCCCCCE
Q 026794          154 SSMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGFE----------KR----VVSQDLQLWLSNAPPSGKK  215 (233)
Q Consensus       154 ~~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~~----------~~----~vg~~~~v~i~~~d~~~~k  215 (233)
                      |..+.|+|+.+.+      +++|+++.++.+|+.    +++....          +.    .+||.+.++|.+++. +++
T Consensus         9 GdiV~G~V~~v~~------~g~~V~I~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~-dg~   81 (95)
T d2nn6h1           9 GDIVVGRITEVQQ------KRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-DGA   81 (95)
T ss_dssp             SBCCCEEEEEEET------TEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-TTE
T ss_pred             CCEEEEEEEEEec------CcEEEEeCCCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECC-CCC
Confidence            4447899999885      478888899999984    3321111          01    579999999999996 589


Q ss_pred             EEEEEcccc
Q 026794          216 FTLLARAGR  224 (233)
Q Consensus       216 i~Ls~r~~~  224 (233)
                      +.||+|..+
T Consensus        82 i~Ls~r~~~   90 (95)
T d2nn6h1          82 VSLHTRSLK   90 (95)
T ss_dssp             EEEECCSST
T ss_pred             EEEEecccc
Confidence            999999653

>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=96.62  E-value=0.0037  Score=42.33  Aligned_cols=74  Identities=34%  Similarity=0.472  Sum_probs=56.5

Q ss_pred             cCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEEEcc-ccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 026794           54 SRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  128 (233)
Q Consensus        54 ~~~~~G~vv~g~----~~G~fV~l~~~~~~~gv~Glv~~s-els~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~LS~k  128 (233)
                      .-+.+|++.+|+    ++-++|.|.+++   |.+|++--+ ++..++..++++.+ +|.+|+++|+.+|.-+|.|.++.|
T Consensus         4 ~lPnigdVtkGiVy~kd~~fyV~L~dY~---g~ea~l~dy~~~~~d~~~klk~kL-VGKtIkvqVIR~d~lKGYIDVr~~   79 (85)
T d1luza_           4 SLPNAGDVIKGRVYEKDYALYIYLFDYP---HFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYK   79 (85)
T ss_dssp             CCCCTTCEEEEEEEEETTEEEEEETTCT---TSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEE
T ss_pred             ccCCCCceeeeEEEEeCCEEEEEecCCC---CceEEeeehhhhhhHHHHHHHHHh-cCceEEEEEEEEcceeeEEEehhh
Confidence            346899999999    666789998643   688887322 22334555666665 799999999999999999999998


Q ss_pred             ccc
Q 026794          129 QLE  131 (233)
Q Consensus       129 ~~~  131 (233)
                      ...
T Consensus        80 ~~~   82 (85)
T d1luza_          80 RMC   82 (85)
T ss_dssp             EEC
T ss_pred             hhh
Confidence            764

>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=96.35  E-value=0.0031  Score=43.61  Aligned_cols=47  Identities=30%  Similarity=0.533  Sum_probs=37.9

Q ss_pred             eeEEEEEccCCCCccEEEEEEccccCccccc---------CcccccCCCCEEEEEEEEEeC
Q 026794           67 YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---------DIRDILNEGDEVRVKVIKIDR  118 (233)
Q Consensus        67 ~G~fV~l~~~~~~~gv~Glv~~sels~~~~~---------~~~~~~~~Gd~V~vkVi~vd~  118 (233)
                      .+|||+++     .+-.||+|.+++.+.+..         +..+.++.||.|-|+|.+=..
T Consensus        16 ~AAFVDiG-----~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~   71 (87)
T d1smxa_          16 EAAFVDYG-----AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEER   71 (87)
T ss_dssp             TEEEEESS-----SSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCB
T ss_pred             eEEEEEeC-----CCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeeccc
Confidence            37999998     478899999999876542         456779999999999988543

>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=95.80  E-value=0.0044  Score=42.77  Aligned_cols=57  Identities=9%  Similarity=-0.059  Sum_probs=41.1

Q ss_pred             cccCCeeeeccCCChhhhhhhhcccC-CeeEEE----eeccccc---------------cc-cccCceEEEEeecCCCCC
Q 026794          156 MSSSNSNTIEPLPGLGAIFEELLQED-GIDDVR----ITRQGFE---------------KR-VVSQDLQLWLSNAPPSGK  214 (233)
Q Consensus       156 ~~~g~v~~v~~~~g~~~~~~~l~~~~-gv~gl~----~~~~~~~---------------~~-~vg~~~~v~i~~~d~~~~  214 (233)
                      ..+|.+..+.++      |.|+++.+ |++|+.    |++++.+               +. .+||.++|++.++|++++
T Consensus         6 ~F~g~Is~v~~~------GifV~L~e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r   79 (87)
T d2ix0a3           6 RFAAEIVDISRG------GMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETR   79 (87)
T ss_dssp             CEEEEEEEEETT------EEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTT
T ss_pred             EEEEEEEEEEcC------eEEEEEecCCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccC
Confidence            356788877754      66777654 799995    4443321               01 579999999999999999


Q ss_pred             EEEE
Q 026794          215 KFTL  218 (233)
Q Consensus       215 ki~L  218 (233)
                      ||..
T Consensus        80 ~I~~   83 (87)
T d2ix0a3          80 SIIA   83 (87)
T ss_dssp             EEEE
T ss_pred             eEEE
Confidence            9853

>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=95.48  E-value=0.0094  Score=41.31  Aligned_cols=67  Identities=13%  Similarity=0.161  Sum_probs=48.9

Q ss_pred             ccCCCCCCEEEEE----eeeEEEEEccCCCCccEEEEE-EccccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 026794           53 SSRVNVEDIFVGR----DYGAFIHLRFPDGLYHLTGLV-HVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL  125 (233)
Q Consensus        53 ~~~~~~G~vv~g~----~~G~fV~l~~~~~~~gv~Glv-~~sels~~~~~~~~~~~~~Gd~V~vkVi~vd~e~~ri~L  125 (233)
                      .-.+-+|++.+|.    ++-++|.|.+++   |.+|++ ..=++..++..+.++.+ +|.+|+++|+.+|  +..|.+
T Consensus        27 ~~~~~~G~V~kGiVy~rd~~fyV~L~dY~---g~eail~dY~n~~~dr~~klkkkL-VGKTIkVqVIRvD--klYIDV   98 (102)
T d1jjga_          27 AMDLSPGSVHEGIVYFKDGIFKVRLLGYE---GHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRAD--GLYVDL   98 (102)
T ss_dssp             CCCCCSSCEEEEEEEEETTEEEEECTTTS---SCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEEC--SSEEEE
T ss_pred             ecccCCCcEeeeEEEEeCCEEEEEecCCC---CceeeeeehhhhhHHHHHHHHHHh-cCceEEEEEEEec--cEEEEE
Confidence            4568899999999    666799998643   788885 33344445666666666 7999999999999  334443

>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=93.95  E-value=0.027  Score=38.49  Aligned_cols=58  Identities=3%  Similarity=-0.033  Sum_probs=40.7

Q ss_pred             ccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eecccc-------------ccc-cccCceEEEEeecCCCCCEE
Q 026794          155 SMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQGF-------------EKR-VVSQDLQLWLSNAPPSGKKF  216 (233)
Q Consensus       155 ~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~~-------------~~~-~vg~~~~v~i~~~d~~~~ki  216 (233)
                      ..++|+|.++.++      |.|+++. .++|+.    ++++..             .+. .+||.++|++.+++.+.+++
T Consensus         5 ev~~g~I~~v~~~------G~fv~lg-~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~i   77 (91)
T d1y14b1           5 EVVDGTVVSCSQH------GFEVQVG-PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSI   77 (91)
T ss_dssp             CEEEEEEEEEETT------EEEEEET-TEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTEE
T ss_pred             CEEEEEEEEEEee------EEEEEEc-CeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccCcc
Confidence            3477999998865      5566665 588884    222211             001 57999999999999999998


Q ss_pred             EEE
Q 026794          217 TLL  219 (233)
Q Consensus       217 ~Ls  219 (233)
                      ...
T Consensus        78 ~~i   80 (91)
T d1y14b1          78 HAI   80 (91)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            654

>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=88.27  E-value=0.24  Score=33.65  Aligned_cols=58  Identities=5%  Similarity=-0.013  Sum_probs=40.0

Q ss_pred             ccccCCeeeeccCCChhhhhhhhcccCCeeEEE----eeccc-c---cc-----------c-cccCceEEEEeecCCCCC
Q 026794          155 SMSSSNSNTIEPLPGLGAIFEELLQEDGIDDVR----ITRQG-F---EK-----------R-VVSQDLQLWLSNAPPSGK  214 (233)
Q Consensus       155 ~~~~g~v~~v~~~~g~~~~~~~l~~~~gv~gl~----~~~~~-~---~~-----------~-~vg~~~~v~i~~~d~~~~  214 (233)
                      ..++|.|.++.++      |.|+++. .++|+.    +.++. .   ++           . .+||.+.++|.+++.+.+
T Consensus         6 ev~~g~V~~v~~~------G~fv~lg-~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~   78 (94)
T d2c35b1           6 EVVDAVVTQVNKV------GLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKN   78 (94)
T ss_dssp             CEEEEEEEEEETT------EEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETT
T ss_pred             CEEEEEEEEEEee------EEEEEec-CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcC
Confidence            3477999998865      5556554 578884    33222 1   10           0 469999999999999999


Q ss_pred             EEEEE
Q 026794          215 KFTLL  219 (233)
Q Consensus       215 ki~Ls  219 (233)
                      ++...
T Consensus        79 ~I~~i   83 (94)
T d2c35b1          79 DIFAI   83 (94)
T ss_dssp             EEEEE
T ss_pred             cceEE
Confidence            98754

>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=81.13  E-value=1.1  Score=29.00  Aligned_cols=45  Identities=11%  Similarity=0.220  Sum_probs=34.5

Q ss_pred             cCCCCCCEEEEE-----eeeEEEEEccCCCCccEEEEEEccccCcccccCcccccCCCCEEEEEEEEE
Q 026794           54 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI  116 (233)
Q Consensus        54 ~~~~~G~vv~g~-----~~G~fV~l~~~~~~~gv~Glv~~sels~~~~~~~~~~~~~Gd~V~vkVi~v  116 (233)
                      ..+++|++=+|.     ..|+||+++       ++-+....           ..|++|+.+.++|.++
T Consensus         6 g~p~vGEiReG~~~rr~~~g~~vDiG-------lD~la~~k-----------~~~~~~~r~tfrIvs~   55 (71)
T d1k3ra1           6 GKPVTGEYRQGLTVKRVKKGTLVDIG-------ADKLALCR-----------EKLTVNRIMSFRVVRL   55 (71)
T ss_dssp             SSCCTTCEEEEEEEEECSSSEEEESS-------SSCEEECS-----------SCCCSSCEEEEEEEEC
T ss_pred             CCCcccceeeEEEEEecCCcEEEEec-------CCceeeee-----------cccccCcEEEEEEEEc
Confidence            457899999998     778999995       44343322           2478999999999997