Citrus Sinensis ID: 022938

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------29
Protein Sequence
MLSLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMV
Secondary Structure (PSIPRED)
cccccccccccEEEEcccEEEEEEEEEEEccEEEEEccEEEEEccccEEEEccccccccccccccEEEEEEccccccccEEEEEccHHHHHHHHHHHHcccEEEEEEEEEEccEEEEEEccEEEEEccccccccccccccccHHHHHHccccccEEEEEEEEEEcccccEEEEEHHHHHHHHHcccccccEEEcEEEEEEEEEcccccccccccEEEEEccccccccccccccccccEEEEEEEEEEccccEEEEEcccccccccHHHHHHHcccccEEEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cccHHHHccccccEEEEEEcccEEEEEEEEEEEEEcccEEEccccccccEcHHEEEEEcccEEEEEEEEccccccEEEEEHHHHccccHHHHHHHHcccccEEEEEEEEEEccEEEEEccccEEEEEcccccccccccccEEEEccccccccccEEEEEEEEEccccccEEEEEccccHHHHHHHcccccEEEcEEEEEEEEEccEEEcccccEEEEEEHccHHccccccHEEEcccEEEEEEEEEcccccEEEEEEccccccHHHHHHHHHcccccEEcccccccccc
Coil and Loop (DISEMBL)
mlslssrigsntcldasscthsslslslslsslvcvnplIIERIcqrnlcpvgkfstnaakitpttvnpilddssdannrqsqsrssADWKAARAYKEsgfiyegkiqgfngGGLLVRFFSLvgflpfpqmspshsckepqKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWnkyssrvnvedifvgrdygafihlrfpdglyhlTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKqleedpllETLEKVIPQGLEPYLKSFYKKMV
Flexible Loop (DISEMBL)
MLSLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFstnaakitpttvnpilddssdannrqsqsrssadwKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDilnegdevrvkvikidreksritlsikqleedplletlekvipqglepylkSFYKKMV
Low Complexity Region (SEG)
MLSLSSRIGSNTCLDASSCTHsslslslslsslVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMV
Disordered region (IsUnstruct)
******************CTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTV************************AARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFP**************IHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSF*****
Disordered Region (DISOPRED)
*************LDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDA*****QSR*SADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMV
Disordered Region (DISEMBL)
*********SNTCL***********LSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDS*******************RAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQ***********KSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMV
Disordered Region (DISPRO)
MLSLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFY****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLSLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLKSFYKKMV
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	289	2.2.26 [Sep-21-2011]
P29344	411	30S ribosomal protein S1,	N/A	no	0.598	0.420	0.313	1e-18
P73530	328	30S ribosomal protein S1	N/A	no	0.546	0.481	0.305	2e-16
Q89AJ3	566	30S ribosomal protein S1	yes	no	0.608	0.310	0.294	2e-15
Q9JZ44	561	30S ribosomal protein S1	yes	no	0.754	0.388	0.277	3e-15
P37985	557	30S ribosomal protein S1	yes	no	0.626	0.324	0.3	4e-15
P46228	307	30S ribosomal protein S1	yes	no	0.546	0.514	0.316	3e-14
P0AG70	557	30S ribosomal protein S1	yes	no	0.626	0.324	0.290	5e-14
P0AG67	557	30S ribosomal protein S1	N/A	no	0.626	0.324	0.290	5e-14
P0AG68	557	30S ribosomal protein S1	yes	no	0.626	0.324	0.290	5e-14
P0AG69	557	30S ribosomal protein S1	N/A	no	0.626	0.324	0.290	5e-14

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

 Score = 94.0 bits (232), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 62/198 (31%), Positives = 102/198 (51%), Gaps = 25/198 (12%)

Query: 72  DDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQM 131
           DDS   + RQ Q   +  W+  R  +    + +GKI G N GG++     L GF+PF Q+
Sbjct: 158 DDSLILSLRQIQYELA--WERCRQLQAEDVVVKGKIVGANKGGVVALVEGLRGFVPFSQI 215

Query: 132 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDI 191
           S   S +E           L    I +K ++ +EE  +LV S + A+ +   +++ +  +
Sbjct: 216 SSKSSAEE-----------LLEKEIPLKFVEVDEEQSRLVMSNRKAMADS-QAQLGIGSV 263

Query: 192 FVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 246
             G     + YGAFI +        + GL+HVS++S D + DI  +L  GD ++V ++  
Sbjct: 264 VTGTVQSLKPYGAFIDI------GGINGLLHVSQISHDRVSDIATVLQPGDTLKVMILSH 317

Query: 247 DREKSRITLSIKQLEEDP 264
           DRE+ R++LS K+LE  P
Sbjct: 318 DRERGRVSLSTKKLEPTP 335

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

 Score = 86.3 bits (212), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 55/180 (30%), Positives = 88/180 (48%), Gaps = 22/180 (12%)

Query: 90  WKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAK 149
           W+  R  +         +   N GG LVR   L GF+P   +S             E  +
Sbjct: 108 WERVRQLQAEDATVRSNVFATNRGGALVRIEGLRGFIPGSHISA-----------REAKE 156

Query: 150 GLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDYGAFIHLR 204
            L G  + +K ++ +EE  +LV S + A+  +  + + V  + VG     + YGAFI + 
Sbjct: 157 DLVGEDLPLKFLEVDEERNRLVLSHRRALVERKMNGLEVAQVVVGSVRGIKPYGAFIDI- 215

Query: 205 FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 264
                  ++GL+H+SE+S D I     + N  DE++V +I +D E+ RI+LS KQLE +P
Sbjct: 216 -----GGVSGLLHISEISHDHIDTPHSVFNVNDEIKVMIIDLDAERGRISLSTKQLEPEP 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 = 83.2 bits (204), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 60/204 (29%), Positives = 104/204 (50%), Gaps = 28/204 (13%)

Query: 80  RQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKE 139
           R+   R  A     +AYK+S  +  G I G   GG  V    +  FLP   +      + 
Sbjct: 86  REKAKRHEAWLTLEQAYKDSKTVV-GLINGKVKGGFTVELEDIRAFLPGSLVD----IRP 140

Query: 140 PQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNV------EDIFV 193
            ++++H     L G  +  KVI+ +++   +V S +  + ++Y++  N+      E + V
Sbjct: 141 VRETMH-----LEGKELEFKVIKLDQKRNNVVVSRRAVIESEYNAERNLLLETLQEGLIV 195

Query: 194 G------RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID 247
                   DYGAF+ L   DGL H+T      +++W  ++   +I+N GDEV++K++K D
Sbjct: 196 SGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNIGDEVKIKILKFD 249

Query: 248 REKSRITLSIKQLEEDPLLETLEK 271
           REK R++L +KQL +DP  +  E+
Sbjct: 250 REKIRVSLGLKQLSDDPWTKISER 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|Q9JZ44|RS1_NEIMB 30S ribosomal protein S1 OS=Neisseria meningitidis serogroup B (strain MC58) GN=rpsA PE=1 SV=1

 Score = 82.4 bits (202), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 107/238 (44%), Gaps = 20/238 (8%)

Query: 53  GKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNG 112
           G+           T+  + +   +    + +++ +ADW A     E+G I  G I G   
Sbjct: 59  GEIEVKVGDFVTVTIESVENGFGETKLSREKAKRAADWIALEEAMENGDILSGIINGKVK 118

Query: 113 GGLLVRFFSLVGFLPF------PQMSPSH-SCKEPQKSIHEIAKGLTGSIISVKVIQANE 165
           GGL V   S+  FLP       P    SH   KE +  + ++ K     ++S + +    
Sbjct: 119 GGLTVMISSIRAFLPGSLVDVRPVKDTSHFEGKEIEFKVIKLDKKRNNVVVSRRAV---- 174

Query: 166 EMKKLVFSEKDAVWNKYSSRVNVEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD 224
            ++  +  E+ A+         ++ I     DYGAF+ L   DGL H+T L      +W 
Sbjct: 175 -LEATLGEERKALLENLQEGSVIKGIVKNITDYGAFVDLGGIDGLLHITDL------AWR 227

Query: 225 LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPYLK 282
            ++   ++L  G EV  KV+K D+EK R++L +KQL EDP    L +  PQG   + K
Sbjct: 228 RVKHPSEVLEVGQEVEAKVLKFDQEKQRVSLGMKQLGEDP-WSGLTRRYPQGTRLFGK 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.

Neisseria meningitidis serogroup B (strain MC58) (taxid: 122586)

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

 Score = 82.0 bits (201), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/210 (30%), Positives = 103/210 (49%), Gaps = 29/210 (13%)

Query: 79  NRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCK 138
           +R+   R  A     +AY+ES  +  G I G   GG  V    +  FLP   +      +
Sbjct: 85  SREKAKRHEAWLMLEKAYEESATVT-GVINGKVKGGFTVELNGIRAFLPGSLVD----VR 139

Query: 139 EPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVN 187
             + ++H     L G  +  KVI+ +++   +V S           E+D +       + 
Sbjct: 140 PVRDTLH-----LEGKELEFKVIKLDQKRNNVVVSRRAVIESENSAERDQLLENLQEGME 194

Query: 188 VEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 246
           V+ I     DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K 
Sbjct: 195 VKGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKF 248

Query: 247 DREKSRITLSIKQLEEDPLLETLEKVIPQG 276
           DRE++R++L +KQL EDP +  + K  P+G
Sbjct: 249 DRERTRVSLGLKQLGEDPWV-AIAKRYPEG 277

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|P46228|RS1_SYNP6 30S ribosomal protein S1 OS=Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) GN=rpsA PE=1 SV=4

 Score = 79.3 bits (194), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 57/180 (31%), Positives = 93/180 (51%), Gaps = 22/180 (12%)

Query: 90  WKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAK 149
           W+  R  +        ++   N GG LVR   L GF+P   +S +   KE          
Sbjct: 109 WERVRQLQTEDATVRSEVFATNRGGALVRIEGLRGFIPGSHIS-TRKAKE---------- 157

Query: 150 GLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDYGAFIHLR 204
            L G  + +K ++ +E+  +LV S + A+  +  +R+ V ++ VG     + YGAFI   
Sbjct: 158 DLVGEELPLKFLEVDEDRNRLVLSHRRALVERKMNRLEVGEVVVGAVRGIKPYGAFI--- 214

Query: 205 FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 264
               +  ++GL+H+SE+S D I+    + N  DEV+V +I +D E+ RI+LS KQLE +P
Sbjct: 215 ---DIGGVSGLLHISEISHDHIETPHSVFNVNDEVKVMIIDLDAERGRISLSTKQLEPEP 271

Binds mRNA.

Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (taxid: 269084)

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

 Score = 78.6 bits (192), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 103/210 (49%), Gaps = 29/210 (13%)

Query: 79  NRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCK 138
           +R+   R  A     +AY+++  +  G I G   GG  V    +  FLP   +      +
Sbjct: 85  SREKAKRHEAWITLEKAYEDAETVT-GVINGKVKGGFTVELNGIRAFLPGSLVD----VR 139

Query: 139 EPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVN 187
             + ++H     L G  +  KVI+ +++   +V S           E+D +       + 
Sbjct: 140 PVRDTLH-----LEGKELEFKVIKLDQKRNNVVVSRRAVIESENSAERDQLLENLQEGME 194

Query: 188 VEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 246
           V+ I     DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K 
Sbjct: 195 VKGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKF 248

Query: 247 DREKSRITLSIKQLEEDPLLETLEKVIPQG 276
           DRE++R++L +KQL EDP +  + K  P+G
Sbjct: 249 DRERTRVSLGLKQLGEDPWV-AIAKRYPEG 277

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 = 78.6 bits (192), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 103/210 (49%), Gaps = 29/210 (13%)

Query: 79  NRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCK 138
           +R+   R  A     +AY+++  +  G I G   GG  V    +  FLP   +      +
Sbjct: 85  SREKAKRHEAWITLEKAYEDAETVT-GVINGKVKGGFTVELNGIRAFLPGSLVD----VR 139

Query: 139 EPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVN 187
             + ++H     L G  +  KVI+ +++   +V S           E+D +       + 
Sbjct: 140 PVRDTLH-----LEGKELEFKVIKLDQKRNNVVVSRRAVIESENSAERDQLLENLQEGME 194

Query: 188 VEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 246
           V+ I     DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K 
Sbjct: 195 VKGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKF 248

Query: 247 DREKSRITLSIKQLEEDPLLETLEKVIPQG 276
           DRE++R++L +KQL EDP +  + K  P+G
Sbjct: 249 DRERTRVSLGLKQLGEDPWV-AIAKRYPEG 277

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 = 78.6 bits (192), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 103/210 (49%), Gaps = 29/210 (13%)

Query: 79  NRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCK 138
           +R+   R  A     +AY+++  +  G I G   GG  V    +  FLP   +      +
Sbjct: 85  SREKAKRHEAWITLEKAYEDAETVT-GVINGKVKGGFTVELNGIRAFLPGSLVD----VR 139

Query: 139 EPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVN 187
             + ++H     L G  +  KVI+ +++   +V S           E+D +       + 
Sbjct: 140 PVRDTLH-----LEGKELEFKVIKLDQKRNNVVVSRRAVIESENSAERDQLLENLQEGME 194

Query: 188 VEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 246
           V+ I     DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K 
Sbjct: 195 VKGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKF 248

Query: 247 DREKSRITLSIKQLEEDPLLETLEKVIPQG 276
           DRE++R++L +KQL EDP +  + K  P+G
Sbjct: 249 DRERTRVSLGLKQLGEDPWV-AIAKRYPEG 277

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 = 78.6 bits (192), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 103/210 (49%), Gaps = 29/210 (13%)

Query: 79  NRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCK 138
           +R+   R  A     +AY+++  +  G I G   GG  V    +  FLP   +      +
Sbjct: 85  SREKAKRHEAWITLEKAYEDAETVT-GVINGKVKGGFTVELNGIRAFLPGSLVD----VR 139

Query: 139 EPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVN 187
             + ++H     L G  +  KVI+ +++   +V S           E+D +       + 
Sbjct: 140 PVRDTLH-----LEGKELEFKVIKLDQKRNNVVVSRRAVIESENSAERDQLLENLQEGME 194

Query: 188 VEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 246
           V+ I     DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K 
Sbjct: 195 VKGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKF 248

Query: 247 DREKSRITLSIKQLEEDPLLETLEKVIPQG 276
           DRE++R++L +KQL EDP +  + K  P+G
Sbjct: 249 DRERTRVSLGLKQLGEDPWV-AIAKRYPEG 277

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)

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	289
225433644	390	PREDICTED: 30S ribosomal protein S1 homo	0.667	0.494	0.787	1e-88
147802809	418	hypothetical protein VITISV_006784 [Viti	0.667	0.461	0.75	1e-86
449468800	378	PREDICTED: 30S ribosomal protein S1-like	0.723	0.552	0.682	5e-81
449484641	379	PREDICTED: 30S ribosomal protein S1-like	0.723	0.551	0.682	5e-81
224131510	299	predicted protein [Populus trichocarpa]	0.650	0.628	0.742	6e-80
356569689	378	PREDICTED: 40S ribosomal protein S1-like	0.705	0.539	0.677	2e-79
356538073	383	PREDICTED: 30S ribosomal protein S1 homo	0.705	0.532	0.672	4e-78
18403854	392	ribosomal protein S1-like RNA-binding do	0.681	0.502	0.689	4e-77
297835412	392	S1 RNA-binding domain-containing protein	0.643	0.474	0.717	9e-76
357462911	399	Polyribonucleotide nucleotidyltransferas	0.705	0.511	0.646	4e-75

>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 =  332 bits (852), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 156/198 (78%), Positives = 180/198 (90%), Gaps = 5/198 (2%)

Query: 83  QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQK 142
           Q+R SADWKAARA+ ESGFIYEG+I+GFNGGGLLVRF+SLVGFLPFPQ+SPSHSCKEP K
Sbjct: 88  QARRSADWKAARAHLESGFIYEGRIEGFNGGGLLVRFYSLVGFLPFPQLSPSHSCKEPHK 147

Query: 143 SIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIF---VG--RDY 197
           +I EIAKGL GS+ISVKVI A+EE +KL+FSEK+A W K+S ++N+ DIF   VG   DY
Sbjct: 148 TIQEIAKGLIGSLISVKVILADEEKRKLIFSEKEAAWLKFSKQINIGDIFEAMVGSVEDY 207

Query: 198 GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI 257
           GAF+HLRFPDGLYHLTGLVHVSEVSWDL+QD+RD+LNEGDEVRVK++K+DR KSRITLSI
Sbjct: 208 GAFVHLRFPDGLYHLTGLVHVSEVSWDLVQDVRDVLNEGDEVRVKIVKVDRVKSRITLSI 267

Query: 258 KQLEEDPLLETLEKVIPQ 275
           KQLEEDPLLETL+KVIPQ
Sbjct: 268 KQLEEDPLLETLDKVIPQ 285

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  325 bits (834), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 156/208 (75%), Positives = 180/208 (86%), Gaps = 15/208 (7%)

Query: 83  QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQK 142
           Q+R SADWKAARA+ ESGFIYEG+I+GFNGGGLLVRF+SLVGFLPFPQ+SPSHSCKEP K
Sbjct: 88  QARRSADWKAARAHLESGFIYEGRIEGFNGGGLLVRFYSLVGFLPFPQLSPSHSCKEPHK 147

Query: 143 SIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIF---VG--RDY 197
           +I EIAKGL GS+ISVKVI A+EE +KL+FSEK+A W K+S ++N+ DIF   VG   DY
Sbjct: 148 TIQEIAKGLIGSLISVKVILADEEKRKLIFSEKEAAWLKFSKQINIGDIFEAMVGSVEDY 207

Query: 198 GAFIHLRFPD----------GLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID 247
           GAF+HLRFPD          GLYHLTGLVHVSEVSWDL+QD+RD+LNEGDEVRVK++K+D
Sbjct: 208 GAFVHLRFPDGTSFSVTYITGLYHLTGLVHVSEVSWDLVQDVRDVLNEGDEVRVKIVKVD 267

Query: 248 REKSRITLSIKQLEEDPLLETLEKVIPQ 275
           R KSRITLSIKQLEEDPLLETL+KVIPQ
Sbjct: 268 RVKSRITLSIKQLEEDPLLETLDKVIPQ 295

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  306 bits (785), Expect = 5e-81,   Method: Compositional matrix adjust.
 Identities = 148/217 (68%), Positives = 180/217 (82%), Gaps = 8/217 (3%)

Query: 64  PTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLV 123
           P  +  +LD S ++  R   +R SADWKAAR Y +SGFIYEG+I+G N GGLLVRF+SLV
Sbjct: 60  PDPIAGVLDTSPESVRR---ARRSADWKAAREYLDSGFIYEGRIEGSNAGGLLVRFYSLV 116

Query: 124 GFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYS 183
           GFLPFPQ+SPSHSCKEP KSI +IAK L GS+ISVKVIQA+E+ +KL+FSEK+A  +K+S
Sbjct: 117 GFLPFPQLSPSHSCKEPYKSIQDIAKSLIGSLISVKVIQADEKNRKLIFSEKEAARSKFS 176

Query: 184 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 238
            +V V D++ G+     DYGAF+HLR  DGLYHLTGLVHVSEVSWDL+QD+RDIL+EGDE
Sbjct: 177 GQVAVGDVYEGKVGSVEDYGAFVHLRLSDGLYHLTGLVHVSEVSWDLVQDVRDILSEGDE 236

Query: 239 VRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ 275
           V VKVI +++ KSRITLSI+QLEEDPLLETL+KVIPQ
Sbjct: 237 VTVKVINVNKNKSRITLSIRQLEEDPLLETLDKVIPQ 273

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  306 bits (785), Expect = 5e-81,   Method: Compositional matrix adjust.
 Identities = 148/217 (68%), Positives = 180/217 (82%), Gaps = 8/217 (3%)

Query: 64  PTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLV 123
           P  +  +LD S ++  R   +R SADWKAAR Y +SGFIYEG+I+G N GGLLVRF+SLV
Sbjct: 61  PDPIAGVLDTSPESVRR---ARRSADWKAAREYLDSGFIYEGRIEGSNAGGLLVRFYSLV 117

Query: 124 GFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYS 183
           GFLPFPQ+SPSHSCKEP KSI +IAK L GS+ISVKVIQA+E+ +KL+FSEK+A  +K+S
Sbjct: 118 GFLPFPQLSPSHSCKEPYKSIQDIAKSLIGSLISVKVIQADEKNRKLIFSEKEAARSKFS 177

Query: 184 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 238
            +V V D++ G+     DYGAF+HLR  DGLYHLTGLVHVSEVSWDL+QD+RDIL+EGDE
Sbjct: 178 GQVAVGDVYEGKVGSVEDYGAFVHLRLSDGLYHLTGLVHVSEVSWDLVQDVRDILSEGDE 237

Query: 239 VRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ 275
           V VKVI +++ KSRITLSI+QLEEDPLLETL+KVIPQ
Sbjct: 238 VTVKVINVNKNKSRITLSIRQLEEDPLLETLDKVIPQ 274

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  303 bits (776), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 144/194 (74%), Positives = 169/194 (87%), Gaps = 6/194 (3%)

Query: 88  ADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEI 147
           ADWKA +AY + G I +G+++GFNGGGL+VRF+SLVGFLPFP +SPSHSCK+PQK+IHEI
Sbjct: 1   ADWKAVKAYYDGGHILQGRVEGFNGGGLIVRFYSLVGFLPFPLLSPSHSCKDPQKTIHEI 60

Query: 148 AKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIH 202
           AK LTG +ISVKVI A EE +KL+FSEK+AVW+K+S  +NV +IF GR     DYGAFIH
Sbjct: 61  AKDLTGLLISVKVIHAEEENRKLIFSEKEAVWSKFSKGINVGEIFAGRVGSVEDYGAFIH 120

Query: 203 LRFPDG-LYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 261
           +RFPDG LYHLTGLVHVSEVSWDL+QD+RDILN GDEV VK+I ID+ KSRITLSIKQLE
Sbjct: 121 MRFPDGSLYHLTGLVHVSEVSWDLVQDVRDILNVGDEVTVKIIDIDQGKSRITLSIKQLE 180

Query: 262 EDPLLETLEKVIPQ 275
           EDPLLETL+KVIPQ
Sbjct: 181 EDPLLETLDKVIPQ 194

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 =  301 bits (771), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 147/217 (67%), Positives = 177/217 (81%), Gaps = 13/217 (5%)

Query: 64  PTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLV 123
           PT  +P LDD+        Q+R S+DWKAA+ Y++S  IY G+++GFN GGLLVRF+S++
Sbjct: 65  PTPPDP-LDDAR-------QARRSSDWKAAKTYQDSKVIYNGRVEGFNSGGLLVRFYSVM 116

Query: 124 GFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYS 183
           GFLPFPQ+SP H+ KEP+KSI EIA+GL GSI+SVKVI A+E+ KKL+FSEK+A W+KYS
Sbjct: 117 GFLPFPQLSPVHASKEPEKSIQEIAQGLIGSIMSVKVILADEDNKKLIFSEKEAAWSKYS 176

Query: 184 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 238
            +VNV DIF  R     DYGAF+HLRFPDGLYHLTGL+HVSEVSWDLIQD+RDIL  GDE
Sbjct: 177 KQVNVGDIFEVRVGYVEDYGAFVHLRFPDGLYHLTGLIHVSEVSWDLIQDVRDILKVGDE 236

Query: 239 VRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ 275
           VR KV+ ID  KSRI LSI+QLEEDPLLETL+KVIPQ
Sbjct: 237 VRAKVVGIDWGKSRINLSIRQLEEDPLLETLDKVIPQ 273

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 =  297 bits (760), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 146/217 (67%), Positives = 176/217 (81%), Gaps = 13/217 (5%)

Query: 64  PTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLV 123
           PT  +P LDD         Q+R S+DWKAA+ Y++S  IY G+++GFN GGLLVRF+S++
Sbjct: 70  PTPPDP-LDDVR-------QARRSSDWKAAKTYQDSKLIYNGRVEGFNSGGLLVRFYSIM 121

Query: 124 GFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYS 183
           GFLPFPQ+SP H+ KEP+KSI EIA+GL GSI+SVKVI A+E+ KKL+FSEK+A W+K+S
Sbjct: 122 GFLPFPQLSPVHASKEPEKSIQEIAQGLIGSIMSVKVILADEDNKKLIFSEKEAAWSKFS 181

Query: 184 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 238
            +VNV DIF  R     DYGAF+HLRFPDGLY LTGL+HVSEVSWDLIQD+RDIL  GDE
Sbjct: 182 KQVNVGDIFEVRVGYVEDYGAFVHLRFPDGLYRLTGLIHVSEVSWDLIQDVRDILKVGDE 241

Query: 239 VRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ 275
           VRVKV+ ID  KSRI LSI+QLEEDPLLETL+KVIPQ
Sbjct: 242 VRVKVVGIDWGKSRINLSIRQLEEDPLLETLDKVIPQ 278

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  294 bits (752), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 142/206 (68%), Positives = 169/206 (82%), Gaps = 9/206 (4%)

Query: 73  DSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMS 132
           D+SD    ++ +   +DWK A+AY +SG  +EG++QGFNGGGLL+RF SLVGFLP+PQ+S
Sbjct: 84  DTSD----EASAAGPSDWKTAKAYCKSGDTFEGEVQGFNGGGLLIRFHSLVGFLPYPQLS 139

Query: 133 PSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIF 192
           PS SCKEPQKSIHEIAK L GS + VKV+QA+EE +KL+ SEK A+W KYS  VNV D+F
Sbjct: 140 PSRSCKEPQKSIHEIAKTLVGSKLPVKVVQADEENRKLILSEKLALWPKYSQNVNVGDVF 199

Query: 193 VGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID 247
            GR     DYGAFIHLRF DGLYHLTGLVHVSEVSWD +QD+RD+L +GDEVRV V  ID
Sbjct: 200 NGRVGSVEDYGAFIHLRFDDGLYHLTGLVHVSEVSWDYVQDVRDVLRDGDEVRVIVTNID 259

Query: 248 REKSRITLSIKQLEEDPLLETLEKVI 273
           +EKSRITLSIKQLE+DPLLETL+KVI
Sbjct: 260 KEKSRITLSIKQLEDDPLLETLDKVI 285

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  289 bits (740), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 137/191 (71%), Positives = 162/191 (84%), Gaps = 5/191 (2%)

Query: 88  ADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEI 147
           +DWK A+AY +SG  +EG+++GFNGGGLL+RF SLVGFLP+PQ+SPS SCKEPQKSIHEI
Sbjct: 95  SDWKTAKAYCKSGDTFEGEVEGFNGGGLLIRFHSLVGFLPYPQLSPSRSCKEPQKSIHEI 154

Query: 148 AKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIH 202
           AK L GS + VKV+QA+EE +KL+ SEK A+W KYS  V+V D+F GR     DYGAFIH
Sbjct: 155 AKTLVGSKLPVKVVQADEENRKLILSEKLALWPKYSQNVSVGDVFTGRVGSVEDYGAFIH 214

Query: 203 LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE 262
           LRF DGLYHLTGLVHVSEVSWD +QD+RD+L +GDEVRV V  ID+EKSRITLSIKQLE+
Sbjct: 215 LRFDDGLYHLTGLVHVSEVSWDYVQDVRDVLRDGDEVRVIVTNIDKEKSRITLSIKQLED 274

Query: 263 DPLLETLEKVI 273
           DPLLETL+KVI
Sbjct: 275 DPLLETLDKVI 285

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 =  287 bits (734), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 137/212 (64%), Positives = 170/212 (80%), Gaps = 8/212 (3%)

Query: 69  PILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPF 128
           P   DS DA     Q+R S+DWKAA AY++SG IY G+++GFN GGLLVRF+S++GFLP+
Sbjct: 86  PSAPDSYDA---LRQARRSSDWKAANAYRDSGLIYNGRVEGFNAGGLLVRFYSIMGFLPY 142

Query: 129 PQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNV 188
           PQ+SP HSC+EP ++I E A+ L G+I+SVKVI  +EE +KLV SEK+A W K+S  +N+
Sbjct: 143 PQLSPVHSCQEPDQTIKERARELIGAILSVKVIIVDEEKRKLVLSEKEASWFKHSKHINI 202

Query: 189 EDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKV 243
            D+F GR     DYGAF+HLRFPDGLYHLTGL+H+SEVSWDL+QD+RD L EG+EVRVKV
Sbjct: 203 GDLFEGRVGSVEDYGAFVHLRFPDGLYHLTGLIHISEVSWDLVQDVRDFLREGEEVRVKV 262

Query: 244 IKIDREKSRITLSIKQLEEDPLLETLEKVIPQ 275
           I ID  K R+TLSIKQLEEDPLLETL+KVI Q
Sbjct: 263 ISIDTVKMRLTLSIKQLEEDPLLETLDKVIRQ 294

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	289
TAIR|locus:2095203	392	AT3G23700 [Arabidopsis thalian	0.698	0.515	0.682	4.6e-73
TAIR|locus:2145860	416	RPS1 "ribosomal protein S1" [A	0.598	0.415	0.313	1.6e-17
TIGR_CMR|SO_2402	555	SO_2402 "ribosomal protein S1"	0.678	0.353	0.297	2e-14
UNIPROTKB|P0AG67	557	rpsA "30S ribosomal subunit pr	0.626	0.324	0.290	2.5e-13
UNIPROTKB|Q9KQT3	556	VC_1915 "30S ribosomal protein	0.737	0.383	0.276	6.8e-13
TIGR_CMR|VC_1915	556	VC_1915 "ribosomal protein S1"	0.737	0.383	0.276	6.8e-13
TIGR_CMR|CPS_2335	553	CPS_2335 "ribosomal protein S1	0.622	0.325	0.293	9.1e-13
TIGR_CMR|CBU_0528	551	CBU_0528 "ribosomal protein S1	0.633	0.332	0.294	4.3e-12
TIGR_CMR|NSE_0408	553	NSE_0408 "ribosomal protein S1	0.387	0.202	0.341	1e-10
UNIPROTKB|Q71X59	117	LMOf2365_2340 "S1 RNA binding	0.249	0.615	0.428	1.6e-10

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

 Score = 738 (264.8 bits), Expect = 4.6e-73, P = 4.6e-73
 Identities = 144/211 (68%), Positives = 172/211 (81%)

Query:    68 NPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLP 127
             N +L D+SD    ++ +   +DWK A+AY +SG  +EG++QGFNGGGLL+RF SLVGFLP
Sbjct:    79 NSLLRDTSD----EASAAGPSDWKTAKAYCKSGDTFEGEVQGFNGGGLLIRFHSLVGFLP 134

Query:   128 FPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVN 187
             +PQ+SPS SCKEPQKSIHEIAK L GS + VKV+QA+EE +KL+ SEK A+W KYS  VN
Sbjct:   135 YPQLSPSRSCKEPQKSIHEIAKTLVGSKLPVKVVQADEENRKLILSEKLALWPKYSQNVN 194

Query:   188 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVK 242
             V D+F GR     DYGAFIHLRF DGLYHLTGLVHVSEVSWD +QD+RD+L +GDEVRV 
Sbjct:   195 VGDVFNGRVGSVEDYGAFIHLRFDDGLYHLTGLVHVSEVSWDYVQDVRDVLRDGDEVRVI 254

Query:   243 VIKIDREKSRITLSIKQLEEDPLLETLEKVI 273
             V  ID+EKSRITLSIKQLE+DPLLETL+KVI
Sbjct:   255 VTNIDKEKSRITLSIKQLEDDPLLETLDKVI 285

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

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0005634 "nucleus" evidence=IDA

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

GO:0009570 "chloroplast stroma" evidence=IDA

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

GO:0006364 "rRNA processing" evidence=RCA

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

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

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

GO:0034660 "ncRNA metabolic process" evidence=RCA

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

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

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

 Score = 219 (82.2 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 62/198 (31%), Positives = 102/198 (51%)

Query:    72 DDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQM 131
             DDS   + R  Q   +  W+  R  +    I + K+ G N GGL+     L GF+PF Q+
Sbjct:   161 DDSLLLSLRNIQYELA--WERCRQLQAEDVIVKAKVIGANKGGLVALVEGLRGFVPFSQI 218

Query:   132 SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDI 191
             S   + +E           L    I +K ++ +EE  KLV S + AV +   +++ +  +
Sbjct:   219 SSKAAAEE-----------LLEKEIPLKFVEVDEEQTKLVLSNRKAVADS-QAQLGIGSV 266

Query:   192 FVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 246
              +G     + YGAFI +    G+    GL+HVS++S D + DI  +L  GD ++V ++  
Sbjct:   267 VLGVVQSLKPYGAFIDI---GGI---NGLLHVSQISHDRVSDIATVLQPGDTLKVMILSH 320

Query:   247 DREKSRITLSIKQLEEDP 264
             DR++ R++LS K+LE  P
Sbjct:   321 DRDRGRVSLSTKKLEPTP 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

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

 Score = 200 (75.5 bits), Expect = 2.0e-14, P = 2.0e-14
 Identities = 66/222 (29%), Positives = 106/222 (47%)

Query:    67 VNPILDDSSDANNRQSQSRSSAD----WKAA-RAYKESGFIYEGKIQGFNGGGLLVRFFS 121
             V+  LD   D       SR  A     W    +AY+++  +  G I G   GG  V    
Sbjct:    68 VDVALDSVEDGFGETQLSREKAKRHEAWIVLEKAYEDAETVI-GIINGKVKGGFTVELNG 126

Query:   122 LVGFLPF------PQMSPSH-SCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE 174
             +  FLP       P    +H   KE +  + ++ +     ++S + +  +E       +E
Sbjct:   127 IRAFLPGSLVDVRPVRDTAHLEYKELEFKVIKLDQKRNNVVVSRRAVIESESS-----AE 181

Query:   175 KDAVWNKYSSRVNVEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDIL 233
             +DA+         V+ I     DYGAF+ L   DGL H+T      +++W  ++   +I+
Sbjct:   182 RDALLENLQEGQAVKGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIV 235

Query:   234 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ 275
             N GDE+ VKV+K DRE++R++L +KQL EDP LE + K  P+
Sbjct:   236 NVGDEINVKVLKYDRERTRVSLGLKQLGEDPWLE-ISKRYPE 276

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

GO:0006412 "translation" evidence=ISS

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

 Score = 194 (73.4 bits), Expect = 2.5e-13, P = 2.5e-13
 Identities = 61/210 (29%), Positives = 103/210 (49%)

Query:    79 NRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCK 138
             +R+   R  A     +AY+++  +  G I G   GG  V    +  FLP   +      +
Sbjct:    85 SREKAKRHEAWITLEKAYEDAETV-TGVINGKVKGGFTVELNGIRAFLPGSLVD----VR 139

Query:   139 EPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVN 187
               + ++H     L G  +  KVI+ +++   +V S           E+D +       + 
Sbjct:   140 PVRDTLH-----LEGKELEFKVIKLDQKRNNVVVSRRAVIESENSAERDQLLENLQEGME 194

Query:   188 VEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKI 246
             V+ I     DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE+ VKV+K 
Sbjct:   195 VKGIVKNLTDYGAFVDLGGVDGLLHIT------DMAWKRVKHPSEIVNVGDEITVKVLKF 248

Query:   247 DREKSRITLSIKQLEEDPLLETLEKVIPQG 276
             DRE++R++L +KQL EDP +  + K  P+G
Sbjct:   249 DRERTRVSLGLKQLGEDPWV-AIAKRYPEG 277

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

GO:0003729 "mRNA binding" evidence=IDA

GO:0016020 "membrane" evidence=IDA

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

GO:0003723 "RNA binding" evidence=IDA

GO:0006412 "translation" evidence=IMP

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

GO:0005737 "cytoplasm" evidence=IDA

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

 Score = 191 (72.3 bits), Expect = 6.8e-13, P = 6.8e-13
 Identities = 67/242 (27%), Positives = 111/242 (45%)

Query:    51 PVGKFSTNAAKI---TPTTVNPILDDSSDANNRQSQSRSSAD----WKAA-RAYKESGFI 102
             P  +F   A ++     + V+  LD   D       SR  A     W    +AY+E+  +
Sbjct:    49 PAEQFKNAAGELEVQVGSQVDVALDAVEDGFGETQLSREKAKRHEAWIVLEKAYEEAATV 108

Query:   103 YEGKIQGFNGGGLLVRFFSLVGFLPF------PQMSPSH-SCKEPQKSIHEIAKGLTGSI 155
               G I G   GG  V    +  FLP       P    +H   KE +  + ++ +     +
Sbjct:   109 I-GIINGKVKGGFTVELNGIRAFLPGSLVDVRPIRDTAHLENKELEFKVIKLDQKRNNVV 167

Query:   156 ISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-RDYGAFIHLRFPDGLYHLTG 214
             +S + +  +E        E+D +         V+ I     DYGAF+ L   DGL H+T 
Sbjct:   168 VSRRAVIESESSV-----ERDELLETLQEGTEVKGIVKNLTDYGAFVDLGGVDGLLHIT- 221

Query:   215 LVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP 274
                  +++W  ++   +I+N GDE+ VKV+K DR+++R++L +KQL EDP +  + K  P
Sbjct:   222 -----DMAWKRVKHPSEIVNVGDEILVKVLKFDRDRTRVSLGLKQLGEDPWV-AIAKRYP 275

Query:   275 QG 276
             +G
Sbjct:   276 EG 277

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|VC_1915 VC_1915 "ribosomal protein S1" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 191 (72.3 bits), Expect = 6.8e-13, P = 6.8e-13
 Identities = 67/242 (27%), Positives = 111/242 (45%)

Query:    51 PVGKFSTNAAKI---TPTTVNPILDDSSDANNRQSQSRSSAD----WKAA-RAYKESGFI 102
             P  +F   A ++     + V+  LD   D       SR  A     W    +AY+E+  +
Sbjct:    49 PAEQFKNAAGELEVQVGSQVDVALDAVEDGFGETQLSREKAKRHEAWIVLEKAYEEAATV 108

Query:   103 YEGKIQGFNGGGLLVRFFSLVGFLPF------PQMSPSH-SCKEPQKSIHEIAKGLTGSI 155
               G I G   GG  V    +  FLP       P    +H   KE +  + ++ +     +
Sbjct:   109 I-GIINGKVKGGFTVELNGIRAFLPGSLVDVRPIRDTAHLENKELEFKVIKLDQKRNNVV 167

Query:   156 ISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-RDYGAFIHLRFPDGLYHLTG 214
             +S + +  +E        E+D +         V+ I     DYGAF+ L   DGL H+T 
Sbjct:   168 VSRRAVIESESSV-----ERDELLETLQEGTEVKGIVKNLTDYGAFVDLGGVDGLLHIT- 221

Query:   215 LVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP 274
                  +++W  ++   +I+N GDE+ VKV+K DR+++R++L +KQL EDP +  + K  P
Sbjct:   222 -----DMAWKRVKHPSEIVNVGDEILVKVLKFDRDRTRVSLGLKQLGEDPWV-AIAKRYP 275

Query:   275 QG 276
             +G
Sbjct:   276 EG 277

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

GO:0006412 "translation" evidence=ISS

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

 Score = 190 (71.9 bits), Expect = 9.1e-13, P = 9.1e-13
 Identities = 62/211 (29%), Positives = 103/211 (48%)

Query:    79 NRQSQSRSSADWKAA-RAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSC 137
             +R+   R  A W+   +AY+E   +  G I G   GG  V    +  FLP   +      
Sbjct:    85 SREKAKRHEA-WQVLEKAYEEKETVI-GVINGKVKGGFTVEVSDIRAFLPGSLVDV---- 138

Query:   138 KEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRV 186
                 + + + A  L G  +  KVI+ +++   +V S           E+D +    +   
Sbjct:   139 ----RPVRDTAH-LEGKPLEFKVIKLDQKRNNVVVSRRAVIEAEGSAERDELLESLAEGQ 193

Query:   187 NVEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 245
              V+ I     DYGAF+ L   DGL H+T      +++W  ++   +I+N GDE++VKV+K
Sbjct:   194 EVKGIVKNLTDYGAFVDLGGIDGLLHIT------DMAWKRVKHPSEIVNVGDEIQVKVLK 247

Query:   246 IDREKSRITLSIKQLEEDPLLETLEKVIPQG 276
              DRE++R++L +KQL EDP +    +  P+G
Sbjct:   248 FDRERTRVSLGMKQLGEDPWVAIANRY-PEG 277

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 = 185 (70.2 bits), Expect = 4.3e-12, P = 4.3e-12
 Identities = 60/204 (29%), Positives = 100/204 (49%)

Query:    79 NRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPF------PQMS 132
             +R+   R+ A  +  +AYK +G + +G I     GG  V   S+  FLP       P   
Sbjct:    81 SREKARRAKAWSELEKAYK-AGEMVKGVIIERVKGGFTVDLNSVRAFLPGSLVDVKPVRD 139

Query:   133 PSH-SCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDI 191
             P +   KE    I ++ +     ++S + +   E       +E+ A   +      ++ +
Sbjct:   140 PGYLEDKEIDFKIIKMDQRRNNVVVSRRAVMEAETS-----AERQARLEELQEGQEIKGV 194

Query:   192 FVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK 250
                  DYGAF+ L   DGL H+T      +++W  ++   D+LN GDEV VKV+K DR+K
Sbjct:   195 IKNITDYGAFVDLGGVDGLLHIT------DMAWGRVKHPSDLLNVGDEVHVKVLKFDRDK 248

Query:   251 SRITLSIKQLEEDPLLETLEKVIP 274
              R++L +KQL +DP  + +E+  P
Sbjct:   249 KRVSLGMKQLADDPWAK-IERRYP 271

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

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

 Score = 174 (66.3 bits), Expect = 1.0e-10, P = 1.0e-10
 Identities = 40/117 (34%), Positives = 65/117 (55%)

Query:   168 KKLVFSEKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVS 222
             +K + +  +A  ++Y S +   DI  GR      YG F+ +   D +  + GL++V+++S
Sbjct:   195 RKALGAVHEAARSEYISTIKEGDIIDGRVKSIASYGVFVQIHESDKVGVVDGLLYVNDIS 254

Query:   223 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP 279
             W  +     I + G EVRVKVI +D EK RI+L +KQL E+P  +  +K  P  + P
Sbjct:   255 WARVTHPSSIYSVGQEVRVKVIAVDPEKGRISLGVKQLTENPWKDVSKKYTPGNVYP 311

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

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

 Score = 151 (58.2 bits), Expect = 1.6e-10, P = 1.6e-10
 Identities = 33/77 (42%), Positives = 49/77 (63%)

Query:   195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT 254
             + YGAF+ L   D      GLVH+SE++   ++DI D L  G EV+VK++ ID EK++I+
Sbjct:    18 QSYGAFVAL---DN--STQGLVHISEITHGFVKDIHDFLEVGQEVKVKILDIDEEKNKIS 72

Query:   255 LSIKQLEEDPLLETLEK 271
             LSI+  EE P  +  +K
Sbjct:    73 LSIRATEEAPKEQPTKK 89

GO:0008150 "biological_process" evidence=ND

---

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	289
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	3e-28
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	1e-27
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	7e-25
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	2e-24
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	3e-23
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	3e-22
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	2e-21
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	8e-21
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	1e-20
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	9e-20
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	3e-19
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-18
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	3e-18
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	2e-17
PRK08059	123	PRK08059, PRK08059, general stress protein 13; Val	3e-16
COG1098	129	COG1098, VacB, Predicted RNA binding protein (cont	4e-16
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	6e-16
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	9e-16
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	2e-15
pfam00575	74	pfam00575, S1, S1 RNA binding domain	6e-15
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	7e-15
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	2e-14
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	1e-13
PRK05807	136	PRK05807, PRK05807, hypothetical protein; Provisio	1e-13
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	2e-13
PRK08582	139	PRK08582, PRK08582, hypothetical protein; Provisio	1e-12
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	2e-12
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	5e-12
cd05708	77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	6e-12
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	1e-11
PRK03987	262	PRK03987, PRK03987, translation initiation factor	2e-11
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	2e-11
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	6e-11
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	6e-11
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-10
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	1e-10
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	2e-10
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	3e-10
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	6e-10
cd05691	73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	6e-10
PRK07252	120	PRK07252, PRK07252, hypothetical protein; Provisio	7e-10
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	2e-09
cd05684	79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	6e-08
cd05690	69	cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: R	7e-08
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	8e-08
cd04461	83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	3e-07
COG2183	780	COG2183, Tex, Transcriptional accessory protein [T	1e-06
cd05689	72	cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: R	1e-06
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	2e-06
cd04465	67	cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec	2e-06
cd05686	73	cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-b	7e-06
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	9e-06
cd05698	70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	1e-05
cd05687	70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	1e-05
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	1e-04
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	3e-04
PRK08563	187	PRK08563, PRK08563, DNA-directed RNA polymerase su	0.001
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	0.003
pfam00575	74	pfam00575, S1, S1 RNA binding domain	0.004

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

 Score =  113 bits (284), Expect = 3e-28
 Identities = 62/203 (30%), Positives = 97/203 (47%), Gaps = 36/203 (17%)

Query: 90  WKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAK 149
           W+      E+G I EGKI G   GGL V    +  FLP   +                  
Sbjct: 96  WEKLEEAFENGEIVEGKITGKVKGGLTVDIEGVRAFLPGSLVDVRPV---------RDLD 146

Query: 150 GLTGSIISVKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVNVEDIFVGR--- 195
            L G  +  K+++ +++   +V S           +++ + NK      V ++  G    
Sbjct: 147 PLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKL----EVGEVVEGVVKN 202

Query: 196 --DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRI 253
             DYGAF+ +        + GL+H+SE+SW  +    +++  GDEV+VKVI +D E+ R+
Sbjct: 203 ITDYGAFVDI------GGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRV 256

Query: 254 TLSIKQLEEDPLLETLEKVIPQG 276
           +LS+KQLEEDP  E +EK  P G
Sbjct: 257 SLSLKQLEEDP-WEGIEKKYPVG 278

Length = 541

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

 Score =  111 bits (280), Expect = 1e-27
 Identities = 69/258 (26%), Positives = 107/258 (41%), Gaps = 44/258 (17%)

Query: 51  PVGKFSTNAAKITPT---TVNPILDDSSDANNRQSQSRSSAD----WKAARAYKESGFIY 103
           P+ +F     ++       V   ++   D       SR  A     W       E+G I 
Sbjct: 59  PLEEFKNEQGELEVKVGDEVEVYVERIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIV 118

Query: 104 EGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163
           EG I G   GG  V    +  FLP      S     P +        L G  +  KVI+ 
Sbjct: 119 EGVINGKVKGGFTVDLNGVEAFLPG-----SQVDVRPVRDT----DPLEGKELEFKVIKL 169

Query: 164 NEEMKKLVFS-------EKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYH 211
           +++   +V S       E+     +    +    +  G      DYGAF+       L  
Sbjct: 170 DKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFV------DLGG 223

Query: 212 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK 271
           + GL+H++++SW  +    +++N GDEV+VKV+K D+EK R++L +KQL EDP  E +EK
Sbjct: 224 VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDP-WEAIEK 282

Query: 272 VIPQG---------LEPY 280
             P G         +  Y
Sbjct: 283 KYPVGSKVKGKVTNITDY 300

Length = 565

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

 Score =  103 bits (259), Expect = 7e-25
 Identities = 53/188 (28%), Positives = 94/188 (50%), Gaps = 28/188 (14%)

Query: 90  WKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAK 149
           WK      E+G   +GK++    GGLLV +  +  FLP   +   +          ++++
Sbjct: 380 WKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVELGYV--------EDLSE 431

Query: 150 GLTGSIISVKVIQANEEMKK-LVFSEKDAVWNKYSSRV-------NVEDIFVGR-----D 196
              G  + VK+I+ N + +K +V S K  +  +   +           D+  G      D
Sbjct: 432 YK-GQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTD 490

Query: 197 YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256
           +GAF+ +    G+    GL+HVSE+SW  ++   D+L  GDE++V ++ ID+E  +++LS
Sbjct: 491 FGAFVDI---GGV---DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLS 544

Query: 257 IKQLEEDP 264
           +K+L  DP
Sbjct: 545 LKKLLPDP 552

Length = 647

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

 Score =  100 bits (252), Expect = 2e-24
 Identities = 54/195 (27%), Positives = 91/195 (46%), Gaps = 36/195 (18%)

Query: 98  ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIIS 157
           E G + E K+     GGL+V    + GF+P   +S             E      G  + 
Sbjct: 104 EEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLISTRFV---------EDFSDFKGKTLE 154

Query: 158 VKVIQANEEMKKLVFS-----------EKDAVWNKYSSRVNVEDIFVG-----RDYGAFI 201
           VK+I+ + E  +++ S           +K+ +     S +   D+  G      D+GAF+
Sbjct: 155 VKIIELDPEKNRVILSRRAVVEEERAAKKEELL----SSLKEGDVVEGTVARLTDFGAFV 210

Query: 202 HLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 261
            +   DGL      VH+SE+S + ++   ++++ G EV VKV+ ID E  RI+LS+K   
Sbjct: 211 DIGGVDGL------VHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTL 264

Query: 262 EDPLLETLEKVIPQG 276
             P  E +E+ +P+G
Sbjct: 265 PGP-WEGVEEKLPEG 278

Length = 390

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

 Score = 98.5 bits (246), Expect = 3e-23
 Identities = 59/187 (31%), Positives = 86/187 (45%), Gaps = 21/187 (11%)

Query: 98  ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIIS 157
           E G + EG ++     G  V    + G L   ++S             E+ K   G  + 
Sbjct: 191 EVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRV-----DHPSEVVK--VGDEVK 243

Query: 158 VKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGL 209
           VKVI  +EE  ++  S K      W     +  V D   G+     DYGAF+ +   +G+
Sbjct: 244 VKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIE--EGV 301

Query: 210 YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETL 269
               GLVHVSE+SW       +++  G EV VKV+ ID E+ RI+L +KQL+E+P  E  
Sbjct: 302 ---EGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENP-WEEF 357

Query: 270 EKVIPQG 276
               P G
Sbjct: 358 ADKHPVG 364

Length = 541

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

 Score = 95.6 bits (238), Expect = 3e-22
 Identities = 65/222 (29%), Positives = 96/222 (43%), Gaps = 31/222 (13%)

Query: 66  TVNPILDDSSDANNRQSQSRSSAD----WKAARAYKESGFIYEGKIQGFNGGGLLVRFFS 121
            V   LD   D       SR  A     W       E G I EGKI G   GG +V    
Sbjct: 63  EVEVYLDRVEDRFGETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNG 122

Query: 122 LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS-------- 173
           +  FLP      S    +P K        L G  +  K+I+ +++   +V S        
Sbjct: 123 VEAFLPG-----SQVDVKPIKD----LDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEE 173

Query: 174 ---EKDAVWNKYSSRVNVEDIFVG-RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI 229
               ++ +         V+ +     D+GAF+ L   DGL      +H++++SW  ++  
Sbjct: 174 RSQAREELLENLKEGDVVKGVVKNITDFGAFVDLGGVDGL------LHITDMSWKRVKHP 227

Query: 230 RDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK 271
            + +  G EV+VKVIK D+EK RI+LS+KQL EDP     +K
Sbjct: 228 SEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKK 269

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

 Score = 93.5 bits (233), Expect = 2e-21
 Identities = 57/191 (29%), Positives = 90/191 (47%), Gaps = 21/191 (10%)

Query: 90  WKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLV-GFLPFPQMSPSHSCKEPQKSIHEIA 148
           W+        G   EGK+      G  V     V G +   ++S +     P + +    
Sbjct: 268 WEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKK-NVPSEVVKV-- 324

Query: 149 KGLTGSIISVKVIQANEEMKKLVFSEKDAVWN---KYSSRVNVEDIFVGR-----DYGAF 200
               G  + VKV+  + E +++    K    N   +++ +  V D+  G+     D+GAF
Sbjct: 325 ----GQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAF 380

Query: 201 IHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL 260
           + L    G+    GLVH+S++SWD   +  +   +GDEV  KV+ +D+EK RI+L IKQL
Sbjct: 381 VEL--EGGI---DGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKERISLGIKQL 435

Query: 261 EEDPLLETLEK 271
           EE P  E  EK
Sbjct: 436 EESPWEEFSEK 446

Length = 541

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

 Score = 89.9 bits (223), Expect = 8e-21
 Identities = 55/160 (34%), Positives = 90/160 (56%), Gaps = 24/160 (15%)

Query: 111 NGGGLLVRFFSLVGFLPFPQMSPSH-SCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKK 169
           N GG LVR   L GF+P      SH S ++P++        L G  + +K ++ +EE  +
Sbjct: 130 NRGGALVRIEGLRGFIP-----GSHISTRKPKEE-------LVGEELPLKFLEVDEERNR 177

Query: 170 LVFSEKDAVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD 224
           LV S + A+  +  +R+ V ++ VG     + YGAFI +        ++GL+H+SE+S +
Sbjct: 178 LVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIG------GVSGLLHISEISHE 231

Query: 225 LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 264
            I+    + N  DE++V +I +D E+ RI+LS KQLE +P
Sbjct: 232 HIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEP 271

Length = 318

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

 Score = 91.4 bits (228), Expect = 1e-20
 Identities = 41/118 (34%), Positives = 64/118 (54%), Gaps = 14/118 (11%)

Query: 156 ISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPD 207
           + VKV++ ++E K++    K      W     +  V     G+     DYGAF+ L   +
Sbjct: 251 VKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELE--E 308

Query: 208 GLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 264
           G+    GLVHVSE+SW    +    +++ G EV V V++ID EK RI+L +KQ +E+P
Sbjct: 309 GI---EGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENP 363

Length = 565

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

 Score = 88.9 bits (221), Expect = 9e-20
 Identities = 54/175 (30%), Positives = 90/175 (51%), Gaps = 20/175 (11%)

Query: 98  ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIIS 157
           E G + EG+++     G  V    + G L   ++S         +   ++ K   G  I 
Sbjct: 476 EEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRV-----EKPSDVLK--VGDEIK 528

Query: 158 VKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGL 209
           V ++  ++E KKL  S K  +   W     +  V  I +G+      +GAF+ L    G+
Sbjct: 529 VYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELE--PGV 586

Query: 210 YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 264
               GLVH+S++SW  I    D+L+EG+EV+ K++++D E+ RI LSIK++EE+P
Sbjct: 587 ---DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP 638

Length = 647

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

 Score = 86.8 bits (216), Expect = 3e-19
 Identities = 45/130 (34%), Positives = 73/130 (56%), Gaps = 14/130 (10%)

Query: 152 TGSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHL 203
            G  + V V++ +EE +++    K      W +++ +  V D+  G+     D+GAF+  
Sbjct: 334 VGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFV-- 391

Query: 204 RFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEE 262
               G+    GLVH+S++SWD   ++  ++  +GDEV   V+K+D EK RI+L IKQLEE
Sbjct: 392 GLEGGI---DGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEE 448

Query: 263 DPLLETLEKV 272
           DP  E  +K 
Sbjct: 449 DPFEEFAKKH 458

Length = 565

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

 Score = 85.2 bits (211), Expect = 1e-18
 Identities = 51/177 (28%), Positives = 81/177 (45%), Gaps = 21/177 (11%)

Query: 104 EGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163
           +G ++     G  V    + G L    MS     K P + +        G  + VKVI+ 
Sbjct: 192 KGVVKNITDFGAFVDLGGVDGLLHITDMSWKRV-KHPSEYVKV------GQEVKVKVIKF 244

Query: 164 NEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL 215
           ++E  ++  S K      W     +  V D   GR     DYG F+ +   +G+    GL
Sbjct: 245 DKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIE--EGI---EGL 299

Query: 216 VHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK 271
           VHVSE+SW         ++ +GDEV V ++ ID E+ R++L +KQ + +P  +  EK
Sbjct: 300 VHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEK 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|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 83.4 bits (207), Expect = 3e-18
 Identities = 42/120 (35%), Positives = 68/120 (56%), Gaps = 13/120 (10%)

Query: 153 GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 204
           G  + VKV+  + E +++  S KD +   W     ++   D+  G      D+GAF+ + 
Sbjct: 239 GQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEV- 297

Query: 205 FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 264
              G+    GLVH+S++S   I    ++L EG EV+VKV++++ E+ RI+LSIK LEE P
Sbjct: 298 -LPGV---EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAP 353

Length = 390

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

 Score = 81.7 bits (202), Expect = 2e-17
 Identities = 53/183 (28%), Positives = 79/183 (43%), Gaps = 30/183 (16%)

Query: 98  ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIIS 157
           E+G   EGK+ G   GG  V       F P  Q+      ++P+           G    
Sbjct: 114 ENGVPVEGKVTGTCKGGFNVEVLGRRAFCPVSQID-LRYVEDPES--------YVGQTFQ 164

Query: 158 VKVIQANEEMKKLVFS-------EKDAVWNKYSSRVNVEDIFVGR-----DYGAFIHLRF 205
             + +  E  + +V S       E+      +   V   D+  G       +GAF+ L  
Sbjct: 165 FLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELA- 223

Query: 206 PDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS----RITLSIKQLE 261
           P     + G+VH+SE+SW  +Q   + ++ GD VRVKV+ I+R K     RI+LSIKQ  
Sbjct: 224 PG----VEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAG 279

Query: 262 EDP 264
            DP
Sbjct: 280 GDP 282

Length = 491

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

 Score = 73.2 bits (180), Expect = 3e-16
 Identities = 33/70 (47%), Positives = 47/70 (67%), Gaps = 5/70 (7%)

Query: 195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT 254
           + YGAF+ L   D      GLVH+SE++   ++DI D L+ GDEV+VKV+ +D EK +I+
Sbjct: 19  QPYGAFVAL---DE--ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKIS 73

Query: 255 LSIKQLEEDP 264
           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 = 72.7 bits (179), Expect = 4e-16
 Identities = 33/69 (47%), Positives = 46/69 (66%), Gaps = 6/69 (8%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
            YGAF+      G    TGLVH+SE++   ++DI D L  G EV+VKV+ ID E  +I+L
Sbjct: 18  PYGAFV--ELEGGK---TGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDID-ENGKISL 71

Query: 256 SIKQLEEDP 264
           SI++LEE+P
Sbjct: 72  SIRKLEEEP 80

Length = 129

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

 Score = 77.1 bits (191), Expect = 6e-16
 Identities = 39/119 (32%), Positives = 62/119 (52%), Gaps = 13/119 (10%)

Query: 153 GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAFIHLR 204
           G  +   V++ + E +++    K      + +++ +     I  G      D GAF+ L 
Sbjct: 422 GDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVKDKGAFVEL- 480

Query: 205 FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEED 263
             DG+    GL+  SE+S D ++D  ++L  GDEV  KVI IDR+  RI+LSIK L+E 
Sbjct: 481 -EDGV---EGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEA 535

Length = 565

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

 Score = 70.0 bits (172), Expect = 9e-16
 Identities = 27/61 (44%), Positives = 42/61 (68%), Gaps = 6/61 (9%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           D+GAF+ L   DGL      +H+S++SW  ++   +++N GDEV VKV+KID+E+ RI+L
Sbjct: 14  DFGAFVDLGGVDGL------LHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67

Query: 256 S 256
            
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|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 75.9 bits (188), Expect = 2e-15
 Identities = 32/83 (38%), Positives = 52/83 (62%), Gaps = 15/83 (18%)

Query: 186 VNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 238
             V +I+ G+     D+GAF+ +  P  DGL      VH+SE++ + ++ + D+L EGDE
Sbjct: 619 PEVGEIYEGKVVRIVDFGAFVEI-LPGKDGL------VHISEIADERVEKVEDVLKEGDE 671

Query: 239 VRVKVIKIDREKSRITLSIKQLE 261
           V+VKV++ID ++ RI LS K + 
Sbjct: 672 VKVKVLEID-KRGRIRLSRKAVL 693

Length = 693

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

 Score = 68.1 bits (167), Expect = 6e-15
 Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 10/79 (12%)

Query: 185 RVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEV 239
           +    D+  G        GAF+ L        + G + +SE+S D ++D  ++L  GDEV
Sbjct: 1   KPEEGDVVKGTVTRVTKGGAFVDL-----GNGVEGFIPISEISDDRVEDPDEVLKVGDEV 55

Query: 240 RVKVIKIDREKSRITLSIK 258
            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|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

 Score = 67.7 bits (166), Expect = 7e-15
 Identities = 28/63 (44%), Positives = 45/63 (71%), Gaps = 6/63 (9%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
            +GAF+ L    G+   +GLVH+S+++   ++D++D+L EGD+V+VKV+ ID    RI+L
Sbjct: 13  PFGAFVEL--GGGI---SGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARG-RISL 66

Query: 256 SIK 258
           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|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 72.8 bits (179), Expect = 2e-14
 Identities = 44/150 (29%), Positives = 72/150 (48%), Gaps = 20/150 (13%)

Query: 124 GFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAV---WN 180
           G +   +MS       P K +        G  + V ++  + E ++L    K      W 
Sbjct: 298 GLVHVSEMSWVKKNSHPSKVVK------KGDEVEVMILDIDPERRRLSLGLKQCKANPWE 351

Query: 181 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNE 235
           ++  +  V D   G+     D+GAF+ L    G+    GL+H+S++SWD      D L +
Sbjct: 352 QFEEKHPVGDRVTGKIKKITDFGAFVELE--GGI---DGLIHLSDISWDKDGREADHLYK 406

Query: 236 -GDEVRVKVIKIDREKSRITLSIKQLEEDP 264
            GDE+   V+ +D+EK RI+L +KQL E+P
Sbjct: 407 KGDEIEAVVLAVDKEKKRISLGVKQLTENP 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|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain

 Score = 64.5 bits (158), Expect = 1e-13
 Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 10/77 (12%)

Query: 187 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 241
            V D+  G        GAF+ L        + GL+ +SE+S   ++D  ++L  GDEV+V
Sbjct: 1   EVGDVVEGTVTEITPGGAFVDL-----GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKV 55

Query: 242 KVIKIDREKSRITLSIK 258
           KV+ +D EK RI LS+K
Sbjct: 56  KVLSVDEEKGRIILSLK 72

Length = 72

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

 Score = 65.9 bits (161), Expect = 1e-13
 Identities = 31/68 (45%), Positives = 47/68 (69%), Gaps = 7/68 (10%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           ++GAF+ +   +G    TGLVH+SEV+   ++DIR+ L E D+V+VKVI ID +  +I+L
Sbjct: 18  NFGAFVEV---EGK---TGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISL 70

Query: 256 SIKQLEED 263
           SIKQ  + 
Sbjct: 71  SIKQAMKQ 78

Length = 136

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

 Score = 69.9 bits (172), Expect = 2e-13
 Identities = 34/82 (41%), Positives = 53/82 (64%), Gaps = 11/82 (13%)

Query: 186 VNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVR 240
           V V +++ G      D+GAF+ L  P       GLVH+S+++ + ++ + D+L EGDEV+
Sbjct: 617 VEVGEVYEGTVVRIVDFGAFVEL-LPGK----DGLVHISQLAKERVEKVEDVLKEGDEVK 671

Query: 241 VKVIKIDREKSRITLSIKQLEE 262
           VKVI+ID ++ RI LSIK + E
Sbjct: 672 VKVIEID-KQGRIRLSIKAVLE 692

Length = 692

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

 Score = 63.5 bits (155), Expect = 1e-12
 Identities = 31/69 (44%), Positives = 48/69 (69%), Gaps = 6/69 (8%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           ++GAF+ L  P+G    TGLVH+SEV+ + ++DI D L  GDEV VKV+ ++ +  +I L
Sbjct: 18  NFGAFVEL--PEGK---TGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDD-GKIGL 71

Query: 256 SIKQLEEDP 264
           SIK+ ++ P
Sbjct: 72  SIKKAKDRP 80

Length = 139

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

 Score = 60.5 bits (147), Expect = 2e-12
 Identities = 27/61 (44%), Positives = 40/61 (65%), Gaps = 5/61 (8%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
            +G F+ L   DG+    GLVH+SE+S   ++D  ++   GDEV VKV+++D EK RI+L
Sbjct: 10  KFGVFVEL--EDGV---EGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64

Query: 256 S 256
           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|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional

 Score = 65.5 bits (160), Expect = 5e-12
 Identities = 44/135 (32%), Positives = 67/135 (49%), Gaps = 18/135 (13%)

Query: 153 GSIISVKV--IQANEEMK--KLVFSEKDAV---WNKYSSRVNVEDIFVGR-----DYGAF 200
           G  + VKV  I+  ++ K  ++  S K A    W+    R+   D   G+      +GAF
Sbjct: 250 GDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAF 309

Query: 201 IHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 259
           + +     L  + GLVHVSE+SW   +    D++  GD V VK+  ID  K RI+LS++ 
Sbjct: 310 VEI-----LPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRD 364

Query: 260 LEEDPLLETLEKVIP 274
            E DP  +  E+  P
Sbjct: 365 AEGDPWADVAERFAP 379

Length = 491

>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 = 60.0 bits (146), Expect = 6e-12
 Identities = 29/63 (46%), Positives = 41/63 (65%), Gaps = 4/63 (6%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           DYG FI +   DG  +++GL H SE+S + + D   +   GD+VR KV+KID EK RI+L
Sbjct: 15  DYGVFIDI---DGT-NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISL 70

Query: 256 SIK 258
            +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|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 64.4 bits (158), Expect = 1e-11
 Identities = 30/79 (37%), Positives = 49/79 (62%), Gaps = 15/79 (18%)

Query: 184 SRVNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDLIQDIRDILNEG 236
           +   V  I+ G+     D+GAF+ +  P  DGL      VH+SE++ + ++ + D+L EG
Sbjct: 614 AEPEVGKIYEGKVVRIMDFGAFVEI-LPGKDGL------VHISEIANERVEKVEDVLKEG 666

Query: 237 DEVRVKVIKIDREKSRITL 255
           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|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha; Validated

 Score = 62.5 bits (153), Expect = 2e-11
 Identities = 28/78 (35%), Positives = 47/78 (60%), Gaps = 8/78 (10%)

Query: 187 NVEDIFVGRDYGAFIHL-RFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 245
            V+++    D+GAF+ L  +P       G +H+SEV+   +++IRD + EG +V  KVI+
Sbjct: 15  TVKEVK---DFGAFVTLDEYPG----KEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIR 67

Query: 246 IDREKSRITLSIKQLEED 263
           +D  K  I LS+K++ E 
Sbjct: 68  VDPRKGHIDLSLKRVNEH 85

Length = 262

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

 Score = 57.9 bits (141), Expect = 2e-11
 Identities = 29/73 (39%), Positives = 47/73 (64%), Gaps = 11/73 (15%)

Query: 190 DIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVI 244
            I+ G+     D+GAF+ +  P       GLVH+SE+S + ++ + D+L  GDEV+VKVI
Sbjct: 2   KIYEGKVVKIKDFGAFVEI-LPGK----DGLVHISELSDERVEKVEDVLKVGDEVKVKVI 56

Query: 245 KIDREKSRITLSI 257
           ++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|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein S1; Provisional

 Score = 62.4 bits (151), Expect = 6e-11
 Identities = 51/181 (28%), Positives = 85/181 (46%), Gaps = 22/181 (12%)

Query: 105 GKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN 164
           G ++ F   G  +      G L    MS  H  + P++ + +      G  I +KVI+ +
Sbjct: 499 GVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVAR-PREFVKK------GQTIELKVIRLD 551

Query: 165 EEMKKLVFSEKD---AVWNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLV 216
           +  K++  S K      W ++ ++  V D+  GR     D+GAFI L   +G+    GL 
Sbjct: 552 QAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIEL--AEGI---EGLA 606

Query: 217 HVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQ 275
           H+SE SW        D++  GDEV   ++  D +  R++L +KQ+  +P  E +E   P 
Sbjct: 607 HISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANP-WEEIEARYPV 665

Query: 276 G 276
           G
Sbjct: 666 G 666

Length = 863

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

 Score = 61.2 bits (149), Expect = 6e-11
 Identities = 26/86 (30%), Positives = 50/86 (58%), Gaps = 6/86 (6%)

Query: 186 VNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIK 245
             V+ +    DYGA++ L    G     G +H+SEV+   +++IRD + EG +V  KV++
Sbjct: 17  GTVKQVA---DYGAYVELDEYPGK---EGFIHISEVASGWVKNIRDYVKEGQKVVAKVLR 70

Query: 246 IDREKSRITLSIKQLEEDPLLETLEK 271
           +D ++  I LS+K++ E    + +++
Sbjct: 71  VDPKRGHIDLSLKRVTEHQRRKKIQE 96

Length = 269

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

 Score = 61.3 bits (149), Expect = 1e-10
 Identities = 34/114 (29%), Positives = 60/114 (52%), Gaps = 13/114 (11%)

Query: 153 GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVG-----RDYGAFIHLR 204
           G  I   V+  ++E K++    K      W K++++  V  +  G     +D+GAF+   
Sbjct: 408 GDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFV--E 465

Query: 205 FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 258
            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 = 60.8 bits (148), Expect = 1e-10
 Identities = 32/82 (39%), Positives = 47/82 (57%), Gaps = 15/82 (18%)

Query: 183 SSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVK 242
           SS VN         +GAF+ L   DGL      VHVSE+SW  I    +++  G EV V+
Sbjct: 217 SSIVN---------FGAFVDLGGVDGL------VHVSELSWKHIDHPSEVVEVGQEVTVE 261

Query: 243 VIKIDREKSRITLSIKQLEEDP 264
           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 = 55.3 bits (134), Expect = 2e-10
 Identities = 24/61 (39%), Positives = 39/61 (63%), Gaps = 5/61 (8%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           D+GAF+ +    G+    GL+H+S+++   +    D+++ GD V VKVI ID E+ RI+L
Sbjct: 13  DFGAFVDI----GV-KQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISL 67

Query: 256 S 256
           S
Sbjct: 68  S 68

The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea. Length = 68

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

 Score = 55.3 bits (134), Expect = 3e-10
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 8/75 (10%)

Query: 186 VNVEDIFVGRDYGAFIHL-RFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVI 244
           V V+ I    D GA++ L  + +    + G++ +SE+S   I+ IR ++  G +  VKVI
Sbjct: 9   VTVKSIA---DMGAYVSLLEYGN----IEGMILLSELSRRRIRSIRKLVKVGRKEVVKVI 61

Query: 245 KIDREKSRITLSIKQ 259
           ++D+EK  I LS K+
Sbjct: 62  RVDKEKGYIDLSKKR 76

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein. Length = 76

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

 Score = 58.9 bits (143), Expect = 6e-10
 Identities = 29/67 (43%), Positives = 43/67 (64%), Gaps = 5/67 (7%)

Query: 197 YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256
           +GAF+  R  +G+    GLVH+SE++   ++    ++  GDEV VKVI ID E+ RI+LS
Sbjct: 307 FGAFV--RVEEGI---EGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLS 361

Query: 257 IKQLEED 263
           +KQ  E 
Sbjct: 362 LKQANEG 368

Length = 486

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

 Score = 54.2 bits (131), Expect = 6e-10
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 211 HLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE 261
            + 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|180908 PRK07252, PRK07252, hypothetical protein; Provisional

 Score = 55.5 bits (134), Expect = 7e-10
 Identities = 34/106 (32%), Positives = 50/106 (47%), Gaps = 26/106 (24%)

Query: 197 YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS 256
           YGAF+ L         TGL+H+SE+    I +I  +L  G+EV V+V+  D    + +LS
Sbjct: 17  YGAFVALENGT-----TGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLS 71

Query: 257 IKQLEED--------------------PLLETLEKVIPQGLEPYLK 282
           ++ LEE+                    PL E L   I + L+ YLK
Sbjct: 72  LRTLEEEKQHFPHRHRFSNSRHKIGFKPLEEQLPIWIEEALQ-YLK 116

Length = 120

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

 Score = 58.2 bits (140), Expect = 2e-09
 Identities = 42/155 (27%), Positives = 74/155 (47%), Gaps = 16/155 (10%)

Query: 122 LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM----KKLVFSEKDA 177
           ++ FLP  Q S       P+  I   +K     I   K  + N+ +    ++ +      
Sbjct: 424 MMAFLPISQ-SDCQKVDAPESLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQ 482

Query: 178 VWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDI 232
              ++ + V++ED   G       +GAFI L   DGL      +HV+++SW  +   R+ 
Sbjct: 483 AREEFFNSVHIEDSVSGVVKSFTSFGAFIDLGGFDGL------LHVNDMSWGHVARPREF 536

Query: 233 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLE 267
           + +G  + +KVI++D+ + RI LS+K  + DP LE
Sbjct: 537 VKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLE 571

Length = 863

>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 = 48.8 bits (117), Expect = 6e-08
 Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 5/64 (7%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRIT 254
           D+G F+ L    G     GLVH+S++S++  + +  D++  G +V+VKVI I   K  I+
Sbjct: 13  DFGCFVQLEGLKG--RKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGK--IS 68

Query: 255 LSIK 258
           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|240195 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain

 Score = 48.3 bits (115), Expect = 7e-08
 Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 6/61 (9%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRIT 254
           D+G F+ L    G+    GLVH+S++SW   ++   +I  +G EV   V+ ID E+ RI+
Sbjct: 13  DFGIFVGL--DGGI---DGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERIS 67

Query: 255 L 255
           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|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 52.7 bits (127), Expect = 8e-08
 Identities = 38/129 (29%), Positives = 60/129 (46%), Gaps = 20/129 (15%)

Query: 153 GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVG-----RDYGAFIHLR 204
           G  +  KV+  ++E +++    K      W ++S +     +  G     +D GAF+   
Sbjct: 411 GDEVEAKVLAVDKEKERISLGIKQLEESPWEEFSEKYKKGSVVKGKVKSVKDKGAFV--E 468

Query: 205 FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 264
              G+    GL+ +SE+S       RD+L  GDEV   V+ ID++  +I LSIK LE   
Sbjct: 469 LGGGV---EGLIRLSELS-------RDVLKVGDEVEAVVVSIDKKNRKILLSIKALERKE 518

Query: 265 LLETLEKVI 273
             E LE   
Sbjct: 519 EKEALESYN 527

Length = 541

>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 = 3e-07
 Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 5/62 (8%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
            YG F+   F      LTGL   S +S + + D      +G  V  KV  +D EK R  L
Sbjct: 27  PYGVFV--EFL---GGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLL 81

Query: 256 SI 257
           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|225094 COG2183, Tex, Transcriptional accessory protein [Transcription]

 Score = 49.2 bits (118), Expect = 1e-06
 Identities = 27/67 (40%), Positives = 45/67 (67%), Gaps = 5/67 (7%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           D+GAF+ +    G+ H  GLVH+S++S   ++D  +++  GD V+VKVI++D  + RI L
Sbjct: 671 DFGAFVDI----GV-HQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIAL 725

Query: 256 SIKQLEE 262
           S++  EE
Sbjct: 726 SMRLDEE 732

Length = 780

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

 Score = 44.9 bits (106), Expect = 1e-06
 Identities = 27/62 (43%), Positives = 39/62 (62%), Gaps = 8/62 (12%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR--DILNEGDEVRVKVIKIDREKSRI 253
           DYG F+ L   +G+    GLVHVSE+ W   ++I    +++ GDEV V V+ ID E+ RI
Sbjct: 16  DYGCFVELE--EGV---EGLVHVSEMDWT-NKNIHPSKVVSLGDEVEVMVLDIDEERRRI 69

Query: 254 TL 255
           +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|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 48.8 bits (117), Expect = 2e-06
 Identities = 17/59 (28%), Positives = 36/59 (61%)

Query: 213 TGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK 271
            G++ + E++ D I  +++ +  GDE+ VKV+K++ E   + LS K+ + +   + LE+
Sbjct: 327 EGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEE 385

Length = 647

>gnl|CDD|239911 cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain

 Score = 44.4 bits (106), Expect = 2e-06
 Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 9/72 (12%)

Query: 104 EGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA 163
           EGK+     GGL+V    +  FLP  Q+              E      G  +  K+I+ 
Sbjct: 5   EGKVTEKVKGGLIVDIEGVRAFLPASQVDLRP---------VEDLDEYVGKELKFKIIEI 55

Query: 164 NEEMKKLVFSEK 175
           + E   +V S +
Sbjct: 56  DRERNNIVLSRR 67

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. Length = 67

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

 Score = 42.9 bits (101), Expect = 7e-06
 Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 5/63 (7%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           +YGAF+ +    G     GLVH S +S   + D  ++++ G++V VKVI  +  K ++ L
Sbjct: 16  EYGAFVKI---PG-CRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGRE-MKDKMKL 70

Query: 256 SIK 258
           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|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 46.4 bits (111), Expect = 9e-06
 Identities = 21/58 (36%), Positives = 39/58 (67%)

Query: 214 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK 271
           G++ +SE+S D I+DI D++  GDE+ V V+K++  +  + LS ++LE +   + LE+
Sbjct: 44  GVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEE 101

Length = 390

>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: 195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT 254
           +  G  +   F + +    G +  SE+S   I+D  +    G  V+VKV+  D E+ R+ 
Sbjct: 12  KPNGCIV--SFYNNV---KGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLL 66

Query: 255 LSIK 258
           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|240192 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain

 Score = 41.7 bits (99), Expect = 1e-05
 Identities = 16/45 (35%), Positives = 29/45 (64%)

Query: 214 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK 258
           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 = 42.4 bits (100), Expect = 1e-04
 Identities = 30/136 (22%), Positives = 57/136 (41%), Gaps = 14/136 (10%)

Query: 153 GSIISVKVIQANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVGR-DYGAFIHLR 204
           G  ++VK+   +   +++  S +DA       V  +++    V      R  +G F++L 
Sbjct: 341 GDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLA 400

Query: 205 FPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE-ED 263
            P     +TGL+  S +S        + L  GD V + V +ID  K +I+L+        
Sbjct: 401 -PG----VTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGAAGSG 455

Query: 264 PLLETLEKVIPQGLEP 279
              +  ++  P+   P
Sbjct: 456 ADDDDWKQFAPKKSAP 471

Length = 491

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 8/77 (10%)

Query: 100 GFIYEGKIQGFNGGGLLVRFFSLV-GFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISV 158
           G + EG +     GG  V   + V G +P  ++S     K+P++ +        G  + V
Sbjct: 3   GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRV-KDPEEVLKV------GDEVKV 55

Query: 159 KVIQANEEMKKLVFSEK 175
           KV+  +EE  +++ S K
Sbjct: 56  KVLSVDEEKGRIILSLK 72

Length = 72

>gnl|CDD|236289 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E'; Provisional

 Score = 38.7 bits (91), Expect = 0.001
 Identities = 19/88 (21%), Positives = 42/88 (47%), Gaps = 25/88 (28%)

Query: 188 VEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEG 236
           V ++    ++GAF+       +  + GL+H+S++  D I           ++ + +L  G
Sbjct: 89  VVEV---VEFGAFV------RIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVG 139

Query: 237 DEVRVKVIKI-----DREKSRITLSIKQ 259
           D VR +++ +         S+I L+++Q
Sbjct: 140 DVVRARIVAVSLKERRPRGSKIGLTMRQ 167

Length = 187

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

 Score = 38.9 bits (90), Expect = 0.003
 Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 15/94 (15%)

Query: 179 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDIL 233
           W +  +R  V   F  R     + GAFI +   +G+    G +HV ++SW  ++  R   
Sbjct: 656 WEEIEARYPVGARFTRRIVKVTNAGAFIEME--EGI---DGFLHVDDLSW--VKRTRPAD 708

Query: 234 NE---GDEVRVKVIKIDREKSRITLSIKQLEEDP 264
           +E   G E+   VI+ D +  RI L +KQL ++P
Sbjct: 709 HELEVGKEIECMVIECDPQARRIRLGVKQLSDNP 742

Length = 863

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 8/77 (10%)

Query: 98  ESGFIYEGKIQGFNGGGLLVRFFSLV-GFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSII 156
           E G + +G +     GG  V   + V GF+P  ++S        +           G  +
Sbjct: 3   EEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVL-------KVGDEV 55

Query: 157 SVKVIQANEEMKKLVFS 173
            VKV++ ++E  +++ S
Sbjct: 56  EVKVLKVDKERGRIILS 72

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	289
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
PRK07400	318	30S ribosomal protein S1; Reviewed	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	100.0
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	100.0
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	100.0
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	100.0
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.98
PRK07400	318	30S ribosomal protein S1; Reviewed	99.91
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.78
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.75
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.64
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.63
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.61
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.6
PRK08582	139	hypothetical protein; Provisional	99.54
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.52
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.49
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.45
PRK09202	470	nusA transcription elongation factor NusA; Validat	99.45
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.44
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.43
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.42
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.42
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.4
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.4
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.4
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.39
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.39
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.38
PRK05807	136	hypothetical protein; Provisional	99.38
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.37
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.37
PRK07252	120	hypothetical protein; Provisional	99.36
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.35
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.34
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.34
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.34
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.33
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.33
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.32
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.32
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.32
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.32
TIGR01953	341	NusA transcription termination factor NusA. This m	99.31
PRK08059	123	general stress protein 13; Validated	99.3
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.29
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.29
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.29
PHA02945	88	interferon resistance protein; Provisional	99.29
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.29
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.28
PRK07252	120	hypothetical protein; Provisional	99.27
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.26
PRK12327	362	nusA transcription elongation factor NusA; Provisi	99.26
PRK08582	139	hypothetical protein; Provisional	99.26
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.25
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.25
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.25
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.24
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.22
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.22
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.22
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	99.22
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.21
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.18
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.18
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.17
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.17
PRK05807	136	hypothetical protein; Provisional	99.17
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.16
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.14
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.14
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.13
PRK08059	123	general stress protein 13; Validated	99.12
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.11
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.11
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.1
PRK03987	262	translation initiation factor IF-2 subunit alpha;	99.09
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.08
PRK12328	374	nusA transcription elongation factor NusA; Provisi	99.08
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.05
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.03
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.02
PHA02945	88	interferon resistance protein; Provisional	99.01
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.01
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.0
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.0
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	98.99
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.98
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	98.98
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.96
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.95
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.94
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.92
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.92
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.9
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.9
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.89
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.88
PRK12329	449	nusA transcription elongation factor NusA; Provisi	98.87
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.87
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.86
COG2183	780	Tex Transcriptional accessory protein [Transcripti	98.86
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.84
COG2183	780	Tex Transcriptional accessory protein [Transcripti	98.84
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.84
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.81
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.8
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.79
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.78
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.77
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.72
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.69
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.67
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.65
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.65
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.64
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.59
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.53
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.49
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.46
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.39
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.29
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.28
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.28
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.27
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.25
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.24
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.22
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	98.22
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.2
PRK11642	813	exoribonuclease R; Provisional	98.19
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.14
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.14
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	98.11
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.1
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.07
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	98.01
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	97.98
PRK11642	813	exoribonuclease R; Provisional	97.96
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	97.91
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	97.89
PRK12327	362	nusA transcription elongation factor NusA; Provisi	97.87
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	97.84
TIGR01953	341	NusA transcription termination factor NusA. This m	97.77
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.74
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.66
KOG2916	304	consensus Translation initiation factor 2, alpha s	97.61
PRK05054	644	exoribonuclease II; Provisional	97.53
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.47
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	97.46
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	97.29
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	97.2
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.17
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.16
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.13
PRK05054	644	exoribonuclease II; Provisional	97.04
COG0557	706	VacB Exoribonuclease R [Transcription]	97.04
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	96.95
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	96.89
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	96.74
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	96.63
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	96.58
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	96.34
KOG2916	304	consensus Translation initiation factor 2, alpha s	96.28
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	96.19
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	96.13
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	96.04
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	95.96
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	95.87
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	95.81
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.64
COG0557	706	VacB Exoribonuclease R [Transcription]	95.38
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	95.29
PRK10811	1068	rne ribonuclease E; Reviewed	95.26
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	95.25
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	95.18
PRK11712	489	ribonuclease G; Provisional	94.63
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	93.79
PRK12329	449	nusA transcription elongation factor NusA; Provisi	93.5
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	92.77
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	90.93
PRK10811	1068	rne ribonuclease E; Reviewed	90.23
PRK11712	489	ribonuclease G; Provisional	88.32
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	87.69
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	85.88
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	85.78
PRK12442	87	translation initiation factor IF-1; Reviewed	84.73
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	82.14
COG4148	352	ModC ABC-type molybdate transport system, ATPase c	81.91
TIGR00008	68	infA translation initiation factor IF-1. This fami	81.51

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

Probab=100.00  E-value=1.7e-43  Score=337.22  Aligned_cols=248  Identities=25%  Similarity=0.400  Sum_probs=233.1

Q ss_pred             ccccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938            3 SLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS   82 (289)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~   82 (289)
                      |-.++|..|+||++.+. -+||++..+++..++.||++.|++||+|+|+|+++|++++|++||+|+..            
T Consensus       198 G~V~~It~~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~------------  264 (541)
T COG0539         198 GVVKNITDYGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLE------------  264 (541)
T ss_pred             EEEEEeecCcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcc------------
Confidence            45688999999999999 99999999999999999999999999999999999999999999998432            


Q ss_pred             hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938           83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI  161 (289)
Q Consensus        83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl  161 (289)
                          +.+|+.+...+.+|+.+.|+|+.++++|+||++. |++||+|+|||+|.+. ..|.+.++      +||.|.|+|+
T Consensus       265 ----~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~-~~P~evv~------~Gq~V~V~Vl  333 (541)
T COG0539         265 ----EDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKK-NVPSEVVK------VGQEVEVKVL  333 (541)
T ss_pred             ----cCcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhccccc-CCHHHhcc------cCCEEEEEEE
Confidence                3589999999999999999999999999999999 9999999999999998 44999998      9999999999


Q ss_pred             EEecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCccccc
Q 022938          162 QANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDIL  233 (289)
Q Consensus       162 ~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~  233 (289)
                      ++|++++||.||+|+   +||+...+.+++|+.++|     +++|+||.++  +|   ++|++|.++++|.....+...|
T Consensus       334 ~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~le--~g---idG~vh~~d~sw~~~~~~~~~~  408 (541)
T COG0539         334 DIDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAFVELE--GG---IDGLVHLSDLSWDRPGEEAEKY  408 (541)
T ss_pred             eeCchhceEEeeehhhhcChhhhhhhhcCCCCeEEEEEeeecccceEEccC--CC---ccceEEHHhcCccccCcHHHhh
Confidence            999999999999997   589999999999999999     9999999996  55   9999999999999877776799


Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChHH
Q 022938          234 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP  279 (289)
Q Consensus       234 ~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~~  279 (289)
                      ++||.++++|+.+|+++++|+|++|++.++||......++.|++.+
T Consensus       409 k~Gd~v~~~vl~vd~~~~~isLgiKql~~~p~~~~~~~~~~~~~v~  454 (541)
T COG0539         409 KKGDEVEAKVLAVDKEKERISLGIKQLEESPWEEFSEKYKKGSVVK  454 (541)
T ss_pred             ccCcEEEEEEEEEecccceeeeehhhhccCchhhhHhhccCCCeEE
Confidence            9999999999999999999999999999999999999999998754

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

Probab=100.00  E-value=5.3e-40  Score=313.32  Aligned_cols=213  Identities=28%  Similarity=0.432  Sum_probs=196.9

Q ss_pred             ccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECC
Q 022938           42 ERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFS  121 (289)
Q Consensus        42 ~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~g  121 (289)
                      -.+|.++.++|+.+|.+++++.+|.+..+            ++.+....+++...+++|+++.|+|++++++|+||+++|
T Consensus       147 ~~~Gk~~~~kiie~d~~~n~vv~SrR~~~------------e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdigG  214 (541)
T COG0539         147 PLIGKELEFKILELDKKRNNVVLSRRAVL------------EEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGG  214 (541)
T ss_pred             ccCCceEEEEEEEEccccCcEEEEhHHHh------------hHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEecC
Confidence            46899999999999999999999987443            222233445567779999999999999999999999999


Q ss_pred             EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec---chhhhcccccccccEEEe----
Q 022938          122 LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG----  194 (289)
Q Consensus       122 v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G----  194 (289)
                      ++|++|++||||.+. .+|++.++      +||.|+|+|+++|.+++|+.||+|+   .||+.....+++|+.+.|    
T Consensus       215 vdGLlHiseiS~~rv-~~P~~vvk------vGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~  287 (541)
T COG0539         215 VDGLLHISEISWKRV-DHPSEVVK------VGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTN  287 (541)
T ss_pred             eeeEEehhhcccccc-CCHHHhcc------cCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEE
Confidence            999999999999998 99999998      9999999999999999999999997   599999999999999999    


Q ss_pred             -eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhC
Q 022938          195 -RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVI  273 (289)
Q Consensus       195 -~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~  273 (289)
                       ++||+||++.  +|   ++||+|+|+|+|.+...|++.+++||.|.|+|+.||++++||+||+|++.+|||+.+.++|+
T Consensus       288 i~~~GafVei~--~G---vEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~  362 (541)
T COG0539         288 LTDYGAFVEIE--EG---VEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHP  362 (541)
T ss_pred             eecCcEEEEec--CC---ccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcC
Confidence             9999999997  66   99999999999999988999999999999999999999999999999999999999999999


Q ss_pred             CCChH
Q 022938          274 PQGLE  278 (289)
Q Consensus       274 ~g~~~  278 (289)
                      +|++.
T Consensus       363 ~g~~v  367 (541)
T COG0539         363 VGDVV  367 (541)
T ss_pred             CCCeE
Confidence            99864

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=6.5e-39  Score=293.80  Aligned_cols=236  Identities=25%  Similarity=0.391  Sum_probs=214.6

Q ss_pred             cccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhh
Q 022938            4 LSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQ   83 (289)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~   83 (289)
                      -+.++.+++|+++++.+..|+..+..+++....+|.+.|++|++++|.|++++++++++.+|+|+.              
T Consensus        38 ~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~--------------  103 (318)
T PRK07400         38 TVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRI--------------  103 (318)
T ss_pred             EEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhh--------------
Confidence            345688999999999999999999999999999999999999999999999999999999998732              


Q ss_pred             hhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938           84 SRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA  163 (289)
Q Consensus        84 ~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v  163 (289)
                       .....|+.+.+.++.|++++|+|+++.++|+||+++|++||||.+++++.+.    .+       ..+|+.++|+|+++
T Consensus       104 -~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~Gv~gfip~s~ls~~~~----~~-------~~vG~~i~~kVl~i  171 (318)
T PRK07400        104 -EYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKP----KE-------ELVGEELPLKFLEV  171 (318)
T ss_pred             -hhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCccCC----cc-------ccCCCEEEEEEEEE
Confidence             2345799999999999999999999999999999999999999999998542    11       23999999999999


Q ss_pred             ecCCcEEEEEeecchhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCE
Q 022938          164 NEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE  238 (289)
Q Consensus       164 d~~~~ri~lS~k~~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~  238 (289)
                      |++++++.||+|.+.++..+.++++|+++.|     +++|+||++   +|   +.|++|+++++|.+..++.+.|++||.
T Consensus       172 d~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i---~g---v~Gllhisels~~~~~~~~~~~~vGd~  245 (318)
T PRK07400        172 DEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDI---GG---VSGLLHISEISHEHIETPHSVFNVNDE  245 (318)
T ss_pred             EcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEE---CC---EEEEEEHHHcccccccChhhccCCCCE
Confidence            9999999999998777778889999999999     999999999   34   999999999999999999999999999


Q ss_pred             EEEEEEEEeCCCCeEEEEEecCCCCchhHHhhh
Q 022938          239 VRVKVIKIDREKSRITLSIKQLEEDPLLETLEK  271 (289)
Q Consensus       239 V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~  271 (289)
                      |+|+|+++|.++++|.||+|++++|||+...+.
T Consensus       246 VkvkVl~iD~e~~rI~LS~K~l~~~P~~~~~~~  278 (318)
T PRK07400        246 MKVMIIDLDAERGRISLSTKQLEPEPGDMLKDP  278 (318)
T ss_pred             EEEEEEEEeCCCCEEEEEEeccccChhhhhhhH
Confidence            999999999999999999999999999876543

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=7.8e-38  Score=299.64  Aligned_cols=245  Identities=23%  Similarity=0.383  Sum_probs=222.0

Q ss_pred             ccccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938            3 SLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS   82 (289)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~   82 (289)
                      |-+.+|...+++++.+.+-.|+.-...++.....||.+.|++|++|+|.|++++..++++.||+++              
T Consensus        41 G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~--------------  106 (486)
T PRK07899         41 GTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKR--------------  106 (486)
T ss_pred             EEEEEEECCcEEEEECCCcEEEEEHHHhcccccCChhhcCCCCCEEEEEEEEEECCCCeEEEEehh--------------
Confidence            446778899999999999999999999999999999999999999999999999999999999873              


Q ss_pred             hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938           83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ  162 (289)
Q Consensus        83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~  162 (289)
                       +..+..|+.+.++++.|++++|+|+++.++|++|++ |++||||.+++++.+. .++..        ++|+.|+|+|++
T Consensus       107 -~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl-Gi~gflP~Sel~~~~~-~~~~~--------~vGq~V~vkVle  175 (486)
T PRK07899        107 -AQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-GLRGFLPASLVEMRRV-RDLQP--------YIGQEIEAKIIE  175 (486)
T ss_pred             -hcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEE-CCEEEEEhhHhccccc-CChhh--------cCCCEEEEEEEE
Confidence             233468999999989999999999999999999999 7999999999998664 44322        499999999999


Q ss_pred             EecCCcEEEEEeec-------chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcc
Q 022938          163 ANEEMKKLVFSEKD-------AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIR  230 (289)
Q Consensus       163 vd~~~~ri~lS~k~-------~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~  230 (289)
                      +|.+++++.+|+|.       .+|+..+.++++|+++.|     +++|+||+|+   |   +.||||+++++|.++.++.
T Consensus       176 id~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlg---g---v~Glv~~Sels~~~v~~~~  249 (486)
T PRK07899        176 LDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG---G---VDGLVHVSELSWKHIDHPS  249 (486)
T ss_pred             EECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC---C---EEEEEEHHHCCCcccCCHH
Confidence            99999999999985       357778889999999999     9999999994   4   9999999999999999999


Q ss_pred             cccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChH
Q 022938          231 DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE  278 (289)
Q Consensus       231 ~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~  278 (289)
                      +.|++||.|+|+|+++|++++||.||+|++.++||..+.+++..|+..
T Consensus       250 ~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv  297 (486)
T PRK07899        250 EVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIV  297 (486)
T ss_pred             HhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEE
Confidence            999999999999999999999999999999999999999988888754

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=7e-38  Score=316.42  Aligned_cols=248  Identities=17%  Similarity=0.241  Sum_probs=223.4

Q ss_pred             ccccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938            3 SLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS   82 (289)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~   82 (289)
                      |-++++-.+++|+++. ...||++...++...+.+|++.|++||+++|+|+++|++++++.+|+|...            
T Consensus       499 G~Vk~i~~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~------------  565 (863)
T PRK12269        499 GVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQ------------  565 (863)
T ss_pred             EEEEEEeCCcEEEEEC-CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccc------------
Confidence            4467788899999994 578999999999999999999999999999999999999999999998431            


Q ss_pred             hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938           83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI  161 (289)
Q Consensus        83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl  161 (289)
                          +.+|+.+.+.+.+|++++|+|+++.++|+||+++ |++|++|.+|++|.....+|.+.|+      +||.|+|+|+
T Consensus       566 ----~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~k------vGd~V~vkVl  635 (863)
T PRK12269        566 ----PDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVK------IGDEVECMIL  635 (863)
T ss_pred             ----cchhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCC------CCCEEEEEEE
Confidence                2478888888999999999999999999999998 9999999999999432377887776      9999999999


Q ss_pred             EEecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-cCcccc
Q 022938          162 QANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDI  232 (289)
Q Consensus       162 ~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-~~~~~~  232 (289)
                      ++|++++++.||+|+   +||+...+++++|+++.|     +++|+||++.  +|   +.|++|.++++|.+. ..+...
T Consensus       636 ~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~--~g---V~GlIh~sels~~~~~~~~~~~  710 (863)
T PRK12269        636 GYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEME--EG---IDGFLHVDDLSWVKRTRPADHE  710 (863)
T ss_pred             EEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEeC--CC---cEEEEEhHHhhccccccchhhc
Confidence            999999999999995   589999899999999999     9999999996  55   999999999999765 445568


Q ss_pred             cCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChH
Q 022938          233 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE  278 (289)
Q Consensus       233 ~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~  278 (289)
                      |++||.|+|+|+++|++++||.||+|++.++||+.+.+++.+|+.-
T Consensus       711 ~kvGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV  756 (863)
T PRK12269        711 LEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTV  756 (863)
T ss_pred             cCCCCEEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCCCCEE
Confidence            9999999999999999999999999999999999999999999764

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=4.5e-37  Score=297.28  Aligned_cols=241  Identities=18%  Similarity=0.256  Sum_probs=216.6

Q ss_pred             ccccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCC----CeEeeeeecccccCCcchh
Q 022938            3 SLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNA----AKITPTTVNPILDDSSDAN   78 (289)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~----~~i~ls~k~~l~~~~~~~~   78 (289)
                      |-+.++..++|+++++....|++++..++.....+|.+.|++||.+.|+|+++|+++    .++.+|+|+.         
T Consensus       208 G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~---------  278 (491)
T PRK13806        208 GTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQA---------  278 (491)
T ss_pred             EEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhh---------
Confidence            345678899999999878899999999999999999999999999999999999986    4799998733         


Q ss_pred             hhhhhhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEE
Q 022938           79 NRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIIS  157 (289)
Q Consensus        79 ~~~~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~  157 (289)
                             .+.+|+.+.+.+..|++++|+|+++.++|+||+++ |++||+|.++++|.....+|.+.++      +||.|+
T Consensus       279 -------~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~------~Gd~v~  345 (491)
T PRK13806        279 -------GGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVA------PGDAVA  345 (491)
T ss_pred             -------hcccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCC------CCCEEE
Confidence                   23468888888999999999999999999999998 9999999999998432266777776      999999


Q ss_pred             EEEEEEecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc
Q 022938          158 VKVIQANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI  229 (289)
Q Consensus       158 vkVl~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~  229 (289)
                      |+|+++|++++++.+|+|+   +||+...+++++|++++|     ++||+||++.  +|   +.||||+++++|.+..++
T Consensus       346 vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~--~g---v~Gli~~se~s~~~~~~~  420 (491)
T PRK13806        346 VKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLA--PG---VTGLLPASVISRAGKPAT  420 (491)
T ss_pred             EEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEEEEecCceEEEcC--CC---cEEEEEHHHcCcccccch
Confidence            9999999999999999996   589999999999999999     9999999996  55   999999999999999999


Q ss_pred             ccccCCCCEEEEEEEEEeCCCCeEEEEEecC-----CCCchhHHhh
Q 022938          230 RDILNEGDEVRVKVIKIDREKSRITLSIKQL-----EEDPLLETLE  270 (289)
Q Consensus       230 ~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~-----~~~p~~~~~~  270 (289)
                      .+.|++||.|+|+|+++|++++||+||+|++     ..+||.++..
T Consensus       421 ~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~~~~~~~~~~~~~~~~~~  466 (491)
T PRK13806        421 YEKLKPGDSVTLVVEEIDTAKRKISLAPAGAAGSGADDDDWKQFAP  466 (491)
T ss_pred             hhcCCCCCEEEEEEEEEeCCCCEEEEEeehhhhhhhhhhHHHhhcc
Confidence            9999999999999999999999999999977     3589999854

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=6.2e-36  Score=289.37  Aligned_cols=247  Identities=22%  Similarity=0.351  Sum_probs=214.4

Q ss_pred             ccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhh
Q 022938            5 SSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQS   84 (289)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~   84 (289)
                      +.++-..++++++. ...|+.-...++.....+|...  +|+++.|+|+.+|++++++.+|.+..+            +.
T Consensus       123 V~~~~~~G~~V~i~-g~~~flP~s~~~~~~~~~~~~~--vG~~i~~~V~~id~~~~~v~lSrk~~~------------~~  187 (491)
T PRK13806        123 VTGTCKGGFNVEVL-GRRAFCPVSQIDLRYVEDPESY--VGQTFQFLITRVEENGRNIVVSRRALL------------ER  187 (491)
T ss_pred             EEEEEcCCEEEEEC-CEEEEEEHHHhccccCCChHHc--CCCeEEEEEEEEECCCCeEEEEeehhh------------hh
Confidence            45566778888864 4566655555666667788753  999999999999999999999977332            22


Q ss_pred             hhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938           85 RSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA  163 (289)
Q Consensus        85 ~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v  163 (289)
                      .....|+.+...++.|++++|+|+++.++|+||+++ |+.||+|.++++|.+. .+|.+.++      +||.++|+|+++
T Consensus       188 ~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~-~~~~~~~~------vGd~i~vkVl~i  260 (491)
T PRK13806        188 EQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRV-QKADEAVS------VGDTVRVKVLGI  260 (491)
T ss_pred             hhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccc-cChhHhcC------CCCEEEEEEEEE
Confidence            344678888888999999999999999999999997 9999999999999886 78887776      999999999999


Q ss_pred             ecCC----cEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCc-ccccCcc
Q 022938          164 NEEM----KKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIR  230 (289)
Q Consensus       164 d~~~----~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~-~~~~~~~  230 (289)
                      |.++    +|+.||+|+   +||.....++++|+++.|     .++|+||+++  +|   +.||+|.++++| .++.++.
T Consensus       261 d~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~--~g---v~Glvh~sels~~~~~~~~~  335 (491)
T PRK13806        261 ERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEIL--PG---IEGLVHVSEMSWTRRVNKPE  335 (491)
T ss_pred             ecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCceEEEEeC--CC---cEEEEEHHHcCcccccCCHH
Confidence            9876    479999987   489999999999999999     9999999996  55   999999999998 4678888


Q ss_pred             cccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChH
Q 022938          231 DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE  278 (289)
Q Consensus       231 ~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~  278 (289)
                      +.|++||.|+|+|+++|+++++|.||+|++.++||+.+.+++.+|++.
T Consensus       336 ~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v  383 (491)
T PRK13806        336 DVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTV  383 (491)
T ss_pred             HcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEE
Confidence            999999999999999999999999999999999999999999999754

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=8.6e-36  Score=281.68  Aligned_cols=247  Identities=22%  Similarity=0.325  Sum_probs=222.0

Q ss_pred             ccccccccceeEeCC-CCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhh
Q 022938            3 SLSSRIGSNTCLDAS-SCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQ   81 (289)
Q Consensus         3 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~   81 (289)
                      |-+.++..++|+++. +....|+....++++....+|.+.|++|++++|+|++++.+++++.+|+++             
T Consensus        23 G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~-------------   89 (390)
T PRK06676         23 GEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRR-------------   89 (390)
T ss_pred             EEEEEEECCeEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEECCCCCEEEEHHH-------------
Confidence            456788999999999 888999999999999899999999999999999999999998899999763             


Q ss_pred             hhhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938           82 SQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI  161 (289)
Q Consensus        82 ~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl  161 (289)
                        ......|+.+.++++.|++++|+|+++.++|++|+++|++||||.+++++.+. .+|.+        .+|+.++|+|+
T Consensus        90 --~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~G~~gflp~~el~~~~~-~~~~~--------~vG~~v~~~Vl  158 (390)
T PRK06676         90 --LEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLISTRFV-EDFSD--------FKGKTLEVKII  158 (390)
T ss_pred             --hhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCCccC-CChHH--------cCCCEEEEEEE
Confidence              23345799999999999999999999999999999999999999999998765 44432        38999999999


Q ss_pred             EEecCCcEEEEEeecc-------hhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc
Q 022938          162 QANEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI  229 (289)
Q Consensus       162 ~vd~~~~ri~lS~k~~-------~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~  229 (289)
                      ++|.+++++.+|+|..       +|...+.++++|+++.|     .++|+||+++   |   +.|++|.++++|.++.++
T Consensus       159 ~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~---~---v~g~v~~sels~~~~~~~  232 (390)
T PRK06676        159 ELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG---G---VDGLVHISELSHERVEKP  232 (390)
T ss_pred             EEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC---C---eEEEEEHHHcCccccCCH
Confidence            9999999999999963       45666788999999999     8999999993   4   999999999999999999


Q ss_pred             ccccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChHH
Q 022938          230 RDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP  279 (289)
Q Consensus       230 ~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~~  279 (289)
                      .+.|++||.|+|+|+++|+++++|.||+|++.++||+.+.+++..|+...
T Consensus       233 ~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~  282 (390)
T PRK06676        233 SEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIE  282 (390)
T ss_pred             HHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEE
Confidence            99999999999999999999999999999999999999998998887643

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=2.9e-35  Score=290.19  Aligned_cols=248  Identities=27%  Similarity=0.428  Sum_probs=222.7

Q ss_pred             ccccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938            3 SLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS   82 (289)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~   82 (289)
                      +-+.+|-.++|+++++ .-.|+++...++...+.+|++.|++||+|.|+|+++|++++++.+|++...            
T Consensus       207 g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~------------  273 (565)
T PRK06299        207 GVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLG------------  273 (565)
T ss_pred             EEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecc------------
Confidence            3457788999999997 788888888888888999999999999999999999999999999988321            


Q ss_pred             hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938           83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI  161 (289)
Q Consensus        83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl  161 (289)
                          +.+|+.+.+.++.|++++|+|+++.++|+||+++ |+.||+|.++++|.....+|.+.+.      +||.|+|+|+
T Consensus       274 ----~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~------~G~~v~v~V~  343 (565)
T PRK06299        274 ----EDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVS------VGQEVEVMVL  343 (565)
T ss_pred             ----cChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcC------CCCEEEEEEE
Confidence                2479888888999999999999999999999998 9999999999998654356766665      9999999999


Q ss_pred             EEecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-cCcccc
Q 022938          162 QANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDI  232 (289)
Q Consensus       162 ~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-~~~~~~  232 (289)
                      ++|++++++.||++.   .||......+++|+++.|     +++|+||+++  +|   +.|++|.++++|.+. .++.+.
T Consensus       344 ~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~--~~---v~g~i~~s~l~~~~~~~~~~~~  418 (565)
T PRK06299        344 EIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLE--GG---IDGLVHLSDISWDKKGEEAVEL  418 (565)
T ss_pred             EEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceEEEECC--CC---CEEEEEHHHcCccccccChHhh
Confidence            999999999999985   488888888999999999     8999999995  45   999999999999876 788899


Q ss_pred             cCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChH
Q 022938          233 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE  278 (289)
Q Consensus       233 ~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~  278 (289)
                      |++||.|+|+|+++|+++++|.||+|++..+||....+.+..|++.
T Consensus       419 ~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV  464 (565)
T PRK06299        419 YKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIV  464 (565)
T ss_pred             CCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEE
Confidence            9999999999999999999999999999999999999888888764

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=2.6e-34  Score=271.54  Aligned_cols=240  Identities=22%  Similarity=0.353  Sum_probs=210.5

Q ss_pred             ccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhh
Q 022938            5 SSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQS   84 (289)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~   84 (289)
                      +..+..++|++++.. ..|+.....++.....+|...  +|+++.|+|+++|++++++.+|++...            ..
T Consensus       113 V~~v~~~G~~V~~~G-~~gflp~~el~~~~~~~~~~~--vG~~v~~~Vl~~d~~~~~i~lS~k~~~------------~~  177 (390)
T PRK06676        113 VTEVVKGGLVVDVEG-VRGFIPASLISTRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVV------------EE  177 (390)
T ss_pred             EEEEECCeEEEEECC-EEEEEEHHHcCCccCCChHHc--CCCEEEEEEEEEECCCCEEEEEeHHHh------------hh
Confidence            456778899999943 388887777777777777653  999999999999999999999987321            12


Q ss_pred             hhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938           85 RSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN  164 (289)
Q Consensus        85 ~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd  164 (289)
                      .....|..+.+.++.|++++|+|+++.++|+||+++|++||||.+++++.+. .+|.+.++      +|+.++|+|+++|
T Consensus       178 ~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~-~~~~~~~~------vGd~i~~~Vl~vd  250 (390)
T PRK06676        178 ERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERV-EKPSEVVS------VGQEVEVKVLSID  250 (390)
T ss_pred             hhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCcccc-CCHHHhcC------CCCEEEEEEEEEe
Confidence            2335677777888999999999999999999999999999999999999876 77777665      9999999999999


Q ss_pred             cCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCC
Q 022938          165 EEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEG  236 (289)
Q Consensus       165 ~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iG  236 (289)
                      ++++++.+|+|.   .||....+++++|+++.|     .++|+||++.  +|   +.|++|.+++++.+..++.+.|++|
T Consensus       251 ~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~--~g---i~Glv~~se~~~~~~~~~~~~~~~G  325 (390)
T PRK06676        251 WETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVL--PG---VEGLVHISQISHKHIATPSEVLEEG  325 (390)
T ss_pred             CCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeCceEEEEEC--CC---CeEEEEhHHcCccccCChhhccCCC
Confidence            999999999995   478888889999999999     8999999995  55   9999999999999888888999999


Q ss_pred             CEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhh
Q 022938          237 DEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEK  271 (289)
Q Consensus       237 d~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~  271 (289)
                      |.|+|+|+++|++++++.||+|++.++||.+..++
T Consensus       326 d~v~v~V~~id~e~~~i~ls~k~~~~~~~~~~~~~  360 (390)
T PRK06676        326 QEVKVKVLEVNEEEKRISLSIKALEEAPAEEEDRR  360 (390)
T ss_pred             CEEEEEEEEEECCCCEEEEEEEecccChhhhhhhh
Confidence            99999999999999999999999999999998554

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=3.2e-34  Score=274.80  Aligned_cols=232  Identities=21%  Similarity=0.302  Sum_probs=202.2

Q ss_pred             ccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhh
Q 022938            5 SSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQS   84 (289)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~   84 (289)
                      +.++-..+|+++++  ..|+.....++.....++..  .+|+++.|+|+++|++++++.+|+|..+            +.
T Consensus       130 V~~v~k~G~~VdlG--i~gflP~Sel~~~~~~~~~~--~vGq~V~vkVleid~~~~~ivLSrr~~l------------~~  193 (486)
T PRK07899        130 VIEVVKGGLILDIG--LRGFLPASLVEMRRVRDLQP--YIGQEIEAKIIELDKNRNNVVLSRRAWL------------EQ  193 (486)
T ss_pred             EEEEECCeEEEEEC--CEEEEEhhHhcccccCChhh--cCCCEEEEEEEEEECCCCEEEEEhHHHH------------Hh
Confidence            45677889999994  56777666565555556654  4999999999999999999999977322            11


Q ss_pred             hhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938           85 RSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN  164 (289)
Q Consensus        85 ~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd  164 (289)
                      .....|+.+...++.|++++|+|+++.++|+||+++|++||||.++++|.+. .+|.+.++      +||.|+|+|+++|
T Consensus       194 ~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v-~~~~~~~k------vGd~V~vkVl~iD  266 (486)
T PRK07899        194 TQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHI-DHPSEVVE------VGQEVTVEVLDVD  266 (486)
T ss_pred             hhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCccc-CCHHHhcC------CCCEEEEEEEEEE
Confidence            2345788888889999999999999999999999999999999999999886 78887776      9999999999999


Q ss_pred             cCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCC
Q 022938          165 EEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEG  236 (289)
Q Consensus       165 ~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iG  236 (289)
                      +++++|.||+|+   +||......+++|+++.|     .++|+||++.  +|   +.||+|++++++.++.++.+.|++|
T Consensus       267 ~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~--~g---ieGLvh~SeLs~~~v~~~~~~~kvG  341 (486)
T PRK07899        267 MDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVE--EG---IEGLVHISELAERHVEVPEQVVQVG  341 (486)
T ss_pred             CCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEeccEEEEEeC--CC---cEEEEEHHHcCcccccCccceeCCC
Confidence            999999999996   589888888999999999     9999999995  55   9999999999999998899999999


Q ss_pred             CEEEEEEEEEeCCCCeEEEEEecCCCCc
Q 022938          237 DEVRVKVIKIDREKSRITLSIKQLEEDP  264 (289)
Q Consensus       237 d~V~vkV~~id~e~~ri~lSlK~~~~~p  264 (289)
                      |.|+|+|+++|++++||.||+|++.++-
T Consensus       342 d~V~VkIi~ID~e~rrI~LSlK~~~~~~  369 (486)
T PRK07899        342 DEVFVKVIDIDLERRRISLSLKQANEGV  369 (486)
T ss_pred             CEEEEEEEEEECCCCEEEEEEEEcccCC
Confidence            9999999999999999999999986543

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=5.4e-34  Score=281.16  Aligned_cols=243  Identities=24%  Similarity=0.379  Sum_probs=213.9

Q ss_pred             cccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhh
Q 022938            4 LSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQ   83 (289)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~   83 (289)
                      -+-++...+|+|+++.+..|+.-.-.+++   .++...|++|++++|.|+++++..+++.+|.+               +
T Consensus        37 ~V~~v~~~~~~Vdig~k~~g~lp~~e~~~---~~~~~~~~vG~~i~~~V~~~~~~~~~i~lS~k---------------~   98 (565)
T PRK06299         37 TVVAIDKDYVLVDVGLKSEGRIPLEEFKN---EQGELEVKVGDEVEVYVERIEDGFGETVLSRE---------------K   98 (565)
T ss_pred             EEEEEECCEEEEEeCCCeEEEEEHHHhcC---ccccccCCCCCEEEEEEEEEECCCCcEEEech---------------H
Confidence            35567789999999888888766555553   23456799999999999999999899999976               2


Q ss_pred             hhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938           84 SRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA  163 (289)
Q Consensus        84 ~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v  163 (289)
                      +.....|+++.++++.|++++|+|.++.++|++|+++|++||||.+++++.+. .++        .+++|++++|+|+++
T Consensus        99 ~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~~~g~~gfip~s~~~~~~~-~~~--------~~~vG~~i~~~V~~~  169 (565)
T PRK06299         99 AKRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAFLPGSQVDVRPV-RDT--------DPLEGKELEFKVIKL  169 (565)
T ss_pred             HHHHHHHHHHHHHhhCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHccCcCC-CCh--------HHhCCCEEEEEEEEE
Confidence            34557899999999999999999999999999999999999999999998764 332        235999999999999


Q ss_pred             ecCCcEEEEEeecc-------hhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCccc
Q 022938          164 NEEMKKLVFSEKDA-------VWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRD  231 (289)
Q Consensus       164 d~~~~ri~lS~k~~-------~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~  231 (289)
                      |.+++++.+|+|..       +|...+.++++|+++.|     .++|+||+++   |   +.|++|+++++|.++.++.+
T Consensus       170 d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~---g---~~glv~~se~s~~~~~~~~~  243 (565)
T PRK06299        170 DKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLG---G---VDGLLHITDISWKRVNHPSE  243 (565)
T ss_pred             ECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC---C---EEEEEEHHHhcccccCCHhh
Confidence            99999999999963       46677889999999999     8999999994   4   99999999999999999999


Q ss_pred             ccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChHH
Q 022938          232 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP  279 (289)
Q Consensus       232 ~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~~  279 (289)
                      .|++||.|+|+|+++|++++++.||+|.+.++||+.+.+.+.+|++..
T Consensus       244 ~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~  291 (565)
T PRK06299        244 VVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVK  291 (565)
T ss_pred             cCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhhCCCCCEEE
Confidence            999999999999999999999999999999999999998999988643

>TIGR00717 rpsA ribosomal protein S1

Probab=100.00  E-value=4e-34  Score=279.34  Aligned_cols=248  Identities=23%  Similarity=0.398  Sum_probs=218.4

Q ss_pred             cccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhh
Q 022938            4 LSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQ   83 (289)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~   83 (289)
                      -++++-.++++++++ ...|+.....++.....+|.+.|++|+++.|+|+++|++++++.+|++..              
T Consensus       194 ~V~~i~~~G~~V~l~-g~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~--------------  258 (516)
T TIGR00717       194 VVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQL--------------  258 (516)
T ss_pred             EEEEEECCeEEEEEC-CEEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEec--------------
Confidence            356777899999985 47888888888888889999999999999999999999999999998732              


Q ss_pred             hhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938           84 SRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ  162 (289)
Q Consensus        84 ~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~  162 (289)
                        ...+|+.+.+.++.|++++|+|+++.++|+||+++ |+.||+|.+++++.+...+|.+.+.      +||.++|+|++
T Consensus       259 --~~~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~------vG~~v~v~V~~  330 (516)
T TIGR00717       259 --GEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVK------KGDEVEVMILD  330 (516)
T ss_pred             --chhHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhcc------CCCEEEEEEEE
Confidence              13478888888999999999999999999999998 9999999999997643355655565      99999999999


Q ss_pred             EecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-cCccccc
Q 022938          163 ANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-QDIRDIL  233 (289)
Q Consensus       163 vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-~~~~~~~  233 (289)
                      +|++++++.||+++   .||....+.+++|+++.|     +++|+||+++  +|   +.|++|.++++|.+. .++...|
T Consensus       331 id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~--~~---v~glv~~s~ls~~~~~~~~~~~~  405 (516)
T TIGR00717       331 IDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELE--GG---IDGLIHLSDISWDKDGREADHLY  405 (516)
T ss_pred             EcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEECC--CC---CEEEEEHHHCcCcccCCCHhHcc
Confidence            99999999999986   588888888999999999     8999999996  55   999999999999754 4567889


Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChHH
Q 022938          234 NEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP  279 (289)
Q Consensus       234 ~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~~  279 (289)
                      ++||.|.|+|+++|+++++|.||+|++.+|||....+.+..|+...
T Consensus       406 ~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~  451 (516)
T TIGR00717       406 KKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVK  451 (516)
T ss_pred             CCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhhccCcceEEE
Confidence            9999999999999999999999999999999999988888887643

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.

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=5.1e-34  Score=288.44  Aligned_cols=243  Identities=15%  Similarity=0.283  Sum_probs=210.3

Q ss_pred             cccccccceeEeCCCCCCccceeEeeccc-ccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938            4 LSSRIGSNTCLDASSCTHSSLSLSLSLSS-LVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS   82 (289)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~   82 (289)
                      -+.+|..+++|+.+.....||++...++. ....+|.+.|++||+|+|+|+++|+++++++||+|+..            
T Consensus       585 ~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~------------  652 (863)
T PRK12269        585 RVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVT------------  652 (863)
T ss_pred             EEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcc------------
Confidence            45788899999999988999999888886 46889999999999999999999999999999987321            


Q ss_pred             hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938           83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI  161 (289)
Q Consensus        83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl  161 (289)
                          ..+|+.+.+.+.+|++++|+|++++++|+||+++ |++||||.++++|.....++.+.|+      +||.|+|+|+
T Consensus       653 ----~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~k------vGq~VkvkVl  722 (863)
T PRK12269        653 ----ANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELE------VGKEIECMVI  722 (863)
T ss_pred             ----cCchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhccccccchhhccC------CCCEEEEEEE
Confidence                2379999899999999999999999999999998 9999999999998664233334454      9999999999


Q ss_pred             EEecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc---c
Q 022938          162 QANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---R  230 (289)
Q Consensus       162 ~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~---~  230 (289)
                      ++|++++++.||+|+   +||+.+...+++|+++.|     +++|+||++.  +|   +.|++|.++++|++..++   .
T Consensus       723 ~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~GkV~~v~~~GvFVeL~--~g---VeGlI~~s~lsdd~~~~~~~~~  797 (863)
T PRK12269        723 ECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVP--GG---VEGLVRKQHLVENRDGDPGEAL  797 (863)
T ss_pred             EEeccCCEEEEEecccccChHHHHHhhCCCCCEEEEEEEEEecCeEEEEcC--CC---eEEEEEHHHcCCcccccchhhc
Confidence            999999999999995   589988888999999999     9999999995  55   999999999999875443   3


Q ss_pred             cccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhC
Q 022938          231 DILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVI  273 (289)
Q Consensus       231 ~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~  273 (289)
                      ..|++||.|+|+|+++|+++++|.||+|+.+..--.+.+++|.
T Consensus       798 ~~f~vGD~V~v~Vl~iD~~~rkI~LSlk~~~~~~~~~~~~~~~  840 (863)
T PRK12269        798 RKYAVGDRVKAVIVDMNVKDRKVAFSVRDYQRKVQRDELSRYM  840 (863)
T ss_pred             cccCCCCEEEEEEEEEEcCCCEEEEEEechhhHHHHHHHHHhh
Confidence            4599999999999999999999999999876544444455553

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

Probab=100.00  E-value=1.1e-33  Score=281.87  Aligned_cols=246  Identities=24%  Similarity=0.371  Sum_probs=221.8

Q ss_pred             ccccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938            3 SLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS   82 (289)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~   82 (289)
                      |-+.++...+++++++.+..|+.-...+++....+|.+.|++|++++|+|++++.+++++.+|+++.             
T Consensus       308 G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~-------------  374 (647)
T PRK00087        308 GTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEA-------------  374 (647)
T ss_pred             EEEEEEECCEEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEeehh-------------
Confidence            4567889999999999999999999999999999999999999999999999999999999998743             


Q ss_pred             hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEE
Q 022938           83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQ  162 (289)
Q Consensus        83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~  162 (289)
                        .....|+.+.++++.|++++|+|+++.++|+||+++|++||||.+++++.+. .+|.+        ++|+.++|+|++
T Consensus       375 --~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lggi~gfiP~sel~~~~~-~d~~~--------~vG~~v~v~Vl~  443 (647)
T PRK00087        375 --DREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVELGYV-EDLSE--------YKGQELEVKIIE  443 (647)
T ss_pred             --cchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHhCcccc-CCHHH--------hCCCEEEEEEEE
Confidence              2345799999999999999999999999999999999999999999998775 55432        389999999999


Q ss_pred             EecCCcE-EEEEeecc-------hhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc
Q 022938          163 ANEEMKK-LVFSEKDA-------VWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI  229 (289)
Q Consensus       163 vd~~~~r-i~lS~k~~-------~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~  229 (289)
                      +|+++++ +.+|+|..       ++...++++++|+++.|     .++|+||++   +|   +.|++|.++++|.++.++
T Consensus       444 vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l---~g---v~Gll~~sels~~~~~~~  517 (647)
T PRK00087        444 FNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI---GG---VDGLLHVSEISWGRVEKP  517 (647)
T ss_pred             EEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEE---CC---EEEEEEHHHcCccccCCH
Confidence            9999988 99999874       34566788999999999     899999999   34   999999999999999999


Q ss_pred             ccccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChH
Q 022938          230 RDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLE  278 (289)
Q Consensus       230 ~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~  278 (289)
                      .+.|++||.|+|+|+++|++++++.||+|++.++||....+++..|+..
T Consensus       518 ~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v  566 (647)
T PRK00087        518 SDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIV  566 (647)
T ss_pred             HHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEE
Confidence            9999999999999999999999999999999999999999888888754

>TIGR00717 rpsA ribosomal protein S1

Probab=100.00  E-value=2.8e-32  Score=266.41  Aligned_cols=228  Identities=21%  Similarity=0.331  Sum_probs=202.8

Q ss_pred             cccccccceeEeCCCCCCccceeEeecccc-cccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhh
Q 022938            4 LSSRIGSNTCLDASSCTHSSLSLSLSLSSL-VCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQS   82 (289)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~   82 (289)
                      -+.++..++|++++.+...|++....++.. ...+|.+.|++||.+.|+|+++|++++++.+|++...            
T Consensus       279 ~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~------------  346 (516)
T TIGR00717       279 RVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCK------------  346 (516)
T ss_pred             EEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcc------------
Confidence            356788999999999888898887777743 4667888899999999999999999999999987321            


Q ss_pred             hhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938           83 QSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI  161 (289)
Q Consensus        83 ~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl  161 (289)
                          ..+|..+.+.+++|++++|+|+++.++|+||+++ |++||+|.++++|.+...++...++      +|+.|.|+|+
T Consensus       347 ----~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~------~G~~V~~~Vl  416 (516)
T TIGR00717       347 ----ANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYK------KGDEIEAVVL  416 (516)
T ss_pred             ----cCcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccC------CCCEEEEEEE
Confidence                2468888888899999999999999999999999 9999999999998764345555554      9999999999


Q ss_pred             EEecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCccccc
Q 022938          162 QANEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDIL  233 (289)
Q Consensus       162 ~vd~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~  233 (289)
                      ++|++++++.+|+|.   +||....+++++|+++.|     +++|+||++.  +|   +.|+||.+++++++..++.+.|
T Consensus       417 ~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~--~~---~~Glv~~s~l~~~~~~~~~~~~  491 (516)
T TIGR00717       417 AVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFVELP--GG---VEGLIRNSELSENRDEDKTDEI  491 (516)
T ss_pred             EEeCcCCEEEEeeccccCCchhhhhhccCcceEEEEEEEEEecceEEEEcC--CC---eEEEEEHHHcCccccccccccC
Confidence            999999999999997   588888888999999999     9999999995  54   9999999999999999999999


Q ss_pred             CCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          234 NEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       234 ~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      ++||.|+++|+++|++++++.||+|
T Consensus       492 ~~Gd~v~~~V~~id~~~~~i~ls~k  516 (516)
T TIGR00717       492 KVGDEVEAKVVDIDKKNRKVSLSVK  516 (516)
T ss_pred             CCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            9999999999999999999999987

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=99.98  E-value=4.4e-31  Score=263.31  Aligned_cols=233  Identities=25%  Similarity=0.393  Sum_probs=203.0

Q ss_pred             ccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCe-EeeeeecccccCCcchhhhhhh
Q 022938            5 SSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAK-ITPTTVNPILDDSSDANNRQSQ   83 (289)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~-i~ls~k~~l~~~~~~~~~~~~~   83 (289)
                      +.++...+|+++++. .+|+.....++.....+|.+ + +|+++.|+|+++|+++++ +.+|++..+            +
T Consensus       397 V~~v~~~G~~V~lgg-i~gfiP~sel~~~~~~d~~~-~-vG~~v~v~Vl~vd~e~~~~l~lS~k~~~------------~  461 (647)
T PRK00087        397 VKEVVKGGLLVDYGG-VRAFLPASHVELGYVEDLSE-Y-KGQELEVKIIEFNRKRRKKVVLSRKAIL------------E  461 (647)
T ss_pred             EEEEECCeEEEEECC-EEEEEEHHHhCccccCCHHH-h-CCCEEEEEEEEEEcCCCcEEEEEeHHHh------------h
Confidence            345678899999985 78887777777777777764 3 999999999999999998 999987432            1


Q ss_pred             hhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938           84 SRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA  163 (289)
Q Consensus        84 ~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v  163 (289)
                      ..+...|....+.++.|+++.|+|+++.++|+||+++|++||+|.++++|.+. .+|.+.|+      +||.++|+|+++
T Consensus       462 ~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~~~-~~~~~~~~------vGd~V~vkV~~i  534 (647)
T PRK00087        462 EEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRV-EKPSDVLK------VGDEIKVYILDI  534 (647)
T ss_pred             hhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCcccc-CCHHHhcC------CCCEEEEEEEEE
Confidence            11233455555668999999999999999999999999999999999999886 77777665      999999999999


Q ss_pred             ecCCcEEEEEeec---chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCC
Q 022938          164 NEEMKKLVFSEKD---AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNE  235 (289)
Q Consensus       164 d~~~~ri~lS~k~---~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~i  235 (289)
                      |++++++.+|+|.   +||.....++++|+++.|     .++|+||++.  +|   +.|++|.+++++.+..++.+.|++
T Consensus       535 d~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~--~~---i~Gli~~sel~~~~~~~~~~~~kv  609 (647)
T PRK00087        535 DKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELE--PG---VDGLVHISQISWKRIDKPEDVLSE  609 (647)
T ss_pred             ECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEECCeEEEEEC--CC---CEEEEEhhhcCccccCCHhhcCCC
Confidence            9999999999996   578888888999999999     8999999995  55   999999999999999999999999


Q ss_pred             CCEEEEEEEEEeCCCCeEEEEEecCCCCc
Q 022938          236 GDEVRVKVIKIDREKSRITLSIKQLEEDP  264 (289)
Q Consensus       236 Gd~V~vkV~~id~e~~ri~lSlK~~~~~p  264 (289)
                      ||.|+|+|+++|++++++.||+|++.++|
T Consensus       610 Gd~V~vkV~~id~e~~rI~lslk~~~~~~  638 (647)
T PRK00087        610 GEEVKAKILEVDPEEKRIRLSIKEVEEEP  638 (647)
T ss_pred             CCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence            99999999999999999999999999999

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.91  E-value=9.3e-24  Score=193.75  Aligned_cols=174  Identities=17%  Similarity=0.291  Sum_probs=146.1

Q ss_pred             hhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938           86 SSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN  164 (289)
Q Consensus        86 ~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd  164 (289)
                      ....|++...+++.|++++|+|+++.++|++|++| +.+||||.+|+++.+. .+|.+.++      +|+.++|+|++++
T Consensus        18 f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~-~~~~~~~~------~G~~v~~~Vi~~~   90 (318)
T PRK07400         18 FAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRV-EGPEEVLQ------PNETREFFILSDE   90 (318)
T ss_pred             HHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccc-cCHHHccC------CCCEEEEEEEEEe
Confidence            33445554455899999999999999999999999 6999999999999886 77877776      9999999999999


Q ss_pred             cCCcEEEEEeec----chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCC
Q 022938          165 EEMKKLVFSEKD----AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNE  235 (289)
Q Consensus       165 ~~~~ri~lS~k~----~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~i  235 (289)
                      .+++++.||+|.    .+|+......+.|+++.|     .++|+||++   +|   +.||+|.|+++|.+..   +. .+
T Consensus        91 ~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l---~G---v~gfip~s~ls~~~~~---~~-~v  160 (318)
T PRK07400         91 NEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRI---EG---LRGFIPGSHISTRKPK---EE-LV  160 (318)
T ss_pred             CCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEE---CC---EEEEEEHHHcCccCCc---cc-cC
Confidence            999999999996    367776667778999999     889999999   35   9999999999986433   33 39


Q ss_pred             CCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhhCCCChHH
Q 022938          236 GDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEP  279 (289)
Q Consensus       236 Gd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~~~g~~~~  279 (289)
                      |+.++|+|+++|+++++|.||+|....+   ...+++..|++..
T Consensus       161 G~~i~~kVl~id~~~~~i~lS~K~~~~~---~~~~~~k~G~vv~  201 (318)
T PRK07400        161 GEELPLKFLEVDEERNRLVLSHRRALVE---RKMNRLEVGEVVV  201 (318)
T ss_pred             CCEEEEEEEEEEcccCEEEEEhhHhhhh---hhhccCCCCCEEE
Confidence            9999999999999999999999976543   3456777777643

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

Probab=99.78  E-value=1.3e-18  Score=176.95  Aligned_cols=193  Identities=22%  Similarity=0.298  Sum_probs=169.4

Q ss_pred             cccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC
Q 022938           41 IERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF  120 (289)
Q Consensus        41 ~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~  120 (289)
                      .|++|.++.||++++.+..+.+.++..+++.........                .++.|+.+.|+|.++.+.|+.|.+-
T Consensus       467 ~~e~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~n----------------DI~iG~~V~~~I~~vt~~Gv~v~v~  530 (1710)
T KOG1070|consen  467 IYEVGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVN----------------DIEIGQLVPGVIRKVTPQGVEVLVT  530 (1710)
T ss_pred             ceecCCcccCccceecccCcEEEEEEehHhhcccccccc----------------cccccceeeeEEEEecCCcEEEEEe
Confidence            589999999999999999999999999888776653222                1689999999999999999999876


Q ss_pred             -C-EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeecc------hhhhcccccccccEE
Q 022938          121 -S-LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA------VWNKYSSRVNVEDIF  192 (289)
Q Consensus       121 -g-v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~~------~~~~~~~~~~~G~iv  192 (289)
                       | +.|++|.+++++.+. .-|...|      .+|..+++||+.++.+.+++.+++|.+      |....+.+..+|+++
T Consensus       531 ~~ni~g~lp~~hlsd~~~-~~p~~~f------~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~  603 (1710)
T KOG1070|consen  531 FGNIKGVLPKEHLSDHPL-QPPLRDF------KVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKIT  603 (1710)
T ss_pred             cCceeeecChHhhhhccc-cccccee------eeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceE
Confidence             4 999999999999875 4454444      488888999999999999999999974      444567788999999


Q ss_pred             Ee-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938          193 VG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  261 (289)
Q Consensus       193 ~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~  261 (289)
                      .|     .++||||.+-  +|   ++||.|.+++++.++.+.++.|.+||+|.|+|.++|++++||.+++|+..
T Consensus       604 ~G~l~~~~~~g~~V~F~--g~---lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~  672 (1710)
T KOG1070|consen  604 KGTLCAIKENGAFVTFT--GG---LSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASS  672 (1710)
T ss_pred             EEEEeeeccCCeEEEec--Cc---cccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhh
Confidence            99     8999999993  54   99999999999999999999999999999999999999999999999975

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

Probab=99.75  E-value=1.7e-17  Score=168.95  Aligned_cols=230  Identities=22%  Similarity=0.244  Sum_probs=192.2

Q ss_pred             eEeCCCCCCccceeEe-ecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHH
Q 022938           13 CLDASSCTHSSLSLSL-SLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWK   91 (289)
Q Consensus        13 ~~~~~~~~~~~~~~~~-~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~   91 (289)
                      -.+++..+-.|=+..+ .+++..-.+|...|..++.+.+.++.++..+..+.++++.+.-.... ..       ....-=
T Consensus      1083 ~~l~~~~~~~G~~~~i~~~~d~~~~~P~~~f~~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~-~~-------~kd~~i 1154 (1710)
T KOG1070|consen 1083 LILQLPFKVFGRVSFIEDMSDSYSMTPVEHFTKIQIVYVCVLSVSALNKGLELSLRESRTKITP-VD-------SKDGSI 1154 (1710)
T ss_pred             eEEecCCccccceEEeeehhccccCChHHhcccccEEEEEEEEEecccccceeecccccccCcc-cc-------ccCCcc
Confidence            4677778888855555 99999999999999999999999999999888899998855432111 00       000000


Q ss_pred             HHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEE
Q 022938           92 AARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKL  170 (289)
Q Consensus        92 ~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri  170 (289)
                      ...++++.|++++|.|..+.+.|+|+.++ ++.||+|++++++.+. ..|...|.      +|+.+..+|++++...+|+
T Consensus      1155 ks~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~-k~w~k~~~------~gklv~~rv~~ve~~s~ri 1227 (1710)
T KOG1070|consen 1155 KSIEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFE-KEWEKHLP------VGKLVTGRVLSVEEDSKRI 1227 (1710)
T ss_pred             cchhhcccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchh-hhhhccCC------ccceeeeEEEEeeccCceE
Confidence            12445799999999999999999999999 9999999999999886 77777776      9999999999999999999


Q ss_pred             EEEeecch------hhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEE
Q 022938          171 VFSEKDAV------WNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEV  239 (289)
Q Consensus       171 ~lS~k~~~------~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V  239 (289)
                      .+|++...      .......++.|+...|     .++|.|+++.. .+  ++.|++|.++.++.+..+....+..|+.|
T Consensus      1228 el~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~-tv--~~~g~~~~~e~~d~~~e~it~~~~~~~~V 1304 (1710)
T KOG1070|consen 1228 ELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDV-TV--NMVGLCHISEEADDRGENITALYYAGDRV 1304 (1710)
T ss_pred             EEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEEEecC-cc--eecccccceeecchhhhhcccceecccee
Confidence            99999742      2345678899999999     89999999962 22  58999999999999999999999999999


Q ss_pred             EEEEEEEeCCCCeEEEEEecC
Q 022938          240 RVKVIKIDREKSRITLSIKQL  260 (289)
Q Consensus       240 ~vkV~~id~e~~ri~lSlK~~  260 (289)
                      +|.++..+.++++|.+.+|..
T Consensus      1305 ~a~~lk~~~ek~rIsl~~k~s 1325 (1710)
T KOG1070|consen 1305 KACVLKEDSEKKRISLGLKSS 1325 (1710)
T ss_pred             eeEeeeccchhhhhhhhhhhh
Confidence            999999999999999998875

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.64  E-value=5.5e-16  Score=140.66  Aligned_cols=92  Identities=25%  Similarity=0.376  Sum_probs=83.5

Q ss_pred             cccc-cccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          184 SRVN-VEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       184 ~~~~-~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      ..++ +|++|.|     .+||+||.|...+   ++.||+|+|++||.++.++++.+++||.|.|+|+++|+++++|.||+
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            3455 7999988     8999999994222   49999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCchhHHhhhhCCCChH
Q 022938          258 KQLEEDPLLETLEKVIPQGLE  278 (289)
Q Consensus       258 K~~~~~p~~~~~~~~~~g~~~  278 (289)
                      |++.++||..+.++|..|...
T Consensus        89 K~v~~~pw~~~~e~~~~g~~v  109 (319)
T PTZ00248         89 KRVSPEDIEACEEKFSKSKKV  109 (319)
T ss_pred             eecccchHHHHHHhCcCCCEE
Confidence            999999999999999998654

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

Probab=99.63  E-value=2e-16  Score=122.36  Aligned_cols=76  Identities=46%  Similarity=0.778  Sum_probs=70.5

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  259 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~  259 (289)
                      .+++|+++.|     ++||+||+|.  +|   -+||+|+|+++.++++++.+.+++||.|.|+|+++|. +++|+||+|.
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~--~g---~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSIr~   75 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELE--GG---KTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRK   75 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEec--CC---CcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHH
Confidence            5789999988     9999999995  55   8999999999999999999999999999999999997 9999999999


Q ss_pred             CCCCchh
Q 022938          260 LEEDPLL  266 (289)
Q Consensus       260 ~~~~p~~  266 (289)
                      ++..|-.
T Consensus        76 ~~e~pe~   82 (129)
T COG1098          76 LEEEPEK   82 (129)
T ss_pred             hhhCccc
Confidence            9887754

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.61  E-value=3.2e-16  Score=142.19  Aligned_cols=135  Identities=13%  Similarity=0.176  Sum_probs=116.6

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      ++|+++.|+|+++.++|+||++.   |++||||.|+++|.+. .+|.+.++      +||.+.|+|+++|+++++|.||.
T Consensus        16 ~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri-~~i~d~vk------vGd~v~vkVl~VD~ekg~IdLS~   88 (319)
T PTZ00248         16 EEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRI-RSINKLIR------VGRHEVVVVLRVDKEKGYIDLSK   88 (319)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhccccc-CCHHHhcC------CCCEEEEEEEEEeCCCCEEEEEe
Confidence            37999999999999999999994   8999999999999887 88998887      99999999999999999999999


Q ss_pred             ec---chhhhcccccccccEEEe------eeeeEEEE------EecCCCceeEEEEEEccCcCcccccCcccccC---CC
Q 022938          175 KD---AVWNKYSSRVNVEDIFVG------RDYGAFIH------LRFPDGLYHLTGLVHVSEVSWDLIQDIRDILN---EG  236 (289)
Q Consensus       175 k~---~~~~~~~~~~~~G~iv~G------~~~G~fV~------i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~---iG  236 (289)
                      |+   .+|......++.|+++.|      ..+|+|++      ..  ++   ..++.|..++....+.++.+.|.   ++
T Consensus        89 K~v~~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~--pl---~~~~gh~y~af~~~v~~~~evl~~l~i~  163 (319)
T PTZ00248         89 KRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIW--PL---YKKYGHALDALKEALTNPDNVFEGLDIP  163 (319)
T ss_pred             eecccchHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHH--HH---HHhcCCHHHHHHHHhcCchhhhccCCCC
Confidence            96   489999999999999999      56999997      33  33   78888988887777777766665   67


Q ss_pred             CEEEEEEE
Q 022938          237 DEVRVKVI  244 (289)
Q Consensus       237 d~V~vkV~  244 (289)
                      +.+...++
T Consensus       164 ~ev~~~l~  171 (319)
T PTZ00248        164 EEVKESLL  171 (319)
T ss_pred             HHHHHHHH
Confidence            66655554

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

Probab=99.60  E-value=1.1e-13  Score=121.07  Aligned_cols=174  Identities=15%  Similarity=0.147  Sum_probs=138.5

Q ss_pred             ccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEEEEEEEE-cCcEEEE
Q 022938           40 IIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFN-GGGLLVR  118 (289)
Q Consensus        40 ~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~-~~G~~V~  118 (289)
                      .-.++||+|++.|.  -..++++.+|++.+.                          .++|+.-+++|+.+. +-|+||+
T Consensus        42 ~e~evGdev~vFiY--~D~~~rl~aTt~~p~--------------------------~tvg~~g~~~Vv~v~~~lGaFlD   93 (287)
T COG2996          42 DELEVGDEVTVFIY--VDSEDRLIATTREPK--------------------------ATVGEYGWLKVVEVNKDLGAFLD   93 (287)
T ss_pred             CccccCcEEEEEEE--ECCCCceeheeecce--------------------------EeecceeEEEEEEEcCCcceEEe
Confidence            35899999999984  345589999988654                          478999999999999 7899999


Q ss_pred             EC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeecchh-hhccccccc---ccEEE
Q 022938          119 FF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVW-NKYSSRVNV---EDIFV  193 (289)
Q Consensus       119 l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~~~~-~~~~~~~~~---G~iv~  193 (289)
                      +| .-+.++|.++++.... .+|          .+|+++-|.+. +|. ++|+...++...+ +........   ++.+.
T Consensus        94 ~Gl~KDl~vp~~elp~~~~-~wp----------q~Gd~l~v~l~-~Dk-k~Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~  160 (287)
T COG2996          94 WGLPKDLLVPLDELPTLKS-LWP----------QKGDKLLVYLY-VDK-KGRIWGTLAIEKILENLATPAYNNLKNQEVD  160 (287)
T ss_pred             cCCCcceeeehhhcccccc-cCC----------CCCCEEEEEEE-Ecc-CCcEEEEecchhHHHhcCCccchhhhcCeee
Confidence            99 9999999999976431 234          29999999985 885 4588888876533 344444444   77777


Q ss_pred             e-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHH
Q 022938          194 G-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLET  268 (289)
Q Consensus       194 G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~  268 (289)
                      |     ...|.||-++  +|   +.|++|.||..        ..++.||.++++|+.+.+ +++|.||++.+..+-.++-
T Consensus       161 ~tVYr~~~~G~fv~~e--~~---~~GfIh~sEr~--------~~prlG~~l~~rVi~~re-Dg~lnLSl~p~~~E~l~~d  226 (287)
T COG2996         161 ATVYRLLESGTFVITE--NG---YLGFIHKSERF--------AEPRLGERLTARVIGVRE-DGKLNLSLRPRAHEMLDED  226 (287)
T ss_pred             eEEEEEeccceEEEEc--CC---eEEEEcchhhc--------ccccCCceEEEEEEEEcc-CCeeecccccccHHhhhhh
Confidence            7     8899999885  54   99999999875        457899999999999997 9999999999866554443

>PRK08582 hypothetical protein; Provisional

Probab=99.54  E-value=6.4e-14  Score=113.76  Aligned_cols=97  Identities=36%  Similarity=0.617  Sum_probs=82.6

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  259 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~  259 (289)
                      .+++|++|.|     +++|+||+|.  +|   +.|+||++++++.++.++.+.|++||.|+|+|+++|. +++|.||+|+
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--EG---KTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKK   75 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEEC--CC---CEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence            3688999998     9999999995  54   9999999999999999999999999999999999997 5999999999


Q ss_pred             CCCCchhHHhh-----------h-hCCCChHHHHHHHhhh
Q 022938          260 LEEDPLLETLE-----------K-VIPQGLEPYLKSFYKK  287 (289)
Q Consensus       260 ~~~~p~~~~~~-----------~-~~~g~~~~~~~~~~~~  287 (289)
                      +.++||.+...           . -...+.+.-|+.|+|.
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~~l~~flk~  115 (139)
T PRK08582         76 AKDRPKRQHDRPRHEDNRGGGNDVAPKEDFEQKMSRFLKD  115 (139)
T ss_pred             cccCchhhccccccccccccccccccccCHHHHHHHHHHH
Confidence            99999975221           0 1125788888888874

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

Probab=99.52  E-value=1e-13  Score=100.34  Aligned_cols=72  Identities=28%  Similarity=0.497  Sum_probs=66.7

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      ++.|++++|+|.+++++|+||+++ +++||||.+++++.+. .+|.+.+.      +||+++|+|+++|.+++++.+|+|
T Consensus         2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~-~~~~~~~~------~G~~v~v~v~~vd~~~~~i~lS~k   74 (74)
T PF00575_consen    2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRI-DDPSEVYK------IGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEE-SSSHGTCE------TTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccc-cccccccC------CCCEEEEEEEEEECCCCeEEEEEC
Confidence            579999999999999999999999 9999999999998865 66777766      999999999999999999999986

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

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

Probab=99.49  E-value=1.2e-13  Score=100.25  Aligned_cols=70  Identities=23%  Similarity=0.439  Sum_probs=62.4

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcc---cchhcccccCCCCEEEEEEEEEecCCcEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQ---KSIHEIAKGLTGSIISVKVIQANEEMKKLVF  172 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~---~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~l  172 (289)
                      +++|+++.|+|+++.++|+||+++ +++|++|.++++|.+. .+|.   +.|+      +||.++|+|+++|++++++.|
T Consensus         1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~-~~~~~~~~~~~------~G~~v~~kVl~id~~~~~i~L   73 (74)
T cd05705           1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFV-SDPSLYNKYLP------EGKLLTAKVLSVNSEKNLVEL   73 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccc-cChhhHhcccC------CCCEEEEEEEEEECCCCEEec
Confidence            368999999999999999999998 9999999999999885 5543   4554      999999999999999999987


Q ss_pred             E
Q 022938          173 S  173 (289)
Q Consensus       173 S  173 (289)
                      |
T Consensus        74 S   74 (74)
T cd05705          74 S   74 (74)
T ss_pred             C
Confidence            6

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.

>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=99.45  E-value=1.8e-13  Score=99.28  Aligned_cols=66  Identities=26%  Similarity=0.446  Sum_probs=59.7

Q ss_pred             cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc---ccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~---~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      +++|+++.|     +++|+||+++  +|   +.|++|+++++|.++.++   .+.|++||.|+|+|+++|+++++|.||
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--SS---IVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeC--CC---CEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            478999999     9999999996  55   999999999999986664   588999999999999999999999886

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

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=99.45  E-value=2.1e-13  Score=130.69  Aligned_cols=142  Identities=15%  Similarity=0.222  Sum_probs=111.6

Q ss_pred             eEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhc--CCCEE
Q 022938           26 LSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKE--SGFIY  103 (289)
Q Consensus        26 ~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~G~iv  103 (289)
                      ..++|+++.-.+|.  +++|+.+.+.|...+.  +|+.++..+..      +.+.+    ++..++.+++.++  .|+++
T Consensus        73 ~eI~L~eAk~~~~~--~~vGD~ie~~I~~~~f--gRia~q~aKq~------i~Qki----re~ere~i~~eyk~~~GeIV  138 (470)
T PRK09202         73 KEISLEEARKIDPD--AEVGDYIEEEIESVDF--GRIAAQTAKQV------IVQKI----REAERERVYEEYKDRVGEII  138 (470)
T ss_pred             ceeeHHHHhhhCcc--ccCCCeEEEEEccccC--ChHHHHHHHHH------HHHHH----HHHHHHHHHHHHHhhcCCEE
Confidence            56778888777775  8999999999977663  66666643222      23333    4445556666665  99999


Q ss_pred             EEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc--EEEEEeecchhhh
Q 022938          104 EGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK--KLVFSEKDAVWNK  181 (289)
Q Consensus       104 ~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~--ri~lS~k~~~~~~  181 (289)
                      +|+|.++.++|++|+++|++||||.++++       |.+.++      +|++++|+|++++++++  ++.|||+...+..
T Consensus       139 ~G~V~ri~~~giiVDLggvea~LP~sE~i-------p~E~~~------~GdrIka~I~~Vd~~~kg~qIilSRt~p~~l~  205 (470)
T PRK09202        139 TGVVKRVERGNIIVDLGRAEAILPRKEQI-------PRENFR------PGDRVRAYVYEVRKEARGPQIILSRTHPEFLK  205 (470)
T ss_pred             EEEEEEEecCCEEEEECCeEEEecHHHcC-------CCccCC------CCCEEEEEEEEEecCCCCCeEEEEeCcHHHHH
Confidence            99999999999999999999999999985       444454      99999999999998877  9999999987777


Q ss_pred             cccccccccEEEe
Q 022938          182 YSSRVNVEDIFVG  194 (289)
Q Consensus       182 ~~~~~~~G~iv~G  194 (289)
                      .+...++-++..|
T Consensus       206 ~Lf~~EVPEI~~G  218 (470)
T PRK09202        206 KLFEQEVPEIADG  218 (470)
T ss_pred             HHHHHhCcccccC
Confidence            7777777777766

>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=99.44  E-value=6.1e-13  Score=96.26  Aligned_cols=70  Identities=20%  Similarity=0.310  Sum_probs=62.5

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCc-cCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSH-SCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~-~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      |++++|+|+++.++|+||.++ +++|+||.+++++.. ...+|.+.|+      +||.++|+|+++|++++++.||.+
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 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFP------IGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCC------CCCEEEEEEEEEeCCCCEEEEEec
Confidence            789999999999999999998 999999999999763 1256666665      999999999999999999999986

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.

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

Probab=99.43  E-value=1.3e-13  Score=106.94  Aligned_cols=73  Identities=22%  Similarity=0.365  Sum_probs=68.8

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      +++|.+++|+|+++.+||+||++. |-+|++|+||+++.++ +|..+.+.      +||.|.|+|+++|. ++++.||+|
T Consensus         3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fV-kdI~d~L~------vG~eV~vKVl~ide-~GKisLSIr   74 (129)
T COG1098           3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFV-KDIHDHLK------VGQEVKVKVLDIDE-NGKISLSIR   74 (129)
T ss_pred             ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhH-HhHHHHhc------CCCEEEEEEEeecc-CCCcceehH
Confidence            579999999999999999999999 8999999999999998 88888887      99999999999996 999999999


Q ss_pred             cc
Q 022938          176 DA  177 (289)
Q Consensus       176 ~~  177 (289)
                      ..
T Consensus        75 ~~   76 (129)
T COG1098          75 KL   76 (129)
T ss_pred             Hh
Confidence            74

>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=99.42  E-value=7.5e-13  Score=98.12  Aligned_cols=72  Identities=22%  Similarity=0.448  Sum_probs=66.4

Q ss_pred             hhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           96 YKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        96 ~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      .++.|+++.|+|+++.++|+||+++ +++||+|.+++++.+. .+|.+.++      +||.++|+|.++|.+++++.+|+
T Consensus        11 ~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~-~~~~~~~~------~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461          11 DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFV-TDPSFGFK------KGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             hCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccc-cCHHHhcC------CCCEEEEEEEEEcCCCCEEEEeC
Confidence            3789999999999999999999998 8999999999999876 67777776      99999999999999999999985

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.

>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=99.42  E-value=7.9e-13  Score=94.60  Aligned_cols=69  Identities=30%  Similarity=0.618  Sum_probs=63.3

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      |++++|+|+++.++|+||+++ +++||+|.+++++.+. .+|.+.++      +||.++|+|+++|++++++.||++
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 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFI-KDPEEHFR------VGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhc-CCHHHccc------CCCEEEEEEEEEcCCCCEEEEEeC
Confidence            789999999999999999998 8999999999998775 67776665      999999999999999999999985

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.

>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=99.40  E-value=6.8e-13  Score=98.34  Aligned_cols=74  Identities=31%  Similarity=0.434  Sum_probs=67.5

Q ss_pred             hhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeE
Q 022938          179 WNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRI  253 (289)
Q Consensus       179 ~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri  253 (289)
                      ....+.++++|+++.|     .++|+||+++  +|   +.|++|.+++++++..++.+.|++||.|+|+|+++|++++++
T Consensus         5 l~~~~~~~~~G~i~~g~V~~v~~~G~fv~l~--~~---~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i   79 (83)
T cd04461           5 LPTNFSDLKPGMVVHGYVRNITPYGVFVEFL--GG---LTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF   79 (83)
T ss_pred             chhhHHhCCCCCEEEEEEEEEeeceEEEEcC--CC---CEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEE
Confidence            3445677999999999     9999999995  54   999999999999999999999999999999999999999999


Q ss_pred             EEEE
Q 022938          254 TLSI  257 (289)
Q Consensus       254 ~lSl  257 (289)
                      .||+
T Consensus        80 ~lsl   83 (83)
T cd04461          80 LLSL   83 (83)
T ss_pred             EEeC
Confidence            9985

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.

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

Probab=99.40  E-value=1.5e-12  Score=93.00  Aligned_cols=68  Identities=24%  Similarity=0.490  Sum_probs=61.8

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      |++++|+|+++.++|+||+++ +++||+|.+++++.+. .+|.+.++      +||.++|+|+++|.+++++.||+
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 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRL-KHPEKKFK------PGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccc-cCHHHcCC------CCCEEEEEEEEEECCCCEEEEEC
Confidence            789999999999999999998 8999999999998775 66666665      99999999999999999999985

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.

>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=99.40  E-value=2.4e-12  Score=93.37  Aligned_cols=68  Identities=15%  Similarity=0.297  Sum_probs=61.0

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      ++.|++++|+|++++++|+||+++  |++||+|.+++++.       +.+      .+||.+.|+|+++|++++++.||+
T Consensus         2 l~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~-------~~~------~~Gq~v~~~V~~vd~~~~~v~ls~   68 (74)
T cd05694           2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKL------KVGQLLLCVVEKVKDDGRVVSLSA   68 (74)
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc-------ccc------CCCCEEEEEEEEEECCCCEEEEEE
Confidence            478999999999999999999997  79999999999864       223      399999999999999999999999


Q ss_pred             ecc
Q 022938          175 KDA  177 (289)
Q Consensus       175 k~~  177 (289)
                      ++.
T Consensus        69 k~~   71 (74)
T cd05694          69 DPS   71 (74)
T ss_pred             eec
Confidence            864

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.

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

Probab=99.39  E-value=1.2e-12  Score=94.59  Aligned_cols=69  Identities=45%  Similarity=0.776  Sum_probs=63.7

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      ++++|+++.|     .++|+||+++  +|   +.|++|.+++++.+..++...|++||+++|+|+++|++++++.||+|
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--NG---IEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             -SSTTSEEEEEEEEEETTEEEEEES--TS---SEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEEC--Cc---EEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            3688999999     8899999996  44   99999999999999999999999999999999999999999999986

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 ....

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

Probab=99.39  E-value=2.4e-12  Score=93.33  Aligned_cols=68  Identities=18%  Similarity=0.212  Sum_probs=60.9

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  259 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~  259 (289)
                      +++.|+++.|     .++|+||+++ .+|   +.||+|.++++|.      +.+++||.+.|+|+++|++++++.||+|+
T Consensus         1 dl~~G~~v~g~V~si~d~G~~v~~g-~~g---v~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~   70 (74)
T cd05694           1 DLVEGMVLSGCVSSVEDHGYILDIG-IPG---TTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADP   70 (74)
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEeC-CCC---cEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            4688999999     9999999995 234   9999999999976      67999999999999999999999999999


Q ss_pred             CCC
Q 022938          260 LEE  262 (289)
Q Consensus       260 ~~~  262 (289)
                      +.+
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.

>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=99.38  E-value=1.4e-12  Score=94.32  Aligned_cols=65  Identities=17%  Similarity=0.331  Sum_probs=59.3

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccc--ccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~--~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      |+++.|     .++|+||.++  +|   +.|++|.+++++..  .+++.+.|++||.|+|+|+++|+++++|.||+|
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--PD---VKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeC--CC---cEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            677777     8999999996  55   99999999999864  788999999999999999999999999999987

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.

>PRK05807 hypothetical protein; Provisional

Probab=99.38  E-value=3.6e-12  Score=103.17  Aligned_cols=96  Identities=40%  Similarity=0.611  Sum_probs=78.4

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  259 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~  259 (289)
                      .+++|+++.|     +++|+||++   +|   ..|++|++++++.++.++.+.|++||.|+|+|+++|+ +++|.||+|.
T Consensus         2 ~~~vG~vv~G~Vt~i~~~GafV~L---~~---~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~   74 (136)
T PRK05807          2 TLKAGSILEGTVVNITNFGAFVEV---EG---KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQ   74 (136)
T ss_pred             CccCCCEEEEEEEEEECCeEEEEE---CC---EEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEe
Confidence            4678999998     999999999   34   8999999999999999999999999999999999998 7999999999


Q ss_pred             CC-CCc--------hhHHhhhhCCCChHHHHHHHhhh
Q 022938          260 LE-EDP--------LLETLEKVIPQGLEPYLKSFYKK  287 (289)
Q Consensus       260 ~~-~~p--------~~~~~~~~~~g~~~~~~~~~~~~  287 (289)
                      +. +.|        |.....+....+.+.-|..|++.
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  111 (136)
T PRK05807         75 AMKQKKSVKPAEIDWQKEKNKNNNGNFEDRLSKFLKD  111 (136)
T ss_pred             ccccccccCccccccccccccCCCcCHHHHHHHHHHH
Confidence            86 222        12111222335888889998874

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

Probab=99.37  E-value=3.8e-12  Score=90.38  Aligned_cols=67  Identities=28%  Similarity=0.469  Sum_probs=59.6

Q ss_pred             CCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938          100 GFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      |++++|+|+++.++|++|+++|++||||.+++++.+. .+|.+        .+||.++|+|+++|.+++++.+|++
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 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPV-EDLDE--------YVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCccc-CChHH--------hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            7899999999999999999999999999999997664 44422        3899999999999999999999985

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.

>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=99.37  E-value=6.3e-12  Score=90.67  Aligned_cols=71  Identities=18%  Similarity=0.201  Sum_probs=64.1

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      +.|+++.|+|+++.++|+||+++ +++|++|.+++++.+. .++.+.++      +||.++|+|+++|.+++++.||.+
T Consensus         2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~-~~~~~~~~------~Gd~v~~~V~~~d~~~~~i~ls~~   73 (73)
T cd05706           2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYS-EALPYKFK------KNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccc-cccccccC------CCCEEEEEEEEEeCCCCEEEEEEC
Confidence            58999999999999999999999 9999999999998774 55656565      999999999999999999999974

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=99.36  E-value=2.4e-12  Score=101.95  Aligned_cols=72  Identities=39%  Similarity=0.753  Sum_probs=66.3

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  261 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~  261 (289)
                      ++|+++.|     .++|+||++.  +|   +.|++|.+++++.++.++.+.|++||.|+|+|+++|++++++.||+|.++
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~--~~---~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~   76 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALE--NG---TTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLE   76 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEEC--CC---CEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence            57888888     8999999995  44   99999999999999989989999999999999999999999999999997


Q ss_pred             CC
Q 022938          262 ED  263 (289)
Q Consensus       262 ~~  263 (289)
                      ++
T Consensus        77 ~~   78 (120)
T PRK07252         77 EE   78 (120)
T ss_pred             cC
Confidence            63

>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=99.35  E-value=4e-12  Score=91.46  Aligned_cols=68  Identities=16%  Similarity=0.239  Sum_probs=60.9

Q ss_pred             CCEEE-EEEEEE-EcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938          100 GFIYE-GKIQGF-NGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus       100 G~iv~-g~V~~v-~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      |++++ |+|+++ .++|+||++. |++||+|.+++++.+. .++.+.++      +||.++|+|+++|+.++++.||+
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~-~~~~~~~~------vG~~v~~kV~~id~~~~~i~lS~   71 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKV-PSDTGPFK------AGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchh-cCcccccC------CCCEEEEEEEEEeCCCCEEEEeC
Confidence            78899 999999 6999999998 9999999999998775 55666665      99999999999999999999985

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.

>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=99.34  E-value=2.8e-12  Score=92.56  Aligned_cols=66  Identities=21%  Similarity=0.299  Sum_probs=59.5

Q ss_pred             cccccEEEe-----e-eeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          186 VNVEDIFVG-----R-DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       186 ~~~G~iv~G-----~-~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      +++|+++.|     . ++|+|+++.  +|   ..|++|++++++++..++.+.|++||.|+|+|+++|.  +++.||+|
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--FG---KTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR   72 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECC--CC---CEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEeC
Confidence            468999999     4 489999995  55   9999999999999999999999999999999999984  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.

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

Probab=99.34  E-value=7.3e-12  Score=90.91  Aligned_cols=70  Identities=34%  Similarity=0.518  Sum_probs=63.1

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  259 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~  259 (289)
                      ++|+++.|     .++|+||++...+|   +.|++|.+++++.+..++.+.|++||.|+|+|.++|.+++++.||+|+
T Consensus         2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~---~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~   76 (76)
T cd04452           2 EEGELVVVTVKSIADMGAYVSLLEYGN---IEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             CCCCEEEEEEEEEEccEEEEEEcCCCC---eEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence            57888888     89999999952223   899999999999999999999999999999999999999999999985

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

>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=99.34  E-value=4.4e-12  Score=90.30  Aligned_cols=67  Identities=15%  Similarity=0.299  Sum_probs=61.2

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      |+++.|+|+++.++|+||+++ +++||+|.+++++.+. .+|.+.++      +||.++|+|+++|++++++.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYL-KDWKKRFK------VGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhh-cCHhhccC------CCCEEEEEEEEEeCCCCEEecC
Confidence            789999999999999999998 8999999999998876 67776665      9999999999999999999876

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.33  E-value=2.9e-12  Score=129.71  Aligned_cols=84  Identities=30%  Similarity=0.491  Sum_probs=76.0

Q ss_pred             cccccccccEEE-e-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 022938          182 YSSRVNVEDIFV-G-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL  255 (289)
Q Consensus       182 ~~~~~~~G~iv~-G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~l  255 (289)
                      .....++|+++. |     .+||+||+|.  +|   ++||||+|+++|+++.++.+.|++||.|+|+|+++|+ ++||.|
T Consensus       747 l~~~~~vG~iy~~g~V~~I~~FGaFVeL~--~g---~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~L  820 (891)
T PLN00207        747 LTMVPTVGDIYRNCEIKSIAPYGAFVEIA--PG---REGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRL  820 (891)
T ss_pred             HhcCcCCCcEEECcEEEEEeccEEEEEeC--CC---CEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEE
Confidence            344578999995 4     9999999996  55   9999999999999999999999999999999999997 899999


Q ss_pred             EEecCCCCchhHHhhh
Q 022938          256 SIKQLEEDPLLETLEK  271 (289)
Q Consensus       256 SlK~~~~~p~~~~~~~  271 (289)
                      |+|++.++||++...+
T Consensus       821 SlK~l~~~Pw~~~~~~  836 (891)
T PLN00207        821 SRRALLPEANSEKSSQ  836 (891)
T ss_pred             EEeccccCchhhhhhh
Confidence            9999999999998763

>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=99.33  E-value=5.2e-12  Score=91.13  Aligned_cols=69  Identities=20%  Similarity=0.347  Sum_probs=62.4

Q ss_pred             cCCCEEEEEEEEEEc-CcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           98 ESGFIYEGKIQGFNG-GGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~-~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      ++|+++.|+|+++.+ +|+||+++ |.+|++|.+++++.+. .+|.+.++      +||.++|+|+++|.  +++.||++
T Consensus         2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~-~~~~~~~~------~Gd~v~~kV~~~~~--~~i~LSl~   72 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYT-ENPLEGFK------PGKIVRCCILSKKD--GKYQLSLR   72 (72)
T ss_pred             CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCccc-CCHHHhCC------CCCEEEEEEEEecC--CEEEEEeC
Confidence            589999999999986 89999999 9999999999999886 77777676      99999999999974  89999985

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=99.32  E-value=8.8e-12  Score=89.91  Aligned_cols=68  Identities=25%  Similarity=0.406  Sum_probs=62.0

Q ss_pred             cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      +++|+++.|     .++|+||++.  +|   +.|++|.+++++++..++.+.|++||.|+|+|+++|++++++.||+|
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--NK---VTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeC--CC---cEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            468999988     8999999996  55   99999999999988778888999999999999999999999999985

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

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

Probab=99.32  E-value=1.1e-11  Score=89.63  Aligned_cols=69  Identities=22%  Similarity=0.314  Sum_probs=62.1

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECC--EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFS--LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~g--v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      +.|++++|+|+++.++|+||++.|  .+||+|.+++++.+. .+|.+.++      +||+++|+|+++|.++ ++.||+
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~-~~~~~~~~------~Gd~v~vkv~~vd~~~-ki~ls~   72 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRV-DDPSEVVD------VGEKVWVKVIGREMKD-KMKLSL   72 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcc-cCHhhEEC------CCCEEEEEEEEECCCC-cEEEEe
Confidence            479999999999999999999975  799999999999876 77777776      9999999999999876 888886

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.

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

Probab=99.32  E-value=9.5e-12  Score=89.00  Aligned_cols=69  Identities=20%  Similarity=0.392  Sum_probs=63.5

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      |++++|+|.++.++|++|+++ +.+|++|.+++++.+. .+|.+.++      +||.++|+|+++|++++++.||++
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~-~~~~~~~~------~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPI-ENGEDEVK------VGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCcccc-CCHhHcCC------CCCEEEEEEEEEECCCCeEEEEeC
Confidence            789999999999999999998 8999999999998876 77777776      999999999999988899999985

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.

>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=99.32  E-value=4.8e-12  Score=90.51  Aligned_cols=65  Identities=29%  Similarity=0.425  Sum_probs=59.4

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      |+++.|     .++|+||++.  +|   +.||+|.+++++++..++.+.|++||.++|+|+++|++++++.||+|
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~--~~---~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k   70 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFY--NN---VKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEEC--CC---CEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            567777     8999999995  44   99999999999998889999999999999999999999999999986

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.

>TIGR01953 NusA transcription termination factor NusA

Probab=99.31  E-value=4.7e-12  Score=116.97  Aligned_cols=143  Identities=19%  Similarity=0.248  Sum_probs=106.3

Q ss_pred             eeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhh--cCCCE
Q 022938           25 SLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYK--ESGFI  102 (289)
Q Consensus        25 ~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~G~i  102 (289)
                      ...++|+++.-.+|+  +++||.+.+.+...+  -+|+.++..+.+      +.+.++++    .++.+++.+  +.|++
T Consensus        69 ~~ei~l~~A~~~d~~--~~vGD~I~~~I~~~~--fgR~aaq~aKqv------i~Qkire~----ere~i~~ey~~k~Gei  134 (341)
T TIGR01953        69 SLEISLEDAREIDPD--VQIGDEVKKEIPPEN--FGRIAAQTAKQV------ILQKIREA----ERERVYDEFSSKEGEI  134 (341)
T ss_pred             cccccHHHHHhhccc--cccCCEEEEEecccC--CCHHHHHHHHHH------HHHHHHHH----HHHHHHHHHHhhcCCE
Confidence            356888999888885  999999999884332  256555543322      33344444    455555555  59999


Q ss_pred             EEEEEEEEEcCc-EEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC--cEEEEEeecchh
Q 022938          103 YEGKIQGFNGGG-LLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM--KKLVFSEKDAVW  179 (289)
Q Consensus       103 v~g~V~~v~~~G-~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~--~ri~lS~k~~~~  179 (289)
                      ++|+|.++.++| ++|++|+++||||.+|+..       .+.+.      +|++++|.|++++.+.  .++.+|++.+.+
T Consensus       135 V~G~V~~v~~~g~v~VdiG~~ea~LP~~E~ip-------~E~~~------~Gd~ik~~V~~V~~~~kg~qIivSRt~~~~  201 (341)
T TIGR01953       135 ISGTVKRVNRRGNLYVELGKTEGILPKKEQIP-------GEKFR------IGDRIKAYVYEVRKTAKGPQIILSRTHPEF  201 (341)
T ss_pred             EEEEEEEEecCCcEEEEECCeEEEecHHHcCC-------CcCCC------CCCEEEEEEEEEEcCCCCCeEEEEeCcHHH
Confidence            999999999988 6999999999999999763       33343      9999999999999553  589999999877


Q ss_pred             hhcccccccccEEEe
Q 022938          180 NKYSSRVNVEDIFVG  194 (289)
Q Consensus       180 ~~~~~~~~~G~iv~G  194 (289)
                      ...+.+.++-++..|
T Consensus       202 v~~Lfe~EVPEI~dG  216 (341)
T TIGR01953       202 VKELLKLEVPEIADG  216 (341)
T ss_pred             HHHHHHHhCccccCC
Confidence            766666666666665

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.

>PRK08059 general stress protein 13; Validated

Probab=99.30  E-value=1.1e-11  Score=98.68  Aligned_cols=77  Identities=45%  Similarity=0.809  Sum_probs=71.1

Q ss_pred             ccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          183 SSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       183 ~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      ++++++|+++.|     .++|+||++.  ++   +.|++|.+++++.+..++.+.|++||.|+|+|.++|++++++.||+
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--EE---TQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSI   76 (123)
T ss_pred             cccCCCCCEEEEEEEEEecceEEEEEC--CC---CEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEE
Confidence            456889999999     8999999996  54   9999999999999888888899999999999999999999999999


Q ss_pred             ecCCCCc
Q 022938          258 KQLEEDP  264 (289)
Q Consensus       258 K~~~~~p  264 (289)
                      |.+..+|
T Consensus        77 k~~~~~~   83 (123)
T PRK08059         77 RATEEAP   83 (123)
T ss_pred             EEcccCc
Confidence            9999888

>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=99.29  E-value=8.8e-12  Score=89.67  Aligned_cols=58  Identities=29%  Similarity=0.479  Sum_probs=54.0

Q ss_pred             eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       195 ~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      .++|+||++.  +|   +.||+|.|++++.+.+++.+.|++||.++|+|+++|++++++.||+
T Consensus        14 ~~~G~~V~l~--~g---v~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~   71 (71)
T cd05696          14 PDLGAVFELK--DG---LLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             cCceEEEEeC--CC---CEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            4799999995  55   9999999999999988899999999999999999999999999995

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.

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

Probab=99.29  E-value=1.4e-11  Score=89.07  Aligned_cols=66  Identities=35%  Similarity=0.615  Sum_probs=58.6

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      +.|+++.|     .+||+||++.   | +..+||+|++++++.++.++.+.|++||.|+|+|+++|.++ ++.||+
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~---~-~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~   72 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIP---G-CRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL   72 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEEC---C-CCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence            47888888     9999999993   2 12699999999999999999999999999999999999965 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.

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

Probab=99.29  E-value=2.7e-11  Score=87.93  Aligned_cols=72  Identities=21%  Similarity=0.320  Sum_probs=65.1

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      +.|+++.|+|+++.++|+||++.   |++|++|.+++++.+. .+|.+.++      +||.++|+|.++|.+.+++.+|+
T Consensus         2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~-~~~~~~~~------~Gd~v~vkv~~~d~~~~~i~ls~   74 (76)
T cd04452           2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRI-RSIRKLVK------VGRKEVVKVIRVDKEKGYIDLSK   74 (76)
T ss_pred             CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCccc-CCHHHeeC------CCCEEEEEEEEEECCCCEEEEEE
Confidence            47999999999999999999995   4999999999998876 77777776      99999999999999899999998


Q ss_pred             ec
Q 022938          175 KD  176 (289)
Q Consensus       175 k~  176 (289)
                      ++
T Consensus        75 k~   76 (76)
T cd04452          75 KR   76 (76)
T ss_pred             cC
Confidence            74

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

>PHA02945 interferon resistance protein; Provisional

Probab=99.29  E-value=1.8e-11  Score=89.57  Aligned_cols=72  Identities=31%  Similarity=0.409  Sum_probs=64.5

Q ss_pred             ccccEEEe----eeeeEEEEEecCCCceeEEEEEEccCc--CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938          187 NVEDIFVG----RDYGAFIHLRFPDGLYHLTGLVHVSEV--SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  260 (289)
Q Consensus       187 ~~G~iv~G----~~~G~fV~i~~~~G~~~i~Glv~~sel--s~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~  260 (289)
                      ++|+++.|    .++|+||.+...+   +..||+|+|+.  +..++++ ++.+ .||++.|+|+.+|+.++.|.||+|+.
T Consensus        10 ~~GelvigtV~~~d~ga~v~L~EY~---g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~V   84 (88)
T PHA02945         10 NVGDVLKGKVYENGYALYIDLFDYP---HSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKRM   84 (88)
T ss_pred             CCCcEEEEEEEecCceEEEEecccC---CcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeEc
Confidence            67888888    8999999996444   49999999955  9999999 9999 99999999999999999999999998


Q ss_pred             CCC
Q 022938          261 EED  263 (289)
Q Consensus       261 ~~~  263 (289)
                      ..+
T Consensus        85 ~~~   87 (88)
T PHA02945         85 CRH   87 (88)
T ss_pred             ccC
Confidence            654

>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=99.29  E-value=1.2e-11  Score=88.32  Aligned_cols=64  Identities=23%  Similarity=0.463  Sum_probs=58.3

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      |+++.|     .++|+||+++  +|   +.|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+
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--DH---IKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEec--CC---cEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            566777     8999999995  55   9999999999999888888999999999999999999999999985

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.

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

Probab=99.28  E-value=2.3e-11  Score=87.50  Aligned_cols=70  Identities=21%  Similarity=0.397  Sum_probs=64.3

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD  176 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~  176 (289)
                      |+++.|+|+++.++|++|+++ +++|++|.+++++.+. .+|.+.++      +||.++|+|+++|.+++++.+|++.
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~-~~~~~~~~------~Gd~v~~~v~~~d~~~~~i~ls~k~   71 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRV-EDATERFK------VGDEVEAKITNVDRKNRKISLSIKA   71 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccc-cCHHHccC------CCCEEEEEEEEEeCCCCEEEEEEEE
Confidence            789999999999999999998 8999999999998875 67777766      9999999999999999999999986

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.

>PRK07252 hypothetical protein; Provisional

Probab=99.27  E-value=3e-11  Score=95.63  Aligned_cols=73  Identities=18%  Similarity=0.272  Sum_probs=66.7

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD  176 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~  176 (289)
                      +.|+++.|+|+++.++|+||+++ ++.|++|.+++++.+. .++.+.++      +||.|+|+|+++|.+.+++.+|++.
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~-~~~~~~~~------vGD~V~VkI~~iD~~~~ri~lSlk~   74 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFI-DNIHQLLK------VGEEVLVQVVDFDEYTGKASLSLRT   74 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccc-cChhhccC------CCCEEEEEEEEEeCCCCEEEEEEee
Confidence            57999999999999999999998 8999999999998876 66666665      9999999999999999999999997


Q ss_pred             c
Q 022938          177 A  177 (289)
Q Consensus       177 ~  177 (289)
                      .
T Consensus        75 ~   75 (120)
T PRK07252         75 L   75 (120)
T ss_pred             c
Confidence            5

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

Probab=99.26  E-value=2e-11  Score=86.89  Aligned_cols=68  Identities=18%  Similarity=0.377  Sum_probs=59.5

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      |+++.|+|+++.++|+||+++ +++|++|.++++|.....+|.+.++      +||.|+|+|.++|.+++++.+|
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~------~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYK------KGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEEC------CCCEEEEEEEEEECCcCEEeCC
Confidence            789999999999999999998 8999999999996432366666665      9999999999999999998774

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=99.26  E-value=1.2e-11  Score=114.92  Aligned_cols=144  Identities=19%  Similarity=0.222  Sum_probs=109.5

Q ss_pred             eEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEE
Q 022938           26 LSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEG  105 (289)
Q Consensus        26 ~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g  105 (289)
                      ..++|+++.-.+|+  .++|+.+...+...+.  +|+.+..      ++..+.+.++++.+...|+++.+  +.|++++|
T Consensus        73 ~eisL~eAk~i~~~--~~vGD~i~~~I~~~~f--gR~aaq~------akqvI~Qkire~ere~v~~ef~~--k~GeiV~G  140 (362)
T PRK12327         73 LEISLEDALAINPA--YELGDVIEIEVTPKDF--GRIAAQT------AKQVIMQRLREAEREIIYNEFSE--REGDIVTG  140 (362)
T ss_pred             ccccHHHHhhhCcc--ccCCCEEEEecCcCCC--ChHHHHH------HHHHHHHHHHHHHHHHHHHHHHH--hcCCEEEE
Confidence            45678888777774  9999999998854443  4544442      23335566777777777766555  69999999


Q ss_pred             EEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc--EEEEEeecchhhhcc
Q 022938          106 KIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK--KLVFSEKDAVWNKYS  183 (289)
Q Consensus       106 ~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~--ri~lS~k~~~~~~~~  183 (289)
                      +|.++.++|++|++|+++||||.+++.       |++.++      +|++++|.|.+++.+.+  ++.+||..+.+...+
T Consensus       141 ~V~~~~~~~~~Vdlg~vEa~LP~~E~i-------p~e~~~------~Gd~Ika~V~~V~~~~kgp~IivSRt~p~~v~~L  207 (362)
T PRK12327        141 VVQRRDNRFVYVNLGKIEAVLPPAEQI-------PGETYK------HGDRIKVYVVKVEKTTKGPQIFVSRTHPGLVKRL  207 (362)
T ss_pred             EEEEEeCCcEEEEeCCeEEEecHHHcC-------CCCCCC------CCCEEEEEEEEEecCCCCCeEEEEeCCHHHHHHH
Confidence            999999999999999999999988864       334444      99999999999996543  799999988776666


Q ss_pred             cccccccEEEe
Q 022938          184 SRVNVEDIFVG  194 (289)
Q Consensus       184 ~~~~~G~iv~G  194 (289)
                      ...++-++..|
T Consensus       208 fe~EVPEI~~G  218 (362)
T PRK12327        208 FELEVPEIYDG  218 (362)
T ss_pred             HHHhCccccCC
Confidence            66666666665

>PRK08582 hypothetical protein; Provisional

Probab=99.26  E-value=3.7e-11  Score=97.59  Aligned_cols=73  Identities=23%  Similarity=0.361  Sum_probs=66.3

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      ++.|+++.|+|++++++|+||+++ +++|+||.+++++.+. .++.+.++      +||.|+|+|+++|. .++|.||++
T Consensus         3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v-~~~~~~l~------vGD~VkvkV~~id~-~gkI~LSlk   74 (139)
T PRK08582          3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYV-KDINDHLK------VGDEVEVKVLNVED-DGKIGLSIK   74 (139)
T ss_pred             CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccc-cccccccC------CCCEEEEEEEEECC-CCcEEEEEE
Confidence            579999999999999999999999 8999999999999886 67766665      99999999999996 489999999


Q ss_pred             cc
Q 022938          176 DA  177 (289)
Q Consensus       176 ~~  177 (289)
                      +.
T Consensus        75 ~~   76 (139)
T PRK08582         75 KA   76 (139)
T ss_pred             ec
Confidence            74

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

Probab=99.25  E-value=2.8e-11  Score=86.98  Aligned_cols=68  Identities=37%  Similarity=0.624  Sum_probs=61.5

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  261 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~  261 (289)
                      |+++.|     .++|+||++.  ++   +.|++|.+++++++..++.+.|++||.++|+|+++|++++++.||+|..+
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--DG---VEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE   73 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeC--CC---CEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEcC
Confidence            566666     8999999996  44   99999999999999889999999999999999999999999999999863

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.

>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=99.25  E-value=3.3e-11  Score=87.47  Aligned_cols=70  Identities=41%  Similarity=0.675  Sum_probs=62.8

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  260 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~  260 (289)
                      ++|+++.|     .++|+||++.  +.  +..|++|.+++++++..++.+.|++||.|+|+|.++|++++++.||+|..
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 KVGQKIDGTVRRVEDYGVFIDID--GT--NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEEC--CC--CeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            35788888     9999999995  21  39999999999999888888999999999999999999999999999975

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.

>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=99.25  E-value=6.1e-11  Score=86.09  Aligned_cols=72  Identities=17%  Similarity=0.327  Sum_probs=65.0

Q ss_pred             CCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938           99 SGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD  176 (289)
Q Consensus        99 ~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~  176 (289)
                      .|+++.|+|+++.++|+||++.  +..|++|.+++++.+. .+|.+.++      +||.|+|+|.++|.+.+++.+|++.
T Consensus         2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~-~~~~~~~~------~Gd~v~v~i~~vd~~~~~i~ls~k~   74 (77)
T cd05708           2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRV-ADASKLFR------VGDKVRAKVLKIDAEKKRISLGLKA   74 (77)
T ss_pred             CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCcc-CCHhHeec------CCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            6999999999999999999997  5999999999998775 66666665      9999999999999999999999987


Q ss_pred             c
Q 022938          177 A  177 (289)
Q Consensus       177 ~  177 (289)
                      +
T Consensus        75 ~   75 (77)
T cd05708          75 S   75 (77)
T ss_pred             e
Confidence            4

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.

>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=99.24  E-value=1.9e-11  Score=87.01  Aligned_cols=63  Identities=30%  Similarity=0.534  Sum_probs=57.3

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      |+++.|     .++|+||++.  +|   +.|++|.+++++++..++.+.|++||.|+|+|+++|++++++.||
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--RG---VDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeC--CC---CEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            566666     8999999995  44   999999999999999999999999999999999999999999886

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.

>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=99.22  E-value=5.7e-11  Score=84.20  Aligned_cols=65  Identities=18%  Similarity=0.459  Sum_probs=56.2

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      |++++|+|+++.++|++|++. +++||+|.++++..+. .  .+.+      .+|+.++|+|+++|++++++.||
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 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKS-S--KSTY------KEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccC-c--ccCc------CCCCEEEEEEEEEeCCCCEEecC
Confidence            789999999999999999997 8999999999975442 1  3334      49999999999999999998876

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.

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

Probab=99.22  E-value=3.2e-11  Score=85.84  Aligned_cols=63  Identities=38%  Similarity=0.796  Sum_probs=55.5

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCc-ccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~-~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      |+++.|     .++|+||++.  +|   ++|++|.++++| .+..++.+.|++||.|+|+|+++|+++++|.||
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--GG---IDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeC--CC---CEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence            556666     9999999996  54   999999999997 467788889999999999999999999999875

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.

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

Probab=99.22  E-value=6.6e-11  Score=85.06  Aligned_cols=70  Identities=20%  Similarity=0.356  Sum_probs=60.0

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      .+|+++.|+|+++.++|+||+++ +++|++|.+++++.....++.+.++      +||.++|+|.++|.+++++.++
T Consensus         2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~------~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVS------LGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeC------CCCEEEEEEEEeeCCcCEEeCC
Confidence            58999999999999999999998 8999999999986522235555555      9999999999999998888764

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.

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

Probab=99.22  E-value=1.1e-11  Score=108.16  Aligned_cols=83  Identities=34%  Similarity=0.623  Sum_probs=73.8

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  261 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~  261 (289)
                      .+|++|-|     .+||+||.|...+|   +.||+|+||++..++++++++++.||.+-|+|+++|++++.|.||+|.+.
T Consensus        10 eeGEiVv~tV~~V~~~GAyv~L~EY~g---~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~   86 (269)
T COG1093          10 EEGEIVVGTVKQVADYGAYVELDEYPG---KEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVT   86 (269)
T ss_pred             CCCcEEEEEEEEeeccccEEEeeccCC---eeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCC
Confidence            67888888     89999999986665   99999999999999999999999999999999999999999999999998


Q ss_pred             CCchhHHhhhh
Q 022938          262 EDPLLETLEKV  272 (289)
Q Consensus       262 ~~p~~~~~~~~  272 (289)
                      ++.-.+.++.+
T Consensus        87 ~~q~~~k~~~w   97 (269)
T COG1093          87 EHQRRKKIQEW   97 (269)
T ss_pred             HHHHHHHHHHH
Confidence            76655544443

>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=99.21  E-value=9.6e-11  Score=85.88  Aligned_cols=71  Identities=35%  Similarity=0.665  Sum_probs=61.0

Q ss_pred             ccEEEe-----eeeeEEEEEecC-CCceeEEEEEEccCcCcccc-cCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938          189 EDIFVG-----RDYGAFIHLRFP-DGLYHLTGLVHVSEVSWDLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  261 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~-~G~~~i~Glv~~sels~~~~-~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~  261 (289)
                      |+++.|     .++|+||+++.. +|   ..|++|.+++++.+. .++.+.|++||.|+|+|.++|  ++++.+|+|+++
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~---~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k~~~   75 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGR---KEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKDVD   75 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCC---cEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEEecc
Confidence            456666     899999999511 13   899999999999986 888899999999999999999  799999999988


Q ss_pred             CCc
Q 022938          262 EDP  264 (289)
Q Consensus       262 ~~p  264 (289)
                      ++.
T Consensus        76 ~~~   78 (79)
T cd05684          76 QDT   78 (79)
T ss_pred             cCC
Confidence            753

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.

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

Probab=99.18  E-value=1.2e-10  Score=82.33  Aligned_cols=68  Identities=21%  Similarity=0.381  Sum_probs=61.1

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      |+++.|+|+++.++|+||+++ +..||+|.+++++.+. .+|.+.++      +||.++++|.++|. .+++.+|++
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRV-KDVKDVLK------EGDKVKVKVLSIDA-RGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCccc-CCHHHccC------CCCEEEEEEEEECC-CCcEEEEEC
Confidence            789999999999999999999 9999999999998775 66666565      99999999999998 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.

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

Probab=99.18  E-value=1.1e-10  Score=82.42  Aligned_cols=68  Identities=25%  Similarity=0.444  Sum_probs=60.8

Q ss_pred             CCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           99 SGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        99 ~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      .|++++|+|.++.++|++|++++.+|++|.+++++.+. .+|.+.++      +||.++|+|.++|.+++++.+|
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 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRV-KHPSEVVN------VGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccc-cCHhHEEC------CCCEEEEEEEEEECCCCEEecC
Confidence            48999999999999999999999999999999997665 66666665      9999999999999988998875

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.

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

Probab=99.17  E-value=1.1e-10  Score=83.44  Aligned_cols=65  Identities=31%  Similarity=0.468  Sum_probs=59.1

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      |+++.|     .++|+||+++  .+   ..|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~--~~---~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIG--YK---SEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeC--CC---ceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            667777     7899999995  43   89999999999999999999999999999999999988999999986

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.

>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=99.17  E-value=5.2e-11  Score=91.39  Aligned_cols=74  Identities=16%  Similarity=0.377  Sum_probs=63.3

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCcc------------------CcCcccchhcccccCCCCEEEE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHS------------------CKEPQKSIHEIAKGLTGSIISV  158 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~------------------~~~p~~~~~~~~~~~vG~~V~v  158 (289)
                      +.|+++.|+|+++.++|++|.++ |++||+|.+++++.+.                  ..++.+.|      .+||.|+|
T Consensus         2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f------~vGd~V~~   75 (100)
T cd05693           2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLF------SVGQLVRC   75 (100)
T ss_pred             CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhc------cCCCEEEE
Confidence            68999999999999999999999 9999999999998652                  02244444      49999999


Q ss_pred             EEEEEecC---CcEEEEEeecc
Q 022938          159 KVIQANEE---MKKLVFSEKDA  177 (289)
Q Consensus       159 kVl~vd~~---~~ri~lS~k~~  177 (289)
                      +|+++|++   ++++.||++.+
T Consensus        76 kVi~~d~~~~~~~~i~LSlr~~   97 (100)
T cd05693          76 KVVSLDKSKSGKKRIELSLEPE   97 (100)
T ss_pred             EEEEccCCcCCCcEEEEEecHH
Confidence            99999987   78999999874

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.

>PRK05807 hypothetical protein; Provisional

Probab=99.17  E-value=2.2e-10  Score=92.78  Aligned_cols=73  Identities=22%  Similarity=0.335  Sum_probs=66.3

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD  176 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~  176 (289)
                      +++|++++|+|+++.++|+||++++..|++|.+++++.+. .++.+.++      +||.|+|+|+++|. .++|.||++.
T Consensus         3 ~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v-~~~~~~~k------vGd~V~VkV~~id~-~gkI~LSlk~   74 (136)
T PRK05807          3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYV-KDIREHLK------EQDKVKVKVISIDD-NGKISLSIKQ   74 (136)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccc-cCccccCC------CCCEEEEEEEEECC-CCcEEEEEEe
Confidence            4789999999999999999999998999999999999886 67666665      99999999999997 7999999987


Q ss_pred             c
Q 022938          177 A  177 (289)
Q Consensus       177 ~  177 (289)
                      .
T Consensus        75 ~   75 (136)
T PRK05807         75 A   75 (136)
T ss_pred             c
Confidence            4

>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=99.16  E-value=1.2e-10  Score=82.11  Aligned_cols=67  Identities=25%  Similarity=0.454  Sum_probs=59.7

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      |+++.|+|+++.++|+||+++ +..|++|.+++++.+. .+|.+.++      +||.++|+|.++|.+.+++.+|
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~-~~~~~~~~------~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFV-SHPSDVVS------VGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccc-cCHHHhcC------CCCEEEEEEEEEECCCCEEecC
Confidence            688999999999999999999 8999999999998765 56665555      9999999999999988888875

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.

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

Probab=99.14  E-value=1.7e-10  Score=82.96  Aligned_cols=66  Identities=41%  Similarity=0.727  Sum_probs=57.3

Q ss_pred             cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcc-cccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~-~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      +++|+++.|     +++|+||++.  +|   ++|++|.++++|. +..++.+.|++||.|+|+|.++|++++++.|+
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~--~~---~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELE--EG---VEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcC--CC---CEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence            467888888     9999999995  55   9999999999875 44467788999999999999999999999874

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.

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

Probab=99.14  E-value=2e-10  Score=81.21  Aligned_cols=64  Identities=45%  Similarity=0.908  Sum_probs=57.6

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      |+++.|     .++|+||+++  ++   ..|++|.+++++.+..++.+.|++||.++|+|.++|+ ++++.||+|
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--GG---ISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEEC--CC---CEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence            556666     8999999996  44   8999999999999888888999999999999999998 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.

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

Probab=99.13  E-value=3.3e-10  Score=80.20  Aligned_cols=70  Identities=26%  Similarity=0.495  Sum_probs=61.9

Q ss_pred             CCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           99 SGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        99 ~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      .|+++.|+|.++.++|++|+++ ++.|++|.+++++.+. .++.+.++      +||.++|+|.+++.+++++.+|++
T Consensus         2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~-~~~~~~~~------~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRV-KDPEEVLK------VGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcccc-CCHHHeec------CCCEEEEEEEEEeCCCCEEEEEeC
Confidence            6999999999999999999999 9999999999998763 44544454      999999999999998899999874

>PRK08059 general stress protein 13; Validated

Probab=99.12  E-value=3.1e-10  Score=90.41  Aligned_cols=74  Identities=23%  Similarity=0.377  Sum_probs=67.1

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      ++.|+++.|+|+++.++|+||+++ +..|++|.+++++.+. .++.+.++      +||.|+|+|.++|.+.+++.+|++
T Consensus         5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~-~~~~~~~~------vGD~I~vkI~~id~~~~~i~lslk   77 (123)
T PRK08059          5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFV-KDIHDFLS------VGDEVKVKVLSVDEEKGKISLSIR   77 (123)
T ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccc-cCHHHcCC------CCCEEEEEEEEEECCCCeEEEEEE
Confidence            678999999999999999999999 8999999999998765 56655555      999999999999999999999999


Q ss_pred             cc
Q 022938          176 DA  177 (289)
Q Consensus       176 ~~  177 (289)
                      ..
T Consensus        78 ~~   79 (123)
T PRK08059         78 AT   79 (123)
T ss_pred             Ec
Confidence            75

>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=99.11  E-value=5.9e-10  Score=81.67  Aligned_cols=69  Identities=29%  Similarity=0.424  Sum_probs=60.5

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC----CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF----SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~----gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      |+++.|+|+++.++|+||+++    +..||+|.+++++.+...++.+.|+      +||.|+|+|.++|  .+++.+|++
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~------~Gd~v~v~v~~vd--~~~i~~s~k   72 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVK------RGQKVKVKVISIQ--NGKISLSMK   72 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeC------CCCEEEEEEEEEe--CCEEEEEEE
Confidence            789999999999999999998    6899999999998763146666665      9999999999999  789999998


Q ss_pred             c
Q 022938          176 D  176 (289)
Q Consensus       176 ~  176 (289)
                      +
T Consensus        73 ~   73 (79)
T cd05684          73 D   73 (79)
T ss_pred             e
Confidence            6

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.

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

Probab=99.11  E-value=3.9e-10  Score=79.71  Aligned_cols=67  Identities=24%  Similarity=0.457  Sum_probs=59.8

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      |+++.|+|+++.++|+||+++ +..||+|.+++++.+. .++.+.++      +||.++|+|.++|+ ++++.+|+
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERV-EKVEDVLK------VGDEVKVKVIEVDD-RGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccc-cCHHHccC------CCCEEEEEEEEECC-CCcEEeeC
Confidence            688999999999999999998 8999999999998765 56665555      99999999999998 88998885

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.

>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=99.10  E-value=1.2e-10  Score=89.37  Aligned_cols=70  Identities=31%  Similarity=0.533  Sum_probs=61.2

Q ss_pred             cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-------------------cCcccccCCCCEEEE
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDEVRV  241 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-------------------~~~~~~~~iGd~V~v  241 (289)
                      +++|+++.|     .++|+||.+.  +|   +.|++|+++++|.+.                   .++.+.|++||.|+|
T Consensus         1 L~~G~vV~G~V~~v~~~gl~v~L~--~g---~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~   75 (100)
T cd05693           1 LSEGMLVLGQVKEITKLDLVISLP--NG---LTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRC   75 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECC--CC---cEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEE
Confidence            478999999     8999999994  44   999999999998652                   347788999999999


Q ss_pred             EEEEEeCC---CCeEEEEEecC
Q 022938          242 KVIKIDRE---KSRITLSIKQL  260 (289)
Q Consensus       242 kV~~id~e---~~ri~lSlK~~  260 (289)
                      +|+++|++   +++|.||+|..
T Consensus        76 kVi~~d~~~~~~~~i~LSlr~~   97 (100)
T cd05693          76 KVVSLDKSKSGKKRIELSLEPE   97 (100)
T ss_pred             EEEEccCCcCCCcEEEEEecHH
Confidence            99999997   79999999974

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.

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

Probab=99.09  E-value=4.4e-10  Score=100.52  Aligned_cols=84  Identities=36%  Similarity=0.621  Sum_probs=71.2

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  261 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~  261 (289)
                      ++|+++.|     .++|+||++...+|   +.|++|.++++++++.++.+.|++||.|.|+|+++|+++++|.||+|.+.
T Consensus         7 ~~GdiV~G~V~~I~~~G~fV~L~e~~g---ieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~   83 (262)
T PRK03987          7 EEGELVVGTVKEVKDFGAFVTLDEYPG---KEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVN   83 (262)
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCCCC---cEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEecc
Confidence            67888888     89999999952224   99999999999999999999999999999999999999999999999987


Q ss_pred             CCchhHHhhhhC
Q 022938          262 EDPLLETLEKVI  273 (289)
Q Consensus       262 ~~p~~~~~~~~~  273 (289)
                      ++.-.+.++++.
T Consensus        84 ~~e~~~~~~~~~   95 (262)
T PRK03987         84 EHQRREKIQEWK   95 (262)
T ss_pred             cchHHHHHHHHH
Confidence            665334333333

>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=99.08  E-value=3.4e-10  Score=80.22  Aligned_cols=61  Identities=18%  Similarity=0.312  Sum_probs=52.7

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      |+++.|     .++|+||++.  +|   +.|++|.++++..+..  .+.|++||.++|+|+++|+++++|.||
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~--~~---v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS   66 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFL--SS---FTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEc--CC---ceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            567777     8999999995  44   9999999999765444  677999999999999999999999886

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

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=99.08  E-value=3e-10  Score=105.20  Aligned_cols=145  Identities=11%  Similarity=0.139  Sum_probs=113.5

Q ss_pred             eeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEE
Q 022938           25 SLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYE  104 (289)
Q Consensus        25 ~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~  104 (289)
                      ...++|+++.-.+|.  +++|+.+...+---+.  +|+.+..-      +..+.+.++++.++..++++.+  +.|++++
T Consensus        76 ~~eI~L~eAk~i~~~--~~vGd~i~~~i~~~~f--gRiaaq~a------kq~i~Qkir~~er~~i~~ey~~--~~Geiv~  143 (374)
T PRK12328         76 EKFISLSEAKEIDPS--VEIGDELTYELSLENM--GRTAANTL------FKELEYHIQRLLEESIFEKYKK--KVGKIVF  143 (374)
T ss_pred             cceeeHHHHHhhCCC--CCCCCEEEEecChhhC--CHHHHHHH------HHHHHHHHHHHHHHHHHHHHHH--hcCcEEE
Confidence            356888999888874  9999999887743222  57666643      3335667777777777877766  5999999


Q ss_pred             EEEEEEEc-CcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc---EEEEEeecchhh
Q 022938          105 GKIQGFNG-GGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK---KLVFSEKDAVWN  180 (289)
Q Consensus       105 g~V~~v~~-~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~---ri~lS~k~~~~~  180 (289)
                      |+|.++.. .+++|++++++|+||.+++.       |.+.|+      +|++++|.|.+|+...+   ++.|||..+.+.
T Consensus       144 g~V~r~~~~~~i~vdlg~~ea~LP~~eqi-------p~E~~~------~Gdrik~~i~~V~~~~k~gp~IilSRt~p~~v  210 (374)
T PRK12328        144 GTVVRVDNEENTFIEIDEIRAVLPMKNRI-------KGEKFK------VGDVVKAVLKRVKIDKNNGILIELSRTSPKFL  210 (374)
T ss_pred             EEEEEEecCCCEEEEcCCeEEEeCHHHcC-------CCCcCC------CCCEEEEEEEEEecCCCCCCEEEEEcCCHHHH
Confidence            99999997 46999999999999999854       555555      99999999999998755   899999998777


Q ss_pred             hcccccccccEEEe
Q 022938          181 KYSSRVNVEDIFVG  194 (289)
Q Consensus       181 ~~~~~~~~G~iv~G  194 (289)
                      ..+.+.++-++..|
T Consensus       211 ~~Lfe~EVPEI~dG  224 (374)
T PRK12328        211 EALLELEVPEIKDG  224 (374)
T ss_pred             HHHHHHhCccccCC
Confidence            66666677776666

>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=99.05  E-value=4.7e-10  Score=79.07  Aligned_cols=63  Identities=38%  Similarity=0.661  Sum_probs=56.0

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      |+++.|     +++|+||+++  ++   ..|++|.+++++.+..++.+.|++||.++|+|.++|++++++.||
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--VK---QDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcC--CC---CEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            455666     8999999996  44   999999999999888888889999999999999999999999876

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.

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

Probab=99.03  E-value=1.1e-09  Score=77.21  Aligned_cols=63  Identities=46%  Similarity=0.907  Sum_probs=56.7

Q ss_pred             cccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          188 VEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       188 ~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      +|+++.|     .++|+||+++   +   +.|++|.+++++.+..++.+.|++||.|+|+|.++|++++++.||
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---G---VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC---C---eEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence            3677777     8999999994   3   899999999998888888899999999999999999999999876

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.

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

Probab=99.02  E-value=1.2e-09  Score=81.27  Aligned_cols=73  Identities=12%  Similarity=0.184  Sum_probs=61.0

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCcc---CcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHS---CKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~---~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      +.|+++.|+|+++.++|++|+++ +.+|++|.+++++...   ..+..+.+      .+||.+.|+|++++++ +++.||
T Consensus         5 ~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l------~vGd~i~~~V~~~~~~-~~i~LS   77 (86)
T cd05789           5 EVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYL------DEGDLIVAEVQSVDSD-GSVSLH   77 (86)
T ss_pred             CCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhC------CCCCEEEEEEEEECCC-CCEEEE
Confidence            68999999999999999999999 8999999999985321   12333334      3999999999999876 899999


Q ss_pred             eecc
Q 022938          174 EKDA  177 (289)
Q Consensus       174 ~k~~  177 (289)
                      ++..
T Consensus        78 ~~~~   81 (86)
T cd05789          78 TRSL   81 (86)
T ss_pred             eCcc
Confidence            9874

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".

>PHA02945 interferon resistance protein; Provisional

Probab=99.01  E-value=2.3e-09  Score=78.55  Aligned_cols=71  Identities=21%  Similarity=0.248  Sum_probs=61.8

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCC--CCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQM--SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLV  171 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sel--s~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~  171 (289)
                      .++|+++-|+|.. .++|+||.+.   |.+||+|.++.  +..+. ++ .+.+       .||++-|+|+++|+.++.|-
T Consensus         9 P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wv-K~-rd~l-------~GqkvV~KVirVd~~kg~ID   78 (88)
T PHA02945          9 PNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYF-KY-RDKL-------VGKTVKVKVIRVDYTKGYID   78 (88)
T ss_pred             CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceE-ee-eeEe-------cCCEEEEEEEEECCCCCEEE
Confidence            3799999999999 9999999985   79999999965  87776 54 4433       89999999999999999999


Q ss_pred             EEeecc
Q 022938          172 FSEKDA  177 (289)
Q Consensus       172 lS~k~~  177 (289)
                      +|+|..
T Consensus        79 lSlK~V   84 (88)
T PHA02945         79 VNYKRM   84 (88)
T ss_pred             eEeeEc
Confidence            999863

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

Probab=99.01  E-value=1.4e-09  Score=76.76  Aligned_cols=63  Identities=46%  Similarity=0.838  Sum_probs=55.8

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      |+++.|     .++|+||+++  ++   ..|++|.+++++.+..++.+.|++||.|+|+|.++|+ ++++.||+
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--PG---KDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeC--CC---CEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence            455666     8999999995  44   8999999999999888888899999999999999999 89999984

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.

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

Probab=99.00  E-value=1.7e-09  Score=76.69  Aligned_cols=62  Identities=29%  Similarity=0.572  Sum_probs=54.1

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      |+++.|     .++|+||++   +|   +.||+|.+++++.+..++.+  .+||.++|+|+++|++++++.||+|
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 GEIVEGKVTEKVKGGLIVDI---EG---VRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE---CC---EEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            566777     899999999   34   99999999999887777665  3899999999999999999999975

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.

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

Probab=99.00  E-value=1.8e-09  Score=76.37  Aligned_cols=67  Identities=45%  Similarity=0.783  Sum_probs=59.7

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      ++|+++.|     .++|+||+++  ++   +.|++|.+++++.+..++...|++||.++|+|.+++++++++.+|++
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~--~~---~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLG--NG---VEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeC--CC---CEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            35888888     8899999995  44   99999999999887777888899999999999999998899999975

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

Probab=98.99  E-value=1.4e-09  Score=80.91  Aligned_cols=69  Identities=22%  Similarity=0.362  Sum_probs=60.0

Q ss_pred             cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCc----ccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSW----DLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~----~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      .++|++|.|     .++|++|+++  ++   +.|++|.+++++    .+..++.+.+++||.++|+|+++|++ +++.||
T Consensus         4 p~~GdiV~g~V~~i~~~g~~v~i~--~~---~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS   77 (86)
T cd05789           4 PEVGDVVIGRVTEVGFKRWKVDIN--SP---YDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLH   77 (86)
T ss_pred             CCCCCEEEEEEEEECCCEEEEECC--CC---eEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEE
Confidence            478999998     8999999995  44   999999999986    34567778899999999999999985 999999


Q ss_pred             EecC
Q 022938          257 IKQL  260 (289)
Q Consensus       257 lK~~  260 (289)
                      +|+.
T Consensus        78 ~~~~   81 (86)
T cd05789          78 TRSL   81 (86)
T ss_pred             eCcc
Confidence            9884

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".

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

Probab=98.98  E-value=2.5e-09  Score=80.17  Aligned_cols=72  Identities=24%  Similarity=0.331  Sum_probs=59.2

Q ss_pred             hcCCCEEEEEEEEEEcC--cEEEEEC-CEEEEeecCCCCC---CccCcCcccchhcccccCCCCEEEEEEEEEecCCcEE
Q 022938           97 KESGFIYEGKIQGFNGG--GLLVRFF-SLVGFLPFPQMSP---SHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKL  170 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~--G~~V~l~-gv~g~ip~sels~---~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri  170 (289)
                      ++.|+++.|+|+++.++  |+||+++ |.+||||.++++|   .+. .++.+.++      +||.|.|+|++.....+..
T Consensus         5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v-~~~~~~~~------~Gd~v~VqV~~~~~~~K~~   77 (88)
T cd04453           5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKH-KKIAKLLK------EGQEILVQVVKEPIGTKGP   77 (88)
T ss_pred             CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhcccc-CCHHHcCC------CCCEEEEEEEEecCCCCCc
Confidence            47999999999999996  9999999 8999999999998   333 55666665      9999999999877666555


Q ss_pred             EEEee
Q 022938          171 VFSEK  175 (289)
Q Consensus       171 ~lS~k  175 (289)
                      .+|..
T Consensus        78 ~lt~~   82 (88)
T cd04453          78 RLTTN   82 (88)
T ss_pred             eEEEE
Confidence            55543

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

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=98.98  E-value=1.2e-09  Score=110.88  Aligned_cols=85  Identities=22%  Similarity=0.323  Sum_probs=73.7

Q ss_pred             HHHhhcCCCEEE-EEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEE
Q 022938           93 ARAYKESGFIYE-GKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKL  170 (289)
Q Consensus        93 l~~~~~~G~iv~-g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri  170 (289)
                      +....+.|++++ |+|+++.++|+||++. |++||||+++++|.++ .++.+.++      +||.|+|+|+++|. .+++
T Consensus       747 l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv-~~~~dv~k------vGD~V~VkVi~ID~-~grI  818 (891)
T PLN00207        747 LTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWL-AKPEDAFK------VGDRIDVKLIEVND-KGQL  818 (891)
T ss_pred             HhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccc-cCHHHhcC------CCCEEEEEEEEECC-CCcE
Confidence            334468999996 6999999999999998 9999999999999886 78877776      99999999999996 7899


Q ss_pred             EEEeec---chhhhcccc
Q 022938          171 VFSEKD---AVWNKYSSR  185 (289)
Q Consensus       171 ~lS~k~---~~~~~~~~~  185 (289)
                      .||+|.   +||+...+.
T Consensus       819 ~LSlK~l~~~Pw~~~~~~  836 (891)
T PLN00207        819 RLSRRALLPEANSEKSSQ  836 (891)
T ss_pred             EEEEeccccCchhhhhhh
Confidence            999986   588866443

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

Probab=98.96  E-value=3.8e-09  Score=77.94  Aligned_cols=72  Identities=22%  Similarity=0.272  Sum_probs=62.9

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD  176 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~  176 (289)
                      +.|+++.|+|+++.+.+++|+++ +.+|++|.++++..+. .++.+.++      +||.+.|+|+++|.+ +++.||.+.
T Consensus         5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~-~~~~~~~~------~GD~i~~~V~~~~~~-~~i~LS~~~   76 (82)
T cd04454           5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDK-KEIRKSLQ------PGDLILAKVISLGDD-MNVLLTTAD   76 (82)
T ss_pred             CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcch-HHHHhcCC------CCCEEEEEEEEeCCC-CCEEEEECC
Confidence            68999999999999999999999 8999999999987654 44445554      999999999999976 899999886


Q ss_pred             c
Q 022938          177 A  177 (289)
Q Consensus       177 ~  177 (289)
                      .
T Consensus        77 ~   77 (82)
T cd04454          77 N   77 (82)
T ss_pred             C
Confidence            4

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".

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

Probab=98.95  E-value=5.1e-09  Score=74.31  Aligned_cols=64  Identities=20%  Similarity=0.373  Sum_probs=54.6

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC--cEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM--KKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~--~ri~lS~  174 (289)
                      ..|++++|+|.++.++|++|++++.+||||.+|++.       .+.++      +|+++++.|.+++.++  .++.+|+
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~-------~~~~~------~Gd~v~v~v~~v~~~~~~~~i~lSr   67 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIP-------GESYR------PGDRIKAYVLEVRKTSKGPQIILSR   67 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCC-------CCcCC------CCCEEEEEEEEEecCCCCCEEEEeC
Confidence            479999999999999999999999999999999863       22233      9999999999999654  4788885

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.

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

Probab=98.94  E-value=4.6e-09  Score=75.14  Aligned_cols=63  Identities=17%  Similarity=0.281  Sum_probs=54.7

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCc-cCcCcccchhcccccCCCCEEEEEEEEEecCCc
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSH-SCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK  168 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~-~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~  168 (289)
                      |+++.|+|+++.++|++|+++ |++|++|.+++++.+ ...+|.+.|+      +||.++|+|+++|.++.
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~------~Gd~i~~kVl~~d~~~~   65 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFK------IGQKIKARVIGGHDAKT   65 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCC------CCCEEEEEEEEEeCccc
Confidence            789999999999999999999 999999999999875 2266666665      99999999999987553

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.

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

Probab=98.92  E-value=9.3e-09  Score=75.64  Aligned_cols=76  Identities=17%  Similarity=0.245  Sum_probs=58.3

Q ss_pred             CCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchh----cccccCCCCEEEEEEEEEecCCcEEEE
Q 022938           99 SGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIH----EIAKGLTGSIISVKVIQANEEMKKLVF  172 (289)
Q Consensus        99 ~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~----~~~~~~vG~~V~vkVl~vd~~~~ri~l  172 (289)
                      .|++++|+|+++.++|+||+++  |++|++|.+++++.+...++.....    ....+.+||.|+|+|.++|.+++++.+
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~   80 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF   80 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence            3889999999999999999999  6999999999986543222211000    001234999999999999998899988


Q ss_pred             Ee
Q 022938          173 SE  174 (289)
Q Consensus       173 S~  174 (289)
                      ++
T Consensus        81 ~l   82 (83)
T cd04471          81 EL   82 (83)
T ss_pred             EE
Confidence            75

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.

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=98.92  E-value=7.1e-09  Score=88.68  Aligned_cols=93  Identities=23%  Similarity=0.320  Sum_probs=75.5

Q ss_pred             EEEecCCcEEEEEeecchhhhcccccccccEEEe-----eeeeEEEEEecCC--C---ceeEEEEEEccCcCcccccCcc
Q 022938          161 IQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPD--G---LYHLTGLVHVSEVSWDLIQDIR  230 (289)
Q Consensus       161 l~vd~~~~ri~lS~k~~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~--G---~~~i~Glv~~sels~~~~~~~~  230 (289)
                      +++|.+++++.+    .||.......++|++|.|     .++|+||+|...+  +   ...+.|++|.+++++.+..++.
T Consensus        41 ~~id~~~~~Isv----~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~  116 (189)
T PRK09521         41 VFIDDINRKISV----IPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLT  116 (189)
T ss_pred             EEEcCCCCEEEE----ecCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHH
Confidence            345666777777    467776778899999999     8999999995210  0   0028899999999998888888


Q ss_pred             cccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938          231 DILNEGDEVRVKVIKIDREKSRITLSIKQL  260 (289)
Q Consensus       231 ~~~~iGd~V~vkV~~id~e~~ri~lSlK~~  260 (289)
                      +.|++||.|.|+|++++   +++.||+|+.
T Consensus       117 ~~~~~GD~V~akV~~i~---~~i~LS~k~~  143 (189)
T PRK09521        117 DAFKIGDIVRAKVISYT---DPLQLSTKGK  143 (189)
T ss_pred             hccCCCCEEEEEEEecC---CcEEEEEecC
Confidence            99999999999999998   7899999974

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

Probab=98.90  E-value=9e-09  Score=75.70  Aligned_cols=64  Identities=30%  Similarity=0.644  Sum_probs=54.2

Q ss_pred             ccEEEe-----eeeeEEEEEecCC-CceeEEEEEEccCcCccccc-----------CcccccCCCCEEEEEEEEEeCCCC
Q 022938          189 EDIFVG-----RDYGAFIHLRFPD-GLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREKS  251 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~-G~~~i~Glv~~sels~~~~~-----------~~~~~~~iGd~V~vkV~~id~e~~  251 (289)
                      |+++.|     +++|+||++.  + |   +.|++|.+++++++..           .....|++||.|+|+|.++|++++
T Consensus         2 g~~~~g~V~~v~~~G~fv~l~--~~~---~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~   76 (83)
T cd04471           2 GEEFDGVISGVTSFGLFVELD--NLT---VEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRR   76 (83)
T ss_pred             CCEEEEEEEeEEeeeEEEEec--CCC---EEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccC
Confidence            667777     9999999996  3 5   9999999999876422           345789999999999999999999


Q ss_pred             eEEEEE
Q 022938          252 RITLSI  257 (289)
Q Consensus       252 ri~lSl  257 (289)
                      ++.+++
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.

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

Probab=98.90  E-value=4.3e-09  Score=72.90  Aligned_cols=64  Identities=22%  Similarity=0.435  Sum_probs=56.0

Q ss_pred             EEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938          103 YEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus       103 v~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      +.|+|+++.++|++|+++ +.+|++|.+++++.+. .++.+.++      +||.++|+|.++|++.+++.+|
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~-~~~~~~~~------~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFV-KDPSEVFK------VGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccc-cCHhhEeC------CCCEEEEEEEEEcCCcCEEecC
Confidence            479999999999999999 9999999999998765 55655555      9999999999999988888775

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.

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

Probab=98.89  E-value=6.8e-09  Score=92.90  Aligned_cols=73  Identities=19%  Similarity=0.307  Sum_probs=66.2

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      .+.|+++.|+|+++.++|+||++.   |++||+|.+++++.+. .++.+.++      +||.+.|+|+++|.+++++.||
T Consensus         6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i-~~i~~~~k------vGd~V~vkVi~VD~~k~~I~LS   78 (262)
T PRK03987          6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWV-KNIRDHVK------EGQKVVCKVIRVDPRKGHIDLS   78 (262)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccc-cCHHHhCC------CCCEEEEEEEEEecccCeEEEE
Confidence            468999999999999999999995   6999999999998876 66766665      9999999999999999999999


Q ss_pred             eec
Q 022938          174 EKD  176 (289)
Q Consensus       174 ~k~  176 (289)
                      ++.
T Consensus        79 lK~   81 (262)
T PRK03987         79 LKR   81 (262)
T ss_pred             EEe
Confidence            984

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=98.88  E-value=5.7e-09  Score=105.33  Aligned_cols=73  Identities=42%  Similarity=0.776  Sum_probs=67.3

Q ss_pred             cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      .....++|+++.|     .++|+||++.  +|   ..|++|+|++++.++.++.+.|++||.|+|+|+++|++ +++.||
T Consensus       615 ~~~~~~vG~v~~G~V~~I~~fGafVei~--~~---~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS  688 (693)
T PRK11824        615 ITAEPEVGEIYEGKVVRIVDFGAFVEIL--PG---KDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLS  688 (693)
T ss_pred             hcccCcCCeEEEEEEEEEECCeEEEEEC--CC---CEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEE
Confidence            3456899999999     9999999996  55   99999999999999999999999999999999999986 999999


Q ss_pred             EecC
Q 022938          257 IKQL  260 (289)
Q Consensus       257 lK~~  260 (289)
                      +|.+
T Consensus       689 ~k~~  692 (693)
T PRK11824        689 RKAV  692 (693)
T ss_pred             EEec
Confidence            9976

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=98.87  E-value=5.7e-09  Score=98.23  Aligned_cols=146  Identities=12%  Similarity=0.109  Sum_probs=110.9

Q ss_pred             eEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEE
Q 022938           26 LSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEG  105 (289)
Q Consensus        26 ~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g  105 (289)
                      ..++|+++.-.+|.  +++|+.+...|.-...+-+|+.+..-+      ..+.+.++.+++...++++.+  +.|++++|
T Consensus        89 ~eIsL~eAk~i~~~--~~iGD~v~~~v~~~~~~fgRiAAq~aK------Qvi~Qkire~ER~~i~~ef~~--~~GeIV~G  158 (449)
T PRK12329         89 HQISLAEVQQVADE--AQLGDTVVLDVTPEQEDFGRMAAIQTK------QVLAQKLRDQQRKMIQEEFQD--LEDTVLTA  158 (449)
T ss_pred             ccccHHHHHhhCCC--CcCCCEEEEecCccccchhHHHHHHHH------HHHHHHHHHHHHHHHHHHHHH--hcCcEEEE
Confidence            45778888877774  999999987762110133677776443      336677888888888888777  59999999


Q ss_pred             EEEEEEcCcEEEEE----C--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC---cEEEEEeec
Q 022938          106 KIQGFNGGGLLVRF----F--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM---KKLVFSEKD  176 (289)
Q Consensus       106 ~V~~v~~~G~~V~l----~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~---~ri~lS~k~  176 (289)
                      +|.++.+.+++|++    |  +++|+||.++..       |++.|+      +|++++|.|.+|+...   -++.|||..
T Consensus       159 ~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi-------p~E~y~------~Gdrika~i~~V~~~~~kGpqIilSRt~  225 (449)
T PRK12329        159 RVLRFERQSVIMAVSSGFGQPEVEAELPKREQL-------PNDNYR------ANATFKVFLKEVSEGPRRGPQLFVSRAN  225 (449)
T ss_pred             EEEEEcCCCEEEEecccCCCcceEEEecHHHcC-------CCCcCC------CCCEEEEEEEEeecCCCCCCEEEEEcCC
Confidence            99999999999998    4  299999999854       555565      9999999999998753   389999998


Q ss_pred             chhhhcccccccccEEEe
Q 022938          177 AVWNKYSSRVNVEDIFVG  194 (289)
Q Consensus       177 ~~~~~~~~~~~~G~iv~G  194 (289)
                      ..+...+...++-++..|
T Consensus       226 p~lv~~Lfe~EVPEI~dG  243 (449)
T PRK12329        226 AGLVVYLFENEVPEIEEG  243 (449)
T ss_pred             HHHHHHHHHhhCcccccC
Confidence            777666666666666555

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

Probab=98.87  E-value=8.8e-09  Score=77.17  Aligned_cols=70  Identities=26%  Similarity=0.383  Sum_probs=59.7

Q ss_pred             ccccccEEEe-----eee--eEEEEEecCCCceeEEEEEEccCcCc---ccccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 022938          185 RVNVEDIFVG-----RDY--GAFIHLRFPDGLYHLTGLVHVSEVSW---DLIQDIRDILNEGDEVRVKVIKIDREKSRIT  254 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~--G~fV~i~~~~G~~~i~Glv~~sels~---~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~  254 (289)
                      .+++|+++.|     .++  |+||+++  +|   .+||+|.++++|   .++.++.+.+++||.|.|+|+......+--.
T Consensus         4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~--~g---~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~   78 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIG--LG---KNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPR   78 (88)
T ss_pred             cCCCCCEEEEEEEEeccCCcEEEEEeC--CC---CEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCce
Confidence            5678999999     665  9999996  55   899999999999   5678888999999999999999887777777


Q ss_pred             EEEec
Q 022938          255 LSIKQ  259 (289)
Q Consensus       255 lSlK~  259 (289)
                      ||.+-
T Consensus        79 lt~~~   83 (88)
T cd04453          79 LTTNI   83 (88)
T ss_pred             EEEEE
Confidence            77654

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

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.86  E-value=9.6e-09  Score=102.44  Aligned_cols=88  Identities=24%  Similarity=0.523  Sum_probs=69.6

Q ss_pred             EEecCCcEEEEEeecch--------hhhccc--ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcC----
Q 022938          162 QANEEMKKLVFSEKDAV--------WNKYSS--RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVS----  222 (289)
Q Consensus       162 ~vd~~~~ri~lS~k~~~--------~~~~~~--~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels----  222 (289)
                      +++ +.+.+.++-....        ......  ..++|+++.|     .+||+||+|.  +|   +.||+|+|+++    
T Consensus       612 di~-d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~--~G---~eGLvHISeisdls~  685 (719)
T TIGR02696       612 SIE-DDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLL--PG---KDGLLHISQIRKLAG  685 (719)
T ss_pred             EEe-cCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEec--CC---ceEEEEhhhcccccc
Confidence            355 3567776655421        112223  4799999999     9999999996  55   99999999996    


Q ss_pred             cccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          223 WDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       223 ~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      +.++.++.+.|++||.|+|+|+++|+ ++||.|+
T Consensus       686 ~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~  718 (719)
T TIGR02696       686 GKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV  718 (719)
T ss_pred             ccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence            46889999999999999999999995 8899886

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.

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=98.86  E-value=3.4e-09  Score=105.22  Aligned_cols=78  Identities=36%  Similarity=0.604  Sum_probs=71.4

Q ss_pred             cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      .++++++|+++.|     .+||+||+|+  -   +..|++|+|++++.++.+|.+.+++||.|+|+|+++|..++||.||
T Consensus       652 ~i~dLk~Gm~leg~Vrnv~~fgafVdIg--v---~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Ls  726 (780)
T COG2183         652 SITDLKPGMILEGTVRNVVDFGAFVDIG--V---HQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALS  726 (780)
T ss_pred             hHhhccCCCEEEEEEEEeeeccceEEec--c---ccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeE
Confidence            3678999999999     9999999997  3   3899999999999999999999999999999999999999999999


Q ss_pred             EecCCCCc
Q 022938          257 IKQLEEDP  264 (289)
Q Consensus       257 lK~~~~~p  264 (289)
                      |+..+..+
T Consensus       727 mr~~~~~~  734 (780)
T COG2183         727 MRLDEEEG  734 (780)
T ss_pred             eeccCCcc
Confidence            99875433

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

Probab=98.84  E-value=3.2e-09  Score=92.81  Aligned_cols=73  Identities=19%  Similarity=0.295  Sum_probs=68.0

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      .++|+++-|+|..|.++|+||.+.   |++||+|.||++..++ .+..++++      +||.+-|+|++||+.++.+-||
T Consensus         9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wV-knIrd~vk------egqkvV~kVlrVd~~rg~IDLS   81 (269)
T COG1093           9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWV-KNIRDYVK------EGQKVVAKVLRVDPKRGHIDLS   81 (269)
T ss_pred             CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHH-HHHHHHhh------cCCeEEEEEEEEcCCCCeEeee
Confidence            369999999999999999999985   7999999999999887 88888887      9999999999999999999999


Q ss_pred             eec
Q 022938          174 EKD  176 (289)
Q Consensus       174 ~k~  176 (289)
                      +|.
T Consensus        82 lkr   84 (269)
T COG1093          82 LKR   84 (269)
T ss_pred             hhh
Confidence            986

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=98.84  E-value=5.9e-09  Score=103.54  Aligned_cols=75  Identities=25%  Similarity=0.416  Sum_probs=71.7

Q ss_pred             hhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           96 YKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        96 ~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      .+++|++++|+|+++.++|+||++| ..+|++|++++++.++ .+|.+.+.      +||.|+|+|+++|..+++|.||+
T Consensus       655 dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv-~~P~~vv~------vGdiV~v~V~~vD~~r~rI~Lsm  727 (780)
T COG2183         655 DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFV-KDPNEVVK------VGDIVKVKVIEVDTARKRIALSM  727 (780)
T ss_pred             hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhc-CChHHhcc------cCCEEEEEEEEEecccCeeeeEe
Confidence            5799999999999999999999999 9999999999999998 99998887      99999999999999999999999


Q ss_pred             ecc
Q 022938          175 KDA  177 (289)
Q Consensus       175 k~~  177 (289)
                      +..
T Consensus       728 r~~  730 (780)
T COG2183         728 RLD  730 (780)
T ss_pred             ecc
Confidence            974

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

Probab=98.84  E-value=3.4e-08  Score=72.04  Aligned_cols=62  Identities=21%  Similarity=0.330  Sum_probs=55.3

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      ++.|+.++|+|.++.++|+||++. +..|++|.+++...         +      .+||.++++|.++ .+.+++.+|+
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 LEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRD---------Y------EVGDEVIVQVTDI-PENGNIDLIP   76 (77)
T ss_pred             CCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhccCc---------C------CCCCEEEEEEEEE-CCCCcEEEEE
Confidence            689999999999999999999999 89999999997432         2      3999999999999 7889998875

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=98.81  E-value=1.9e-08  Score=101.53  Aligned_cols=74  Identities=23%  Similarity=0.401  Sum_probs=68.3

Q ss_pred             HhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           95 AYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        95 ~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      ...+.|+++.|+|+++.++|+||++. |.+|++|++++++.+. .++.+.++      +||.|+|+|+++|.+ +++.||
T Consensus       617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v-~~~~~v~k------vGD~V~VkV~~iD~~-grI~LS  688 (693)
T PRK11824        617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERV-EKVEDVLK------EGDEVKVKVLEIDKR-GRIRLS  688 (693)
T ss_pred             ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccc-cCccceeC------CCCEEEEEEEEECCC-CcEEEE
Confidence            44689999999999999999999998 9999999999999886 78888776      999999999999977 999999


Q ss_pred             eec
Q 022938          174 EKD  176 (289)
Q Consensus       174 ~k~  176 (289)
                      +|.
T Consensus       689 ~k~  691 (693)
T PRK11824        689 RKA  691 (693)
T ss_pred             EEe
Confidence            986

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

Probab=98.80  E-value=2.1e-08  Score=73.93  Aligned_cols=68  Identities=22%  Similarity=0.245  Sum_probs=61.0

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  260 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~  260 (289)
                      ++|+++.|     .+.+++|+++  .   ...|++|.++++.....++.+.|++||.+.|+|+++|.+ +++.||++..
T Consensus         5 ~~GdiV~G~V~~v~~~~~~V~i~--~---~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~~   77 (82)
T cd04454           5 DVGDIVIGIVTEVNSRFWKVDIL--S---RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTADN   77 (82)
T ss_pred             CCCCEEEEEEEEEcCCEEEEEeC--C---CceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECCC
Confidence            68888888     8999999996  3   399999999999887888889999999999999999986 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".

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=98.79  E-value=2.9e-08  Score=84.89  Aligned_cols=104  Identities=20%  Similarity=0.209  Sum_probs=77.3

Q ss_pred             cccCCCeEEEEEEEE---eCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEE
Q 022938           41 IERICQRNLCPVGKF---STNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGKIQGFNGGGLLV  117 (289)
Q Consensus        41 ~~~vG~~v~~~Vl~~---d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V  117 (289)
                      .|..+..+.+.+...   |.++.++++.                       +|.......+.|+++.|+|+++.++|++|
T Consensus        26 ty~~~~~i~as~~G~~~id~~~~~Isv~-----------------------P~~~~~~~~~~GdiV~GkV~~i~~~g~~V   82 (189)
T PRK09521         26 TYEDNGEVYASVVGKVFIDDINRKISVI-----------------------PFKKTPPLLKKGDIVYGRVVDVKEQRALV   82 (189)
T ss_pred             EEeeCCEEEEEeeEEEEEcCCCCEEEEe-----------------------cCcCCCCCCCCCCEEEEEEEEEcCCeEEE
Confidence            455666777766654   4555566553                       12221223579999999999999999999


Q ss_pred             EEC-----------CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeecc
Q 022938          118 RFF-----------SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA  177 (289)
Q Consensus       118 ~l~-----------gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~~  177 (289)
                      +++           +..|++|.+++++.+. .++.+.|+      +||.|.|+|++++   +++.||.+..
T Consensus        83 ~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~-~~~~~~~~------~GD~V~akV~~i~---~~i~LS~k~~  143 (189)
T PRK09521         83 RIVSIEGSERELATSKLAYIHISQVSDGYV-ESLTDAFK------IGDIVRAKVISYT---DPLQLSTKGK  143 (189)
T ss_pred             EEEEecccccccCCCceeeEEhhHcChhhh-hhHHhccC------CCCEEEEEEEecC---CcEEEEEecC
Confidence            985           5789999999988664 44555555      9999999999997   7899999863

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

Probab=98.78  E-value=4.2e-08  Score=71.57  Aligned_cols=62  Identities=34%  Similarity=0.542  Sum_probs=54.2

Q ss_pred             cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      .+.+++.|+.+.|     +++|+||++.  ++   ..|++|.+++.        +.+++||.++++|.++ .+++++.+|
T Consensus        10 ~~~~~~~G~~~~g~V~~i~~~G~fV~l~--~~---~~Glv~~se~~--------~~~~iGd~v~v~I~~i-~e~~~i~l~   75 (77)
T cd04473          10 TMEDLEVGKLYKGKVNGVAKYGVFVDLN--DH---VRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLI   75 (77)
T ss_pred             chhhCCCCCEEEEEEEeEecceEEEEEC--CC---cEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEE
Confidence            4556889999999     9999999996  44   99999999864        5699999999999999 789999998


Q ss_pred             E
Q 022938          257 I  257 (289)
Q Consensus       257 l  257 (289)
                      +
T Consensus        76 ~   76 (77)
T cd04473          76 P   76 (77)
T ss_pred             E
Confidence            5

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.77  E-value=1.9e-08  Score=100.42  Aligned_cols=69  Identities=19%  Similarity=0.295  Sum_probs=61.2

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCC---C-CccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMS---P-SHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLV  171 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels---~-~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~  171 (289)
                      .+.|++++|+|+++.++|+||++. |++||+|+||++   | .+. .+|.+.++      +||.|+|+|+++|. ++|+.
T Consensus       645 ~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv-~~~~dv~k------vGd~V~VKVl~ID~-~gKI~  716 (719)
T TIGR02696       645 PEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRV-ENVEDVLS------VGQKIQVEIADIDD-RGKLS  716 (719)
T ss_pred             CCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCc-CCHHHcCC------CCCEEEEEEEEECC-CCCee
Confidence            579999999999999999999998 999999999996   3 444 77888776      99999999999994 77888


Q ss_pred             EE
Q 022938          172 FS  173 (289)
Q Consensus       172 lS  173 (289)
                      |+
T Consensus       717 L~  718 (719)
T TIGR02696       717 LV  718 (719)
T ss_pred             ec
Confidence            76

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.

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

Probab=98.72  E-value=3.6e-08  Score=70.45  Aligned_cols=58  Identities=22%  Similarity=0.298  Sum_probs=50.0

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccc--ccCcccccCCCCEEEEEEEEEeCCCC
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDIRDILNEGDEVRVKVIKIDREKS  251 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~--~~~~~~~~~iGd~V~vkV~~id~e~~  251 (289)
                      |+++.|     .++|+||++.  +|   ++|++|.+++++.+  ..++.+.|++||.|+|+|+++|.++.
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--DN---VHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT   65 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeC--CC---cEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence            566777     8899999995  55   99999999999884  77888899999999999999998543

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=98.69  E-value=6.4e-08  Score=66.92  Aligned_cols=57  Identities=47%  Similarity=0.857  Sum_probs=51.7

Q ss_pred             eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       195 ~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      .++|+||+++  +|   ..|++|.+++++.+..++.+.|++||.|+|+|+++|++++++.||
T Consensus         9 ~~~g~~v~l~--~~---~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           9 TKFGVFVELE--DG---VEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             EeeeEEEEec--CC---CEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            7899999996  44   999999999998877788889999999999999999999998875

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.67  E-value=2.8e-08  Score=95.68  Aligned_cols=160  Identities=13%  Similarity=0.137  Sum_probs=111.0

Q ss_pred             EeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEEE
Q 022938           27 SLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEGK  106 (289)
Q Consensus        27 ~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g~  106 (289)
                      +-.+++++.....+.|.....+.+.   +|+++|.+.+-....+++.                                 
T Consensus        24 ~~~le~al~~a~~k~~~~~~~~~v~---id~~~g~~~~~~~~~vV~~---------------------------------   67 (470)
T PRK09202         24 IEALEEALATAYKKKYGPEANIRVE---IDRKTGDIEVFRRWEVVEE---------------------------------   67 (470)
T ss_pred             HHHHHHHHHHHHHhhcCCcccEEEE---EeCCCCeEEEEEEEEEecc---------------------------------
Confidence            3445666666666777555555554   4888887777654333211                                 


Q ss_pred             EEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee-c--------c
Q 022938          107 IQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK-D--------A  177 (289)
Q Consensus       107 V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k-~--------~  177 (289)
                                  +..-.+.+|.++...    .+|        ...+|+.+.+.|...+  .+|+.++.. +        .
T Consensus        68 ------------v~~~~~eI~L~eAk~----~~~--------~~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~  121 (470)
T PRK09202         68 ------------VEDPTKEISLEEARK----IDP--------DAEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREA  121 (470)
T ss_pred             ------------ccCCcceeeHHHHhh----hCc--------cccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHH
Confidence                        112235666666532    122        2349999999998775  444443322 2        2


Q ss_pred             hhhhcccccc--cccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCC
Q 022938          178 VWNKYSSRVN--VEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK  250 (289)
Q Consensus       178 ~~~~~~~~~~--~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~  250 (289)
                      .++..++.++  .|+++.|     .++|+||+++   |   +.|++|.++++      |.+.|++||.|+|+|+++++++
T Consensus       122 ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLg---g---vea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~  189 (470)
T PRK09202        122 ERERVYEEYKDRVGEIITGVVKRVERGNIIVDLG---R---AEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEA  189 (470)
T ss_pred             HHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEEC---C---eEEEecHHHcC------CCccCCCCCEEEEEEEEEecCC
Confidence            3446678887  9999999     8899999994   4   99999999985      6688999999999999999987


Q ss_pred             C--eEEEEEecC
Q 022938          251 S--RITLSIKQL  260 (289)
Q Consensus       251 ~--ri~lSlK~~  260 (289)
                      +  .|.||.+..
T Consensus       190 kg~qIilSRt~p  201 (470)
T PRK09202        190 RGPQIILSRTHP  201 (470)
T ss_pred             CCCeEEEEeCcH
Confidence            7  899998763

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

Probab=98.65  E-value=1.6e-07  Score=71.88  Aligned_cols=69  Identities=29%  Similarity=0.501  Sum_probs=58.6

Q ss_pred             eeeeEEEEEecCCCceeEEEEEEccCcCcccccC-----------cccccCCCCEEEEEEEEEeCCC-----CeEEEEEe
Q 022938          195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-----------IRDILNEGDEVRVKVIKIDREK-----SRITLSIK  258 (289)
Q Consensus       195 ~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~-----------~~~~~~iGd~V~vkV~~id~e~-----~ri~lSlK  258 (289)
                      .++|+||++.   +   +.|++|.+++++++...           ....|++||.|+|+|.++|.+.     .++.||+|
T Consensus        11 ~~~GifV~l~---~---v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k   84 (99)
T cd04460          11 VDFGAFVRIG---P---VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIGLTMR   84 (99)
T ss_pred             EeccEEEEEc---C---eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEEEEEe
Confidence            8999999994   3   89999999998776543           3477999999999999999864     58999999


Q ss_pred             cCCCCchhHHh
Q 022938          259 QLEEDPLLETL  269 (289)
Q Consensus       259 ~~~~~p~~~~~  269 (289)
                      +....||+-+.
T Consensus        85 ~~~~g~~~~~~   95 (99)
T cd04460          85 QPGLGKLEWIE   95 (99)
T ss_pred             cCCCCcHHHhh
Confidence            99888887654

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.

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

Probab=98.65  E-value=6.6e-08  Score=94.82  Aligned_cols=92  Identities=37%  Similarity=0.658  Sum_probs=77.2

Q ss_pred             EecCCcEEEEEeecc--------hhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc
Q 022938          163 ANEEMKKLVFSEKDA--------VWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI  229 (289)
Q Consensus       163 vd~~~~ri~lS~k~~--------~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~  229 (289)
                      ++ +.+.+.++-...        .......++++|+++.|     .+||+||.+.  +|   -.|+||+|++++.++...
T Consensus       587 ie-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~--~g---kdgl~hiS~~~~~rv~kv  660 (692)
T COG1185         587 IE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELL--PG---KDGLVHISQLAKERVEKV  660 (692)
T ss_pred             ec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEec--CC---cceeEEehhhhhhhhhcc
Confidence            44 556666655432        23345688999999999     8999999995  65   899999999999999999


Q ss_pred             ccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938          230 RDILNEGDEVRVKVIKIDREKSRITLSIKQLE  261 (289)
Q Consensus       230 ~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~  261 (289)
                      .+.++.||.|.||+..+|+ ++|+.||+|..+
T Consensus       661 ~dvlk~Gd~v~Vkv~~iD~-~Gri~ls~~~~~  691 (692)
T COG1185         661 EDVLKEGDEVKVKVIEIDK-QGRIRLSIKAVL  691 (692)
T ss_pred             cceeecCceEEEEEeeecc-cCCccceehhcc
Confidence            9999999999999999997 899999999764

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

Probab=98.64  E-value=1.7e-07  Score=71.63  Aligned_cols=71  Identities=15%  Similarity=0.311  Sum_probs=58.5

Q ss_pred             CEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCc----------ccchhcccccCCCCEEEEEEEEEecCC---
Q 022938          101 FIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEP----------QKSIHEIAKGLTGSIISVKVIQANEEM---  167 (289)
Q Consensus       101 ~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p----------~~~~~~~~~~~vG~~V~vkVl~vd~~~---  167 (289)
                      +++.|+|+++.++|+||+++++.|++|.+++++.+...++          ...+      .+||.++|+|.++|.+.   
T Consensus         1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~------~~Gd~v~vkI~~vd~~~~~~   74 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVL------KVGDVVRARIVAVSLKERRP   74 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCEE------CCCCEEEEEEEEEeHHHCcC
Confidence            4789999999999999999999999999999876542221          2333      49999999999999764   


Q ss_pred             --cEEEEEeecc
Q 022938          168 --KKLVFSEKDA  177 (289)
Q Consensus       168 --~ri~lS~k~~  177 (289)
                        .++.||++..
T Consensus        75 ~~~~i~ls~k~~   86 (99)
T cd04460          75 RESKIGLTMRQP   86 (99)
T ss_pred             CCceEEEEEecC
Confidence              5899999975

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.59  E-value=1.4e-07  Score=95.17  Aligned_cols=68  Identities=43%  Similarity=0.815  Sum_probs=61.1

Q ss_pred             cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 022938          182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL  255 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~l  255 (289)
                      .....++|+++.|     .++|+||++.  +|   ..||+|+|++++.++.++.+.|++||.|+|+|+++|+ ++++.|
T Consensus       612 ~~~~~~~G~i~~G~V~~I~~~GafVei~--~g---~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L  684 (684)
T TIGR03591       612 ITAEPEVGKIYEGKVVRIMDFGAFVEIL--PG---KDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL  684 (684)
T ss_pred             hhcccccCcEEEEEEEEEeCCEEEEEEC--CC---cEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence            3456799999999     9999999995  55   9999999999999999999999999999999999997 777754

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).

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.53  E-value=2.3e-07  Score=93.70  Aligned_cols=70  Identities=21%  Similarity=0.384  Sum_probs=62.0

Q ss_pred             HHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEE
Q 022938           94 RAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLV  171 (289)
Q Consensus        94 ~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~  171 (289)
                      ....+.|+++.|+|+++.++|+||++. |.+||+|.+++++.+. .++.+.++      +||.|+|+|+++|. ++++.
T Consensus       613 ~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v-~~~~~~~k------vGD~V~VkVi~id~-~gki~  683 (684)
T TIGR03591       613 TAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERV-EKVEDVLK------EGDEVKVKVLEIDK-QGRIK  683 (684)
T ss_pred             hcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcc-cChhhccC------CCCEEEEEEEEECC-CCCcc
Confidence            344689999999999999999999998 8999999999999886 77887776      99999999999996 56654

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).

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

Probab=98.49  E-value=7.3e-07  Score=75.60  Aligned_cols=80  Identities=18%  Similarity=0.234  Sum_probs=62.4

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccch----hcccccCCCCEEEEEEEEEe-----cCCc
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSI----HEIAKGLTGSIISVKVIQAN-----EEMK  168 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~----~~~~~~~vG~~V~vkVl~vd-----~~~~  168 (289)
                      ..|++++|+|++++++|+||+++.++|++|.+++.+.+..-++.+..    .....+.+|+.|+++|.+++     ++..
T Consensus        80 ~~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~  159 (179)
T TIGR00448        80 ELGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEGS  159 (179)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCcc
Confidence            58999999999999999999998899999999998655322222100    00123459999999999998     5567


Q ss_pred             EEEEEeecc
Q 022938          169 KLVFSEKDA  177 (289)
Q Consensus       169 ri~lS~k~~  177 (289)
                      ++.+|+|++
T Consensus       160 ~I~lt~k~~  168 (179)
T TIGR00448       160 KIGLTMRQP  168 (179)
T ss_pred             eEEEEeccC
Confidence            999999985

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

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

Probab=98.46  E-value=7.9e-07  Score=87.39  Aligned_cols=78  Identities=22%  Similarity=0.353  Sum_probs=68.9

Q ss_pred             HHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcE
Q 022938           91 KAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKK  169 (289)
Q Consensus        91 ~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~r  169 (289)
                      +.+....++|+++.|+|+++.++|+||.+. |-+|++|.+++++.++ ...++.++      +||.+.|++..+| ..+|
T Consensus       611 ~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv-~kv~dvlk------~Gd~v~Vkv~~iD-~~Gr  682 (692)
T COG1185         611 EAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERV-EKVEDVLK------EGDEVKVKVIEID-KQGR  682 (692)
T ss_pred             HHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhh-hcccceee------cCceEEEEEeeec-ccCC
Confidence            345566799999999999999999999998 9999999999999876 66667766      9999999999999 5789


Q ss_pred             EEEEeec
Q 022938          170 LVFSEKD  176 (289)
Q Consensus       170 i~lS~k~  176 (289)
                      +.+|++.
T Consensus       683 i~ls~~~  689 (692)
T COG1185         683 IRLSIKA  689 (692)
T ss_pred             ccceehh
Confidence            9999875

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.39  E-value=7.6e-07  Score=78.70  Aligned_cols=70  Identities=27%  Similarity=0.364  Sum_probs=60.9

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc----cCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRITL  255 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~----~~~~~~~~iGd~V~vkV~~id~e~~ri~l  255 (289)
                      ..++||+|.|     .++|+||+|+  .+   ..|++|.+++++.+.    .++.+.|++||.|.|+|++++++ +.+.|
T Consensus        60 ~P~vGDiViG~V~~i~~~~~~vdI~--~~---~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~-~~~~L  133 (235)
T PRK04163         60 IPKVGDLVIGKVTDVTFSGWEVDIN--SP---YKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRT-RDVVL  133 (235)
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEeC--CC---ceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCC-CcEEE
Confidence            3488999999     8999999996  33   899999999999876    78888999999999999999974 46999


Q ss_pred             EEecC
Q 022938          256 SIKQL  260 (289)
Q Consensus       256 SlK~~  260 (289)
                      |+|+.
T Consensus       134 S~k~~  138 (235)
T PRK04163        134 TLKGK  138 (235)
T ss_pred             EEcCC
Confidence            99874

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

Probab=98.29  E-value=3.2e-06  Score=70.75  Aligned_cols=80  Identities=16%  Similarity=0.162  Sum_probs=61.8

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcc--cchhcc--cccCCCCEEEEEEEEEecCC-----c
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQ--KSIHEI--AKGLTGSIISVKVIQANEEM-----K  168 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~--~~~~~~--~~~~vG~~V~vkVl~vd~~~-----~  168 (289)
                      ..|+++.|.|+++.++|+||.++-.+||+|.+++.+.+...++.  ....+.  ..+.+|+.|++||..+....     .
T Consensus        80 ~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~  159 (183)
T COG1095          80 FRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRES  159 (183)
T ss_pred             ccccEEEEEEEEEeecceEEEeccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCccccc
Confidence            57999999999999999999999999999999999874422221  111110  12349999999999887655     4


Q ss_pred             EEEEEeecc
Q 022938          169 KLVFSEKDA  177 (289)
Q Consensus       169 ri~lS~k~~  177 (289)
                      ++.++++++
T Consensus       160 ~I~lTmrq~  168 (183)
T COG1095         160 KIGLTMRQP  168 (183)
T ss_pred             eEEEEeccc
Confidence            788999985

>TIGR02063 RNase_R ribonuclease R

Probab=98.28  E-value=5.2e-06  Score=84.56  Aligned_cols=79  Identities=20%  Similarity=0.286  Sum_probs=60.6

Q ss_pred             hhcCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCccc-ch-hc--ccccCCCCEEEEEEEEEecCCcE
Q 022938           96 YKESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQK-SI-HE--IAKGLTGSIISVKVIQANEEMKK  169 (289)
Q Consensus        96 ~~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~-~~-~~--~~~~~vG~~V~vkVl~vd~~~~r  169 (289)
                      ..+.|++++|+|++++++|+||++.  |++|++|.+++++.+..-+... .+ .+  ...+.+||.|+|+|.++|..+++
T Consensus       624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~  703 (709)
T TIGR02063       624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGK  703 (709)
T ss_pred             hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence            3478999999999999999999997  6999999999986543111110 00 00  01245999999999999999999


Q ss_pred             EEEEe
Q 022938          170 LVFSE  174 (289)
Q Consensus       170 i~lS~  174 (289)
                      +.+++
T Consensus       704 I~~~l  708 (709)
T TIGR02063       704 IDFEL  708 (709)
T ss_pred             EEEEE
Confidence            99875

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.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.28  E-value=3.3e-06  Score=74.65  Aligned_cols=73  Identities=19%  Similarity=0.278  Sum_probs=61.5

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCcc---CcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHS---CKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~---~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      +.|+++.|+|+++.++|++|+++ +..|++|.+++++.+.   ..++.+.|+      +||.|.|+|++++++ +.+.||
T Consensus        62 ~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~------~GDlV~akV~~i~~~-~~~~LS  134 (235)
T PRK04163         62 KVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLD------IGDYIIAKVKDVDRT-RDVVLT  134 (235)
T ss_pred             CCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCC------CCCEEEEEEEEECCC-CcEEEE
Confidence            79999999999999999999999 8999999999998653   134444454      999999999999854 458999


Q ss_pred             eecc
Q 022938          174 EKDA  177 (289)
Q Consensus       174 ~k~~  177 (289)
                      .+..
T Consensus       135 ~k~~  138 (235)
T PRK04163        135 LKGK  138 (235)
T ss_pred             EcCC
Confidence            8764

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

Probab=98.27  E-value=3.5e-06  Score=59.63  Aligned_cols=58  Identities=17%  Similarity=0.302  Sum_probs=47.6

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEEE
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITLS  256 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~--~ri~lS  256 (289)
                      ..|++++|     .++|+||+++   +   ++|++|.++++.      .+.|++||.|++.|.+++.++  ..|.||
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig---~---~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS   66 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLG---K---VEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILS   66 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcC---C---eEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence            46888888     7899999994   3   899999999863      356899999999999999654  457776

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.

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

Probab=98.25  E-value=5.2e-06  Score=70.40  Aligned_cols=73  Identities=34%  Similarity=0.626  Sum_probs=58.7

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccccc-----------CcccccCCCCEEEEEEEEEe---
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKID---  247 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~-----------~~~~~~~iGd~V~vkV~~id---  247 (289)
                      .+|+++.|     +++|+||+++  +    +.|++|.+++.+++..           +....+++||.|+++|.++|   
T Consensus        80 ~~gEvv~G~V~~v~~~GifV~lg--~----~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~  153 (179)
T TIGR00448        80 ELGEIVEGEVIEIVEFGAFVSLG--P----FDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKD  153 (179)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEeC--C----ceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccC
Confidence            46888888     9999999995  2    8999999998865431           23467999999999999998   


Q ss_pred             --CCCCeEEEEEecCCCCch
Q 022938          248 --REKSRITLSIKQLEEDPL  265 (289)
Q Consensus       248 --~e~~ri~lSlK~~~~~p~  265 (289)
                        ++..+|.+|+|+----|+
T Consensus       154 ~~~~~~~I~lt~k~~~LG~~  173 (179)
T TIGR00448       154 RRPEGSKIGLTMRQPLLGKL  173 (179)
T ss_pred             CCCCcceEEEEeccCcCCcc
Confidence              678899999998544443

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

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

Probab=98.24  E-value=8.2e-06  Score=82.31  Aligned_cols=78  Identities=18%  Similarity=0.302  Sum_probs=60.8

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccc-h-hc--ccccCCCCEEEEEEEEEecCCcEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKS-I-HE--IAKGLTGSIISVKVIQANEEMKKL  170 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~-~-~~--~~~~~vG~~V~vkVl~vd~~~~ri  170 (289)
                      -+.|++++|+|++++++|+||++.  +++|++|.+++.+.+..-++... + .+  ...+.+||+|+|+|.++|.++++|
T Consensus       570 ~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I  649 (654)
T TIGR00358       570 DKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSI  649 (654)
T ss_pred             hCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeE
Confidence            378999999999999999999997  79999999999876431222110 0 00  023459999999999999999999


Q ss_pred             EEEe
Q 022938          171 VFSE  174 (289)
Q Consensus       171 ~lS~  174 (289)
                      .+++
T Consensus       650 ~f~l  653 (654)
T TIGR00358       650 IFEL  653 (654)
T ss_pred             EEEE
Confidence            8875

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.

>TIGR02063 RNase_R ribonuclease R

Probab=98.22  E-value=4.1e-06  Score=85.29  Aligned_cols=70  Identities=27%  Similarity=0.562  Sum_probs=58.7

Q ss_pred             ccccccccEEEe-----eeeeEEEEEecCC-CceeEEEEEEccCcCcccc-----------cCcccccCCCCEEEEEEEE
Q 022938          183 SSRVNVEDIFVG-----RDYGAFIHLRFPD-GLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIK  245 (289)
Q Consensus       183 ~~~~~~G~iv~G-----~~~G~fV~i~~~~-G~~~i~Glv~~sels~~~~-----------~~~~~~~~iGd~V~vkV~~  245 (289)
                      +..-++|+++.|     +++|+||++.  + |   ++|++|++++++++.           .+....|++||.|+|+|.+
T Consensus       622 yl~~~iG~~~~g~V~~v~~fGifV~L~--~~~---~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~  696 (709)
T TIGR02063       622 YMSEKIGEEFEGVISGVTSFGLFVELE--NNT---IEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVK  696 (709)
T ss_pred             hhhccCCcEEEEEEEEEEeCCEEEEec--CCc---eEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEE
Confidence            334578999999     8999999995  3 4   999999999986543           2344679999999999999


Q ss_pred             EeCCCCeEEEEE
Q 022938          246 IDREKSRITLSI  257 (289)
Q Consensus       246 id~e~~ri~lSl  257 (289)
                      +|.++++|.+++
T Consensus       697 vd~~~~~I~~~l  708 (709)
T TIGR02063       697 ADLDTGKIDFEL  708 (709)
T ss_pred             EecccCeEEEEE
Confidence            999999999986

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.

>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=98.22  E-value=6.4e-06  Score=58.75  Aligned_cols=69  Identities=19%  Similarity=0.301  Sum_probs=56.4

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEE-EEEEEEEecCCcEEEEEee
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSII-SVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V-~vkVl~vd~~~~ri~lS~k  175 (289)
                      |++++|+|..-++.+++|++.  |+.|++|..++++ ...+++. .+   .+.++||++ ++.|+  +...+.+.+|.|
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 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD-HVSNCPL-LW---HCLQEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-chhhCHH-HH---hhhhcCCCccceEEE--eccccEEEEecC
Confidence            689999999999999999998  7999999999999 5434432 22   245699999 99998  777888888865

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=98.20  E-value=1.2e-06  Score=83.88  Aligned_cols=81  Identities=28%  Similarity=0.443  Sum_probs=70.6

Q ss_pred             ccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          183 SSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       183 ~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      ..++..|-+++|     .++|+||++-  +|   ..||+|.++|+..++.+|++.+.+||.|.++.+..|+ .+.+.+|.
T Consensus       663 ~~~l~~g~vy~~tIt~~rd~G~~V~l~--p~---~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~-~g~~~ls~  736 (760)
T KOG1067|consen  663 VQDLEFGGVYTATITEIRDTGVMVELY--PM---QQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSS  736 (760)
T ss_pred             ccceEeeeEEEEEEeeecccceEEEec--CC---chhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehh
Confidence            346777777777     8999999995  55   9999999999999999999999999999999999998 67788888


Q ss_pred             ecCCCCchhHHh
Q 022938          258 KQLEEDPLLETL  269 (289)
Q Consensus       258 K~~~~~p~~~~~  269 (289)
                      |.+.++|-...-
T Consensus       737 ralLp~p~~~~~  748 (760)
T KOG1067|consen  737 RALLPDPATKES  748 (760)
T ss_pred             hhhcCCcccCCc
Confidence            888999976543

>PRK11642 exoribonuclease R; Provisional

Probab=98.19  E-value=7.3e-06  Score=84.23  Aligned_cols=79  Identities=22%  Similarity=0.277  Sum_probs=61.6

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcc--cchhc--ccccCCCCEEEEEEEEEecCCcEEE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQ--KSIHE--IAKGLTGSIISVKVIQANEEMKKLV  171 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~--~~~~~--~~~~~vG~~V~vkVl~vd~~~~ri~  171 (289)
                      +.|++++|+|++++++|+||++.  +++|++|.+++++.++.-+..  ....+  ...+.+||.|+|+|.++|.+.++|.
T Consensus       642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~  721 (813)
T PRK11642        642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKID  721 (813)
T ss_pred             cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEE
Confidence            68999999999999999999997  499999999998764312211  00000  0124599999999999999999999


Q ss_pred             EEeec
Q 022938          172 FSEKD  176 (289)
Q Consensus       172 lS~k~  176 (289)
                      +++..
T Consensus       722 f~l~~  726 (813)
T PRK11642        722 FSLIS  726 (813)
T ss_pred             EEEec
Confidence            99854

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

Probab=98.14  E-value=7.5e-06  Score=68.55  Aligned_cols=76  Identities=30%  Similarity=0.566  Sum_probs=56.5

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc----------cC-cccccCCCCEEEEEEEEEeCCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----------QD-IRDILNEGDEVRVKVIKIDREK  250 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~----------~~-~~~~~~iGd~V~vkV~~id~e~  250 (289)
                      ..|+++.|     .++|+||.++  +    .+||+|.+++.++++          -. -...+++||.|++||+.+....
T Consensus        80 ~~gEVV~GeVv~~~~~G~fV~ig--p----~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~  153 (183)
T COG1095          80 FRGEVVEGEVVEVVEFGAFVRIG--P----LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKS  153 (183)
T ss_pred             ccccEEEEEEEEEeecceEEEec--c----ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEeccc
Confidence            34555555     9999999997  4    899999999988732          11 2336999999999999987544


Q ss_pred             -----CeEEEEEecC--CCCchhHH
Q 022938          251 -----SRITLSIKQL--EEDPLLET  268 (289)
Q Consensus       251 -----~ri~lSlK~~--~~~p~~~~  268 (289)
                           -+|.++||+.  -.-+|-+.
T Consensus       154 ~~~~~~~I~lTmrq~~LGklew~~~  178 (183)
T COG1095         154 RRPRESKIGLTMRQPGLGKLEWIEE  178 (183)
T ss_pred             CccccceEEEEeccccCCcchhhhh
Confidence                 6789999984  34455543

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

Probab=98.14  E-value=1.6e-05  Score=67.79  Aligned_cols=80  Identities=15%  Similarity=0.228  Sum_probs=60.4

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCccc-ch-h--cccccCCCCEEEEEEEEEecCC-----c
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQK-SI-H--EIAKGLTGSIISVKVIQANEEM-----K  168 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~-~~-~--~~~~~~vG~~V~vkVl~vd~~~-----~  168 (289)
                      ..|+++.|+|++++++|++|+++.++|+++.+++.+.+..-++.+ .+ .  ....+.+|+.|+|+|.+++.+.     .
T Consensus        80 ~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~  159 (187)
T PRK08563         80 ELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRGS  159 (187)
T ss_pred             cCCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCC
Confidence            589999999999999999999999999999999976543111110 00 0  0012349999999999998754     3


Q ss_pred             EEEEEeecc
Q 022938          169 KLVFSEKDA  177 (289)
Q Consensus       169 ri~lS~k~~  177 (289)
                      ++.+|++.+
T Consensus       160 ~I~ls~~~~  168 (187)
T PRK08563        160 KIGLTMRQP  168 (187)
T ss_pred             EEEEEecCC
Confidence            788899975

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=98.11  E-value=6.9e-06  Score=59.72  Aligned_cols=67  Identities=25%  Similarity=0.399  Sum_probs=59.9

Q ss_pred             cccccEEEe----eeeeEEEEEecCCCceeEEEEEE-ccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          186 VNVEDIFVG----RDYGAFIHLRFPDGLYHLTGLVH-VSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       186 ~~~G~iv~G----~~~G~fV~i~~~~G~~~i~Glv~-~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      -++|+++.|    .+.|+||.+-    .|+++|++. .++++..++.++.+.+ +|-+..|+|+.+|++++-|.||.
T Consensus        14 P~v~dvv~~Vv~i~d~~~YV~Ll----eY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         14 PNINEVTKGIVFVKDNIFYVKLI----DYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             CCCCeEEEEEEEEeccEEEEEEe----cCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence            367888878    8999999995    256999998 8999999999999989 99999999999999999999984

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

Probab=98.10  E-value=8.3e-06  Score=61.56  Aligned_cols=48  Identities=23%  Similarity=0.335  Sum_probs=41.0

Q ss_pred             EEEEEEccCcCccccc--CcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938          212 LTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  260 (289)
Q Consensus       212 i~Glv~~sels~~~~~--~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~  260 (289)
                      ..|++|.+++...+..  ++.+.|++||.|+|+|++++. ...+.||++.-
T Consensus        38 ~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~~~Lst~~~   87 (92)
T cd05791          38 FRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASSYYLSTAEN   87 (92)
T ss_pred             cccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCCcEEEecCC
Confidence            7899999998877665  688999999999999999985 46799998763

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".

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

Probab=98.07  E-value=6e-05  Score=64.27  Aligned_cols=79  Identities=25%  Similarity=0.544  Sum_probs=61.0

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccccc-----------CcccccCCCCEEEEEEEEEeC
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDR  248 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~-----------~~~~~~~iGd~V~vkV~~id~  248 (289)
                      .-.+|+++.|     .++|+||+++  +    +.|++|.+++.+++..           +....+++||.|+++|.+++.
T Consensus        78 ~P~~GEVv~g~V~~v~~~Gi~V~lg--~----~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~  151 (187)
T PRK08563         78 KPELQEVVEGEVVEVVEFGAFVRIG--P----VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSL  151 (187)
T ss_pred             eccCCCEEEEEEEEEEccEEEEEEe--C----ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEc
Confidence            3457999999     8999999996  2    8999999999866432           345679999999999999997


Q ss_pred             CC-----CeEEEEEecCC---CCchhHHh
Q 022938          249 EK-----SRITLSIKQLE---EDPLLETL  269 (289)
Q Consensus       249 e~-----~ri~lSlK~~~---~~p~~~~~  269 (289)
                      +.     .+|.+|+|+--   -+.|.+..
T Consensus       152 ~~~~~~~~~I~ls~~~~~LG~~~w~~~~~  180 (187)
T PRK08563        152 KERRPRGSKIGLTMRQPGLGKLEWIEEEK  180 (187)
T ss_pred             ccCCCCCCEEEEEecCCCCCcHHHHHHHH
Confidence            54     38999999842   34455433

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

Probab=98.01  E-value=5.7e-05  Score=56.49  Aligned_cols=69  Identities=13%  Similarity=0.175  Sum_probs=53.2

Q ss_pred             CCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCccc---chh--cccccCCCCEEEEEEEEEecCCc
Q 022938           99 SGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQK---SIH--EIAKGLTGSIISVKVIQANEEMK  168 (289)
Q Consensus        99 ~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~---~~~--~~~~~~vG~~V~vkVl~vd~~~~  168 (289)
                      .|+++.|+|+++++.|+||.+|.+++|++..++.+... .+|.+   .+.  .......|+.|++||..+..+.+
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~-~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~   74 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDME-FDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT   74 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccce-ECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence            48999999999999999999999999999999976654 34421   121  12345689999999998876544

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.

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

Probab=97.98  E-value=0.00012  Score=64.76  Aligned_cols=121  Identities=14%  Similarity=0.126  Sum_probs=83.4

Q ss_pred             eEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEE
Q 022938           26 LSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEG  105 (289)
Q Consensus        26 ~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g  105 (289)
                      +++++++.+-..+ -=.++||.+-|.+. +|.. +|+..+++..      ..++.+.    ....+.     -.++.++|
T Consensus       100 l~vp~~elp~~~~-~wpq~Gd~l~v~l~-~Dkk-~Ri~g~~a~~------~~l~~l~----~~~~~~-----l~nq~v~~  161 (287)
T COG2996         100 LLVPLDELPTLKS-LWPQKGDKLLVYLY-VDKK-GRIWGTLAIE------KILENLA----TPAYNN-----LKNQEVDA  161 (287)
T ss_pred             eeeehhhcccccc-cCCCCCCEEEEEEE-EccC-CcEEEEecch------hHHHhcC----Cccchh-----hhcCeeee
Confidence            3455555543211 12689999999873 4544 6999987622      0111100    001111     14899999


Q ss_pred             EEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeecchhh
Q 022938          106 KIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWN  180 (289)
Q Consensus       106 ~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~~~~~  180 (289)
                      +|-+....|.||-.. +..||||.||.-..+               +.|+++.++|+.+.. .+++.||++....+
T Consensus       162 tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~p---------------rlG~~l~~rVi~~re-Dg~lnLSl~p~~~E  221 (287)
T COG2996         162 TVYRLLESGTFVITENGYLGFIHKSERFAEP---------------RLGERLTARVIGVRE-DGKLNLSLRPRAHE  221 (287)
T ss_pred             EEEEEeccceEEEEcCCeEEEEcchhhcccc---------------cCCceEEEEEEEEcc-CCeeecccccccHH
Confidence            999999999999999 899999999864332               399999999999985 89999999875443

>PRK11642 exoribonuclease R; Provisional

Probab=97.96  E-value=2.9e-05  Score=79.91  Aligned_cols=70  Identities=30%  Similarity=0.532  Sum_probs=58.8

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccccc-----------CcccccCCCCEEEEEEEEEeCCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDREK  250 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~-----------~~~~~~~iGd~V~vkV~~id~e~  250 (289)
                      ++|+++.|     +++|+||+|.  ++  .++|+||.+++.+++..           +....|++||.|+|+|.++|.++
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 QVGNVFKGVISSVTGFGFFVRLD--DL--FIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDE  717 (813)
T ss_pred             cCCcEEEEEEEEeecCceEEEEC--CC--CeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCC
Confidence            78999999     9999999995  32  49999999999876321           23467999999999999999999


Q ss_pred             CeEEEEEecC
Q 022938          251 SRITLSIKQL  260 (289)
Q Consensus       251 ~ri~lSlK~~  260 (289)
                      ++|.+++-..
T Consensus       718 rkI~f~l~~~  727 (813)
T PRK11642        718 RKIDFSLISS  727 (813)
T ss_pred             CeEEEEEecc
Confidence            9999998543

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

Probab=97.91  E-value=3.5e-05  Score=77.80  Aligned_cols=69  Identities=26%  Similarity=0.482  Sum_probs=57.3

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-----------cCcccccCCCCEEEEEEEEEeC
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDR  248 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-----------~~~~~~~~iGd~V~vkV~~id~  248 (289)
                      +-++|+++.|     +++|+||++.. .   +++|++|.+++.+++.           ++....|++||.|+|+|.++|+
T Consensus       569 ~~~iG~~~~g~I~~v~~~GifV~L~~-~---~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~  644 (654)
T TIGR00358       569 LDKVGTEFSGEISSVTRFGMFVRLDD-N---GIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNM  644 (654)
T ss_pred             hhCCCcEEEEEEEeEEcCcEEEEecC-C---ceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEec
Confidence            3367999888     99999999951 3   4999999999987641           2234679999999999999999


Q ss_pred             CCCeEEEEE
Q 022938          249 EKSRITLSI  257 (289)
Q Consensus       249 e~~ri~lSl  257 (289)
                      ++++|.+++
T Consensus       645 ~~~~I~f~l  653 (654)
T TIGR00358       645 ETRSIIFEL  653 (654)
T ss_pred             ccCeEEEEE
Confidence            999999985

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=97.89  E-value=5.3e-05  Score=57.12  Aligned_cols=72  Identities=19%  Similarity=0.233  Sum_probs=57.9

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEE--------C-CEEEEeecCCCCCCccCc--CcccchhcccccCCCCEEEEEEEEEecC
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRF--------F-SLVGFLPFPQMSPSHSCK--EPQKSIHEIAKGLTGSIISVKVIQANEE  166 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l--------~-gv~g~ip~sels~~~~~~--~p~~~~~~~~~~~vG~~V~vkVl~vd~~  166 (289)
                      +.|+++.|+|+++....+.|++        . ...|++|.+++...+. .  +..+.|      .+||.|+++|.+++. 
T Consensus         5 ~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~-d~~~~~~~f------~~GDiV~AkVis~~~-   76 (92)
T cd05791           5 KVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEK-DKVEMYKCF------RPGDIVRAKVISLGD-   76 (92)
T ss_pred             CCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHcccccc-chHHHHhhc------CCCCEEEEEEEEcCC-
Confidence            6899999999999999999999        6 6899999999876553 2  233334      499999999999974 


Q ss_pred             CcEEEEEeecc
Q 022938          167 MKKLVFSEKDA  177 (289)
Q Consensus       167 ~~ri~lS~k~~  177 (289)
                      .+.+.||.+..
T Consensus        77 ~~~~~Lst~~~   87 (92)
T cd05791          77 ASSYYLSTAEN   87 (92)
T ss_pred             CCCcEEEecCC
Confidence            35688887754

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".

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=97.87  E-value=1.2e-05  Score=75.24  Aligned_cols=96  Identities=17%  Similarity=0.242  Sum_probs=68.9

Q ss_pred             cCCCCEEEEEEEEEecCCcEEEEEe-------ecchhhhccccc--ccccEEEe-----eeeeEEEEEecCCCceeEEEE
Q 022938          150 GLTGSIISVKVIQANEEMKKLVFSE-------KDAVWNKYSSRV--NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGL  215 (289)
Q Consensus       150 ~~vG~~V~vkVl~vd~~~~ri~lS~-------k~~~~~~~~~~~--~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Gl  215 (289)
                      ..+|+.+.+.+...+..+..+..+.       ++...+..++++  +.|+++.|     .+.|+||+++   |   +.|+
T Consensus        87 ~~vGD~i~~~I~~~~fgR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg---~---vEa~  160 (362)
T PRK12327         87 YELGDVIEIEVTPKDFGRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG---K---IEAV  160 (362)
T ss_pred             ccCCCEEEEecCcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC---C---eEEE
Confidence            3489999998865442221111111       112345667788  99999999     7789999994   3   9999


Q ss_pred             EEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCe--EEEEE
Q 022938          216 VHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR--ITLSI  257 (289)
Q Consensus       216 v~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~r--i~lSl  257 (289)
                      +|.+++.      +.+.|++||.++|.|.+++.+++.  |.||.
T Consensus       161 LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSR  198 (362)
T PRK12327        161 LPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSR  198 (362)
T ss_pred             ecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEe
Confidence            9988774      357799999999999999976654  55554

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

Probab=97.84  E-value=2e-05  Score=75.78  Aligned_cols=74  Identities=22%  Similarity=0.307  Sum_probs=64.2

Q ss_pred             hhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           96 YKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        96 ~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      .+..|-+++|+|+++.++|+||++. +..|++|.+|++..++ ..|++.+.      +||.+.++..+.|+..+...+|+
T Consensus       665 ~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~i-akpsd~le------vGq~I~vk~ie~d~~g~~~ls~r  737 (760)
T KOG1067|consen  665 DLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKI-AKPSDLLE------VGQEIQVKYIERDPRGGIMLSSR  737 (760)
T ss_pred             ceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccc-cChHHHHh------hcceeEEEEEeecCccceeehhh
Confidence            3567889999999999999999999 8999999999999987 88988876      99999999999997666555555


Q ss_pred             ec
Q 022938          175 KD  176 (289)
Q Consensus       175 k~  176 (289)
                      +-
T Consensus       738 al  739 (760)
T KOG1067|consen  738 AL  739 (760)
T ss_pred             hh
Confidence            43

>TIGR01953 NusA transcription termination factor NusA

Probab=97.77  E-value=3.2e-05  Score=71.83  Aligned_cols=98  Identities=16%  Similarity=0.263  Sum_probs=71.4

Q ss_pred             ccCCCCEEEEEEEEEecCCcEEEEEe-ec--------chhhhccccc--ccccEEEe-----eeee-EEEEEecCCCcee
Q 022938          149 KGLTGSIISVKVIQANEEMKKLVFSE-KD--------AVWNKYSSRV--NVEDIFVG-----RDYG-AFIHLRFPDGLYH  211 (289)
Q Consensus       149 ~~~vG~~V~vkVl~vd~~~~ri~lS~-k~--------~~~~~~~~~~--~~G~iv~G-----~~~G-~fV~i~~~~G~~~  211 (289)
                      ++.+|+.+.+.+...+  .+|+.++. |+        ..++..++++  +.|++++|     .+.| +||+++   |   
T Consensus        83 ~~~vGD~I~~~I~~~~--fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG---~---  154 (341)
T TIGR01953        83 DVQIGDEVKKEIPPEN--FGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG---K---  154 (341)
T ss_pred             ccccCCEEEEEecccC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC---C---
Confidence            3459999999885432  34433332 22        2455667777  59999999     5556 699994   3   


Q ss_pred             EEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEEEEecC
Q 022938          212 LTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITLSIKQL  260 (289)
Q Consensus       212 i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~--~ri~lSlK~~  260 (289)
                      +.|++|.++..      +.+.|++||.++|.|.+++.+.  ..|.||.+..
T Consensus       155 ~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~  199 (341)
T TIGR01953       155 TEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP  199 (341)
T ss_pred             eEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence            99999999886      3466999999999999999543  5689998763

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.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=97.74  E-value=0.00018  Score=49.97  Aligned_cols=60  Identities=22%  Similarity=0.144  Sum_probs=36.3

Q ss_pred             CCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           99 SGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        99 ~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      .|++.+.+|...++.|+|++.+ +-+.++|.+++....               .+|+.|.|.|. .| ..+|+.+|++
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~~---------------~~Gd~v~VFvY-~D-~~~rl~AT~k   61 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEPL---------------KVGDEVEVFVY-LD-KEGRLVATTK   61 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG---------------------TTSEEEEEEE-E--TTS-EEEE--
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCCC---------------CCCCEEEEEEE-EC-CCCCEEEecC
Confidence            3888899999999999999999 699999999975332               29999999996 56 3558888764

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

Probab=97.66  E-value=0.00033  Score=59.23  Aligned_cols=79  Identities=6%  Similarity=0.062  Sum_probs=57.5

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCccc---ch-h--cccccCCCCEEEEEEEEEecCC--cE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQK---SI-H--EIAKGLTGSIISVKVIQANEEM--KK  169 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~---~~-~--~~~~~~vG~~V~vkVl~vd~~~--~r  169 (289)
                      ..|+++.|.|+++++.|+||.+|=.++|+|.++|.+... -++.+   .+ .  .......|+.|++||..+..+.  .+
T Consensus        80 f~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~-fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~  158 (176)
T PTZ00162         80 FKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFV-YDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLF  158 (176)
T ss_pred             CCCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccE-ECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcE
Confidence            589999999999999999999997889999999975432 22211   11 1  1233558999999998776443  35


Q ss_pred             EEEEeecc
Q 022938          170 LVFSEKDA  177 (289)
Q Consensus       170 i~lS~k~~  177 (289)
                      +.+|++.+
T Consensus       159 ~i~T~~~~  166 (176)
T PTZ00162        159 AIATINSD  166 (176)
T ss_pred             EEEEecCC
Confidence            66677764

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

Probab=97.61  E-value=4.1e-05  Score=67.15  Aligned_cols=89  Identities=26%  Similarity=0.427  Sum_probs=75.8

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  261 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~  261 (289)
                      .++++|-+     .+.|+||.+...+   ++.|++-.|+||..++.+++...++|-.=.|.|+.+|++++-|.||.+.+.
T Consensus        15 ev~e~VmvnV~sIaemGayv~LlEYn---niEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs   91 (304)
T KOG2916|consen   15 EVEEIVMVNVRSIAEMGAYVKLLEYN---NIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVS   91 (304)
T ss_pred             CcccEEEEEeeEehhccceEeeeecC---CcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCC
Confidence            45566655     7899999996444   599999999999999999999999999999999999999999999999998


Q ss_pred             CCchhHHhhhhCCCChH
Q 022938          262 EDPLLETLEKVIPQGLE  278 (289)
Q Consensus       262 ~~p~~~~~~~~~~g~~~  278 (289)
                      ++--....+++-.--..
T Consensus        92 ~ed~~kC~Er~~ksK~v  108 (304)
T KOG2916|consen   92 PEDKEKCEERFAKSKLV  108 (304)
T ss_pred             HHHHHHHHHHHHHhHHH
Confidence            88777777776554333

>PRK05054 exoribonuclease II; Provisional

Probab=97.53  E-value=0.00079  Score=67.93  Aligned_cols=77  Identities=18%  Similarity=0.312  Sum_probs=57.5

Q ss_pred             cCC--CEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCc--c--CcCcccch-hcccccCCCCEEEEEEEEEecCCc
Q 022938           98 ESG--FIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSH--S--CKEPQKSI-HEIAKGLTGSIISVKVIQANEEMK  168 (289)
Q Consensus        98 ~~G--~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~--~--~~~p~~~~-~~~~~~~vG~~V~vkVl~vd~~~~  168 (289)
                      ..|  +.++|.|++++++|+||++.  |++|+||.+.+.+.+  .  ..+..... .....+.+||+|+|+|.++|.+.+
T Consensus       558 ~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~  637 (644)
T PRK05054        558 KAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR  637 (644)
T ss_pred             ccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence            455  59999999999999999997  799999999996531  1  01111111 001246799999999999999999


Q ss_pred             EEEEEe
Q 022938          169 KLVFSE  174 (289)
Q Consensus       169 ri~lS~  174 (289)
                      +|.++.
T Consensus       638 ~i~~~~  643 (644)
T PRK05054        638 SIIARP  643 (644)
T ss_pred             eEEEEE
Confidence            988764

>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=97.47  E-value=0.00033  Score=50.03  Aligned_cols=63  Identities=17%  Similarity=0.256  Sum_probs=50.8

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccC---cccccCCCCEE-EEEEEEEeCCCCeEEEEEe
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD---IRDILNEGDEV-RVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~---~~~~~~iGd~V-~vkV~~id~e~~ri~lSlK  258 (289)
                      |++++|     ++.+++|+++  +.  ++.|+++..++++ +.++   .-..+++||++ .+.|+  ++..+.|.+|.|
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 GKLVDARVLKKTLNGLEVAIL--PE--EIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEec--CC--CcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence            567777     8889999997  42  4999999999998 5433   33558999999 99999  877888898875

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.

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=97.46  E-value=0.00031  Score=51.24  Aligned_cols=69  Identities=14%  Similarity=0.223  Sum_probs=56.9

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC--CEEEEee-cCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF--SLVGFLP-FPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip-~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      .++|+++. .|+.+.+.|++|.+-  |++|.|+ .+|++..+. ....       +..+|....|+|+.+|++++-|-||
T Consensus        14 P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~ri-rsi~-------kllVGk~e~v~ViRVDk~KGYIDLs   84 (86)
T PHA02858         14 PNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRA-EKLK-------KKLVGKTINVQVIRTDKLKGYIDVR   84 (86)
T ss_pred             CCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHH-Hhhh-------hhhcCCeeEEEEEEECCCCCEEEeE
Confidence            36899998 899999999999975  8999998 999986654 2222       2339999999999999999999887


Q ss_pred             e
Q 022938          174 E  174 (289)
Q Consensus       174 ~  174 (289)
                      .
T Consensus        85 ~   85 (86)
T PHA02858         85 H   85 (86)
T ss_pred             c
Confidence            4

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

Probab=97.29  E-value=0.0024  Score=53.73  Aligned_cols=77  Identities=29%  Similarity=0.343  Sum_probs=57.7

Q ss_pred             hhcccccccccEEEe-----eeeeEEEEEecCCC-----ceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCC
Q 022938          180 NKYSSRVNVEDIFVG-----RDYGAFIHLRFPDG-----LYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDRE  249 (289)
Q Consensus       180 ~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G-----~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e  249 (289)
                      .....-.+.|++|-|     ....+.|++-+..+     .+-..|-+|+|+.+..+++++++.|++||.|+|+|++.-  
T Consensus        56 ~~~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--  133 (188)
T COG1096          56 KKTPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--  133 (188)
T ss_pred             CCCCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--
Confidence            335566788898888     56666776642111     002567899999999999999999999999999999984  


Q ss_pred             CCeEEEEEec
Q 022938          250 KSRITLSIKQ  259 (289)
Q Consensus       250 ~~ri~lSlK~  259 (289)
                       -.+.||.+.
T Consensus       134 -~~~~Lst~~  142 (188)
T COG1096         134 -DPIQLSTKG  142 (188)
T ss_pred             -CCeEEEecC
Confidence             347777764

>TIGR02062 RNase_B exoribonuclease II

Probab=97.20  E-value=0.0022  Score=64.65  Aligned_cols=76  Identities=17%  Similarity=0.315  Sum_probs=55.6

Q ss_pred             cCC--CEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCC--C-c-cCcCcc-cchhcccccCCCCEEEEEEEEEecCCc
Q 022938           98 ESG--FIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSP--S-H-SCKEPQ-KSIHEIAKGLTGSIISVKVIQANEEMK  168 (289)
Q Consensus        98 ~~G--~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~--~-~-~~~~p~-~~~~~~~~~~vG~~V~vkVl~vd~~~~  168 (289)
                      +.|  +.+.|.|++++++|+||++.  |++|+||.+.+.+  . + ...+.. -.+.-...+.+||+|+|+|.++|.+.+
T Consensus       554 ~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~  633 (639)
T TIGR02062       554 KAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETR  633 (639)
T ss_pred             ccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccC
Confidence            454  59999999999999999995  8999999999965  1 1 111111 011000136699999999999999988


Q ss_pred             EEEEE
Q 022938          169 KLVFS  173 (289)
Q Consensus       169 ri~lS  173 (289)
                      +|.+.
T Consensus       634 ~i~~~  638 (639)
T TIGR02062       634 SIIAR  638 (639)
T ss_pred             cEeee
Confidence            88764

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.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.17  E-value=0.0011  Score=63.20  Aligned_cols=59  Identities=20%  Similarity=0.323  Sum_probs=47.1

Q ss_pred             cCCCEEEEEEEEEEcC--cEEEEEC-CEEEEeecCCCCCCcc-----------CcCcccchhcccccCCCCEEEEEEEE
Q 022938           98 ESGFIYEGKIQGFNGG--GLLVRFF-SLVGFLPFPQMSPSHS-----------CKEPQKSIHEIAKGLTGSIISVKVIQ  162 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~--G~~V~l~-gv~g~ip~sels~~~~-----------~~~p~~~~~~~~~~~vG~~V~vkVl~  162 (289)
                      ..|.++.|+|.++.++  |+||++| +..||+|.+++.+...           .+++.+.+      .+||.|.|.|.+
T Consensus        24 ~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l------~~G~~IlVQV~K   96 (414)
T TIGR00757        24 LKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELL------RPGQSVLVQVVK   96 (414)
T ss_pred             CCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhC------cCCCEEEEEEee
Confidence            5899999999999998  9999999 8999999999865311           01222233      389999999986

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.

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

Probab=97.16  E-value=0.019  Score=50.34  Aligned_cols=86  Identities=17%  Similarity=0.197  Sum_probs=65.2

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCcc---CcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHS---CKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~---~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      +.|+.+-|.|..+...+..|+++ -..|++|.+++.+...   ..+....++      +||.|.++|..+|+ .....|+
T Consensus        63 ~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~------vGD~v~AkV~~vd~-~~~~~L~  135 (239)
T COG1097          63 EVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLN------VGDLVYAKVVDVDR-DGEVELT  135 (239)
T ss_pred             CCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccc------cCCEEEEEEEEccC-CCceEEE
Confidence            79999999999999999999999 5999999999954432   123334444      99999999999995 5677777


Q ss_pred             eecchhhhcccccccccEEEe
Q 022938          174 EKDAVWNKYSSRVNVEDIFVG  194 (289)
Q Consensus       174 ~k~~~~~~~~~~~~~G~iv~G  194 (289)
                      .|..    -+-.++.|.++..
T Consensus       136 ~k~~----~~GkL~~G~iv~i  152 (239)
T COG1097         136 LKDE----GLGKLKNGQIVKI  152 (239)
T ss_pred             eecC----CCccccCCEEEEE
Confidence            7543    3445566666554

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

Probab=97.13  E-value=0.0027  Score=47.45  Aligned_cols=59  Identities=17%  Similarity=0.247  Sum_probs=45.5

Q ss_pred             cccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccC-----------cccccCCCCEEEEEEEEEeCCCC
Q 022938          188 VEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-----------IRDILNEGDEVRVKVIKIDREKS  251 (289)
Q Consensus       188 ~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~-----------~~~~~~iGd~V~vkV~~id~e~~  251 (289)
                      +|+++.|     +++|+||.++  +    +.+|+|.+.+..+..-+           -...+.+|+.|++||..+..+.+
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G--p----l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~   74 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG--P----LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT   74 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc--C----ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence            4788888     8999999996  3    88999998886553222           13458899999999999987655


Q ss_pred             e
Q 022938          252 R  252 (289)
Q Consensus       252 r  252 (289)
                      .
T Consensus        75 ~   75 (88)
T cd04462          75 D   75 (88)
T ss_pred             c
Confidence            4

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.

>PRK05054 exoribonuclease II; Provisional

Probab=97.04  E-value=0.0024  Score=64.54  Aligned_cols=67  Identities=15%  Similarity=0.155  Sum_probs=52.2

Q ss_pred             ccc--cEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccc--c---cC-------cccccCCCCEEEEEEEEEe
Q 022938          187 NVE--DIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--I---QD-------IRDILNEGDEVRVKVIKID  247 (289)
Q Consensus       187 ~~G--~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~--~---~~-------~~~~~~iGd~V~vkV~~id  247 (289)
                      ++|  +.+.|     +++|+||+|. ..   ++.|+||.+.+...+  .   .+       -...|++||.|+|+|.++|
T Consensus       558 ~~G~~~~f~g~I~~v~~~G~fV~l~-~~---~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd  633 (644)
T PRK05054        558 KAGTDTRFAAEIIDISRGGMRVRLL-EN---GAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVR  633 (644)
T ss_pred             ccCCCeEEEEEEEeeecCcEEEEEe-CC---ceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEc
Confidence            455  47777     8999999996 23   499999999996531  1   01       1246999999999999999


Q ss_pred             CCCCeEEEEE
Q 022938          248 REKSRITLSI  257 (289)
Q Consensus       248 ~e~~ri~lSl  257 (289)
                      .++++|.+++
T Consensus       634 ~~~~~i~~~~  643 (644)
T PRK05054        634 METRSIIARP  643 (644)
T ss_pred             cccCeEEEEE
Confidence            9999998874

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=97.04  E-value=0.0042  Score=63.48  Aligned_cols=81  Identities=17%  Similarity=0.213  Sum_probs=62.3

Q ss_pred             HhhcCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCccc----chhcccccCCCCEEEEEEEEEecCCc
Q 022938           95 AYKESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQK----SIHEIAKGLTGSIISVKVIQANEEMK  168 (289)
Q Consensus        95 ~~~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~----~~~~~~~~~vG~~V~vkVl~vd~~~~  168 (289)
                      -..+.|+.++|+|+++..+|+||.+.  +++|++|.+.+...++.-++..    .-+....++.|+.|++++.+++...+
T Consensus       618 m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~  697 (706)
T COG0557         618 MKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDER  697 (706)
T ss_pred             HHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEccccc
Confidence            33589999999999999999999998  5999999999996444222211    00111246699999999999999888


Q ss_pred             EEEEEee
Q 022938          169 KLVFSEK  175 (289)
Q Consensus       169 ri~lS~k  175 (289)
                      ++.+++.
T Consensus       698 ~i~~~~v  704 (706)
T COG0557         698 KIDFELV  704 (706)
T ss_pred             ceEEEec
Confidence            8887653

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

Probab=96.95  E-value=0.0012  Score=68.38  Aligned_cols=74  Identities=19%  Similarity=0.252  Sum_probs=62.6

Q ss_pred             hhcCCCEEEEEEEEEEcC--c-EEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEE
Q 022938           96 YKESGFIYEGKIQGFNGG--G-LLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLV  171 (289)
Q Consensus        96 ~~~~G~iv~g~V~~v~~~--G-~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~  171 (289)
                      .+..|.++.++|++|+..  + +-|.+. |+.||||..++|+..+ .+|...+.      +||.|.|+|+++|.++=-+.
T Consensus       982 t~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v-~~p~~~v~------vgq~v~~kvi~id~e~f~v~ 1054 (1299)
T KOG1856|consen  982 TFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDV-RRPENRVK------VGQTVYCKVIKIDKERFSVE 1054 (1299)
T ss_pred             HhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhc-cCHHHhhc------cCceEEEEeeeeeHhhhhhh
Confidence            467899999999999954  2 467788 9999999999999776 88887776      99999999999998776677


Q ss_pred             EEeec
Q 022938          172 FSEKD  176 (289)
Q Consensus       172 lS~k~  176 (289)
                      ||.+.
T Consensus      1055 Ls~r~ 1059 (1299)
T KOG1856|consen 1055 LSCRT 1059 (1299)
T ss_pred             hhhhh
Confidence            77664

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

Probab=96.89  E-value=0.003  Score=55.31  Aligned_cols=69  Identities=29%  Similarity=0.485  Sum_probs=57.4

Q ss_pred             cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc----cCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~----~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      -++||+|-|     ...+..|+|+.+     ..+++|.|++.+...    .+++..|++||.|.|+|..+|+ .....|+
T Consensus        62 P~~gD~VIG~I~~v~~~~W~VDI~sp-----~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~  135 (239)
T COG1097          62 PEVGDVVIGKIIEVGPSGWKVDIGSP-----YPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELT  135 (239)
T ss_pred             CCCCCEEEEEEEEEcccceEEEcCCc-----cceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceEEE
Confidence            367888888     788999999743     789999999855542    4678889999999999999997 7889999


Q ss_pred             EecC
Q 022938          257 IKQL  260 (289)
Q Consensus       257 lK~~  260 (289)
                      +|..
T Consensus       136 ~k~~  139 (239)
T COG1097         136 LKDE  139 (239)
T ss_pred             eecC
Confidence            9765

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

Probab=96.74  E-value=0.012  Score=43.63  Aligned_cols=70  Identities=19%  Similarity=0.203  Sum_probs=55.2

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD  176 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~  176 (289)
                      +.|+.+-|+|+.+......|+++ -..|++|..++.-..  ++....++      +|+.|-|+|.++++. ....||...
T Consensus         5 ~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gat--k~~rp~L~------~GDlV~ArV~~~~~~-~~~eLtc~~   75 (86)
T cd05790           5 AKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGAT--KRNRPNLN------VGDLVYARVVKANRD-MEPELSCVD   75 (86)
T ss_pred             CCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHccccc--ccccccCC------CCCEEEEEEEecCCC-CCeEEEEeC
Confidence            68999999999999999999999 689999998774332  22233344      999999999999864 456777765

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".

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

Probab=96.63  E-value=0.009  Score=44.36  Aligned_cols=67  Identities=19%  Similarity=0.103  Sum_probs=52.0

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  260 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~  260 (289)
                      ++||+|-|     ...+.+|+|+.     ...|++|..++... .+..+..+++||.|-|+|.++|+. ....||+...
T Consensus         5 ~~gD~VIG~V~~~~~~~~~VdI~s-----~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~-~~~eLtc~~~   76 (86)
T cd05790           5 AKGDHVIGIVVAKAGDFFKVDIGG-----SEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRD-MEPELSCVDS   76 (86)
T ss_pred             CCCCEEEEEEEEEcCCeEEEEcCC-----CcceEechHHcccc-cccccccCCCCCEEEEEEEecCCC-CCeEEEEeCC
Confidence            57888888     66788999963     26799998776433 344567799999999999999984 5689998773

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".

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

Probab=96.58  E-value=0.0099  Score=50.24  Aligned_cols=68  Identities=18%  Similarity=0.232  Sum_probs=49.3

Q ss_pred             cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccc-----------c-cCcccccCCCCEEEEEEEEEeC
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-----------I-QDIRDILNEGDEVRVKVIKIDR  248 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~-----------~-~~~~~~~~iGd~V~vkV~~id~  248 (289)
                      -..|++++|     +++|+||.++  +    .++++|.++|..+.           . ++-...+..|+.|++||..+..
T Consensus        79 Pf~gEVv~g~V~~v~~~G~~v~~G--p----~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~  152 (176)
T PTZ00162         79 PFKDEVLDAIVTDVNKLGFFAQAG--P----LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRY  152 (176)
T ss_pred             cCCCCEEEEEEEEEecceEEEEee--C----eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEe
Confidence            356777777     8999999997  3    77999999997441           1 1224568999999999988865


Q ss_pred             CC--CeEEEEEec
Q 022938          249 EK--SRITLSIKQ  259 (289)
Q Consensus       249 e~--~ri~lSlK~  259 (289)
                      +.  .+...|||+
T Consensus       153 ~~~~~~~i~T~~~  165 (176)
T PTZ00162        153 DASNLFAIATINS  165 (176)
T ss_pred             cCCCcEEEEEecC
Confidence            43  345556665

>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=96.34  E-value=0.0072  Score=44.47  Aligned_cols=76  Identities=22%  Similarity=0.340  Sum_probs=38.1

Q ss_pred             CCCCEEEEEEEEEecCCcEEEEEeec--chhhhcccccccccEEEeeeeeEEEEEecCCCceeEEEEEEccCcCcccccC
Q 022938          151 LTGSIISVKVIQANEEMKKLVFSEKD--AVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD  228 (289)
Q Consensus       151 ~vG~~V~vkVl~vd~~~~ri~lS~k~--~~~~~~~~~~~~G~iv~G~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~  228 (289)
                      .+|+.|-++|+++.+  +...+..-.  ..+.   .....+..          .+.  .   ...|+++.+++.....+.
T Consensus         3 ~vGdiV~~rVtrv~~--~~a~v~Il~v~~~~~---~~~~~~~~----------~l~--~---~f~GiIR~~DVR~te~Dk   62 (82)
T PF10447_consen    3 KVGDIVIARVTRVNP--RQAKVEILCVEGKGN---DSINAGDR----------PLK--E---PFQGIIRKQDVRATEKDK   62 (82)
T ss_dssp             -TT-EEEEEEEEE-S--SEEEEEEEES-------------SSS-------------------SS-S-EEEEGGGT-SS--
T ss_pred             CCCCEEEEEEEEEec--cEEEEEEEEEEeccc---cccccCCc----------ccc--c---ccEEEEEeeeecccccch
Confidence            489999999999954  333333322  1111   00000110          122  1   277999999887665443


Q ss_pred             --cccccCCCCEEEEEEEEE
Q 022938          229 --IRDILNEGDEVRVKVIKI  246 (289)
Q Consensus       229 --~~~~~~iGd~V~vkV~~i  246 (289)
                        +.+.|++||.|+|+|+++
T Consensus        63 v~~~~~FrpGDIVrA~ViSl   82 (82)
T PF10447_consen   63 VKMYDCFRPGDIVRARVISL   82 (82)
T ss_dssp             --GGGT--SSSEEEEEEEEE
T ss_pred             hhHHhccCCCCEEEEEEeeC
Confidence              578899999999999975

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.

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

Probab=96.28  E-value=0.0031  Score=55.63  Aligned_cols=73  Identities=19%  Similarity=0.250  Sum_probs=64.0

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEE---CCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRF---FSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l---~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      .++++++-+.|.++...|++|.+   ++++|.+-.+|+|..++ ....+.++      +|..=.|.|+.||.+++-|-||
T Consensus        14 Pev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRI-RSI~klir------VGr~E~vvVlrVDkekGYIDLS   86 (304)
T KOG2916|consen   14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRI-RSIQKLIR------VGRNEPVVVLRVDKEKGYIDLS   86 (304)
T ss_pred             CCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHH-HHHHHHHh------cCCcceEEEEEEcCCCCceech
Confidence            37899999999999999999986   37999999999998776 44555555      9999999999999999999999


Q ss_pred             eec
Q 022938          174 EKD  176 (289)
Q Consensus       174 ~k~  176 (289)
                      .+.
T Consensus        87 krr   89 (304)
T KOG2916|consen   87 KRR   89 (304)
T ss_pred             hcc
Confidence            875

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=96.19  E-value=0.012  Score=56.29  Aligned_cols=58  Identities=28%  Similarity=0.407  Sum_probs=45.8

Q ss_pred             cccccccEEEe-----eee--eEEEEEecCCCceeEEEEEEccCcCcc------------cccCcccccCCCCEEEEEEE
Q 022938          184 SRVNVEDIFVG-----RDY--GAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI  244 (289)
Q Consensus       184 ~~~~~G~iv~G-----~~~--G~fV~i~~~~G~~~i~Glv~~sels~~------------~~~~~~~~~~iGd~V~vkV~  244 (289)
                      ....+|++|.|     .+.  |+||+|+  .|   -.||+|.+++.+.            ...++.+.+++||.|.|.|.
T Consensus        21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG--~~---k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~   95 (414)
T TIGR00757        21 SRQLKGNIYKGRVTRILPSLQAAFVDIG--LE---KNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVV   95 (414)
T ss_pred             CcCCCCCEEEEEEeeecCCCceEEEEcC--CC---ceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEe
Confidence            34578999999     555  9999997  54   8999999998653            23345667999999999999


Q ss_pred             EE
Q 022938          245 KI  246 (289)
Q Consensus       245 ~i  246 (289)
                      .=
T Consensus        96 Ke   97 (414)
T TIGR00757        96 KE   97 (414)
T ss_pred             eC
Confidence            83

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.

>TIGR02062 RNase_B exoribonuclease II

Probab=96.13  E-value=0.016  Score=58.55  Aligned_cols=66  Identities=14%  Similarity=0.207  Sum_probs=50.0

Q ss_pred             ccc--cEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCc--ccc-----c---Cc--ccccCCCCEEEEEEEEEe
Q 022938          187 NVE--DIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSW--DLI-----Q---DI--RDILNEGDEVRVKVIKID  247 (289)
Q Consensus       187 ~~G--~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~--~~~-----~---~~--~~~~~iGd~V~vkV~~id  247 (289)
                      ++|  +.+.|     +++|+||++. ..   ++.|++|.+.+..  +..     .   .+  ...|++||.|+|+|.++|
T Consensus       554 ~~g~~~~f~g~I~~v~~~g~~v~l~-~~---~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd  629 (639)
T TIGR02062       554 KAAKNTRFAAEIVDISRGGMRVRLL-EN---GAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVR  629 (639)
T ss_pred             ccCCCcEEEEEEEeeeCCcEEEEEe-cC---ceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEec
Confidence            454  36666     8999999996 23   4999999999865  211     1   11  126999999999999999


Q ss_pred             CCCCeEEEE
Q 022938          248 REKSRITLS  256 (289)
Q Consensus       248 ~e~~ri~lS  256 (289)
                      .++++|.+.
T Consensus       630 ~~~~~i~~~  638 (639)
T TIGR02062       630 METRSIIAR  638 (639)
T ss_pred             cccCcEeee
Confidence            999998764

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.

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

Probab=96.04  E-value=0.074  Score=44.89  Aligned_cols=70  Identities=19%  Similarity=0.274  Sum_probs=56.2

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEECC-----------EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEec
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFFS-----------LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANE  165 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~g-----------v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~  165 (289)
                      .+.|+++-|.|+++....+.|++-+           ..|-+|.++.+..+. .+..+.|+      +||.|+++|++.- 
T Consensus        62 ~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~-~~~~d~f~------~GDivrA~Vis~~-  133 (188)
T COG1096          62 PKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYV-EKLSDAFR------IGDIVRARVISTG-  133 (188)
T ss_pred             CCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccc-cccccccc------cccEEEEEEEecC-
Confidence            5789999999999999999998753           346789999988876 66666665      9999999999863 


Q ss_pred             CCcEEEEEeec
Q 022938          166 EMKKLVFSEKD  176 (289)
Q Consensus       166 ~~~ri~lS~k~  176 (289)
                        ..+.||.+.
T Consensus       134 --~~~~Lst~~  142 (188)
T COG1096         134 --DPIQLSTKG  142 (188)
T ss_pred             --CCeEEEecC
Confidence              456676665

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

Probab=95.96  E-value=0.0056  Score=63.67  Aligned_cols=75  Identities=24%  Similarity=0.332  Sum_probs=59.7

Q ss_pred             cccccccEEEe------eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          184 SRVNVEDIFVG------RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       184 ~~~~~G~iv~G------~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      +.+..|.+|.+      ...|.-|.+-..+|   +.|+|+.+++|+..+.+|...+++||+|.|+|+++|.++=.+.||+
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~Ls~ 1057 (1299)
T KOG1856|consen  981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCG---VTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSC 1057 (1299)
T ss_pred             hHhccCceEEEeeeEEEecccceeEEEecCC---CceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhh
Confidence            45778888876      33333333322366   9999999999999999999999999999999999999888888998


Q ss_pred             ecCC
Q 022938          258 KQLE  261 (289)
Q Consensus       258 K~~~  261 (289)
                      |.++
T Consensus      1058 r~sd 1061 (1299)
T KOG1856|consen 1058 RTSD 1061 (1299)
T ss_pred             hhHH
Confidence            8753

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

Probab=95.87  E-value=0.075  Score=43.72  Aligned_cols=70  Identities=19%  Similarity=0.200  Sum_probs=45.8

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcc---cchh-cc-cccCCCCEEEEEEEEEecCCc
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQ---KSIH-EI-AKGLTGSIISVKVIQANEEMK  168 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~---~~~~-~~-~~~~vG~~V~vkVl~vd~~~~  168 (289)
                      -.|++++|+|+++++.|+|++.|-++-|+..-.....+. -+|+   ..|. ++ ....+|.+|+++|+.......
T Consensus        80 fKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~-f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~  154 (170)
T KOG3298|consen   80 FKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYE-FDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDET  154 (170)
T ss_pred             cCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcc-cCCCCCCCcccccccceeeeCcEEEEEEEEEEEeee
Confidence            479999999999999999999997777765433332221 1122   1121 11 134589999999987654333

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

Probab=95.81  E-value=0.0076  Score=58.78  Aligned_cols=74  Identities=30%  Similarity=0.482  Sum_probs=59.9

Q ss_pred             cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      .+.+++.|.++.|     ..||+||+++  .   ++.|++|.++++..      ..|.+||.+-+.+..+.++++.+.+.
T Consensus       116 ~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln--~---~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~  184 (715)
T COG1107         116 TMEDVEAGKYYKGIVSRVEKYGVFVELN--S---HVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFE  184 (715)
T ss_pred             chhhcccceeeeccccchhhhcceeecC--h---hhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCcccee
Confidence            4678899999999     8999999996  3   59999999998752      34889999999999999988877765


Q ss_pred             EecCCCCchhHH
Q 022938          257 IKQLEEDPLLET  268 (289)
Q Consensus       257 lK~~~~~p~~~~  268 (289)
                      ...+  ++|...
T Consensus       185 ~~~~--~~Y~~~  194 (715)
T COG1107         185 PVGL--DRYREV  194 (715)
T ss_pred             ecCC--ccchhh
Confidence            5544  455543

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.64  E-value=0.035  Score=52.03  Aligned_cols=61  Identities=20%  Similarity=0.334  Sum_probs=49.1

Q ss_pred             ccccEEEe-----ee-eeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCC---eEEEEE
Q 022938          187 NVEDIFVG-----RD-YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS---RITLSI  257 (289)
Q Consensus       187 ~~G~iv~G-----~~-~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~---ri~lSl  257 (289)
                      ++|+++.|     .. .++||+++   +   +.|++|.++..      +.+.|++||.++|.|.+++...+   .|.||.
T Consensus       137 ~~Geiv~g~V~r~~~~~~i~vdlg---~---~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSR  204 (374)
T PRK12328        137 KVGKIVFGTVVRVDNEENTFIEID---E---IRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSR  204 (374)
T ss_pred             hcCcEEEEEEEEEecCCCEEEEcC---C---eEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEc
Confidence            78999999     22 35899984   3   99999988765      56889999999999999998765   677775


Q ss_pred             ec
Q 022938          258 KQ  259 (289)
Q Consensus       258 K~  259 (289)
                      ..
T Consensus       205 t~  206 (374)
T PRK12328        205 TS  206 (374)
T ss_pred             CC
Confidence            43

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=95.38  E-value=0.046  Score=55.98  Aligned_cols=71  Identities=31%  Similarity=0.507  Sum_probs=56.4

Q ss_pred             cccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-----------cCcccccCCCCEEEEEEEEEe
Q 022938          184 SRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKID  247 (289)
Q Consensus       184 ~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-----------~~~~~~~~iGd~V~vkV~~id  247 (289)
                      -+-.+|+.+.|     +.+|+||.+.. .   +++|++|++.+...+.           ......|+.||.|++++.+++
T Consensus       618 m~~~vg~~f~g~V~~v~~~g~~V~l~~-~---~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~  693 (706)
T COG0557         618 MKKRVGEEFDGVVTGVTSFGFFVELPE-L---GLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVD  693 (706)
T ss_pred             HHHhcCCEEEEEEEEEEeccEEEEecc-c---ccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEc
Confidence            34578888777     89999999952 2   4999999999986422           233446999999999999999


Q ss_pred             CCCCeEEEEEe
Q 022938          248 REKSRITLSIK  258 (289)
Q Consensus       248 ~e~~ri~lSlK  258 (289)
                      ...+++.+++-
T Consensus       694 ~~~~~i~~~~v  704 (706)
T COG0557         694 LDERKIDFELV  704 (706)
T ss_pred             ccccceEEEec
Confidence            99999988763

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

Probab=95.29  E-value=0.054  Score=39.83  Aligned_cols=60  Identities=17%  Similarity=0.206  Sum_probs=37.3

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-------------------CEEEEeecCCCCCCccCc-CcccchhcccccCCCCEEE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-------------------SLVGFLPFPQMSPSHSCK-EPQKSIHEIAKGLTGSIIS  157 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-------------------gv~g~ip~sels~~~~~~-~p~~~~~~~~~~~vG~~V~  157 (289)
                      ++|.++.|+|+++++.-+.+++-                   ...|.++.+++......+ ...+.      |++||.|+
T Consensus         3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~------FrpGDIVr   76 (82)
T PF10447_consen    3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDC------FRPGDIVR   76 (82)
T ss_dssp             -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--------SSSEEE
T ss_pred             CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhc------cCCCCEEE
Confidence            58999999999999987766541                   257888888876543200 12333      45999999


Q ss_pred             EEEEEE
Q 022938          158 VKVIQA  163 (289)
Q Consensus       158 vkVl~v  163 (289)
                      ++|+++
T Consensus        77 A~ViSl   82 (82)
T PF10447_consen   77 ARVISL   82 (82)
T ss_dssp             EEEEEE
T ss_pred             EEEeeC
Confidence            999874

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.

>PRK10811 rne ribonuclease E; Reviewed

Probab=95.26  E-value=0.049  Score=56.44  Aligned_cols=62  Identities=19%  Similarity=0.335  Sum_probs=47.2

Q ss_pred             cCCCEEEEEEEEEEc--CcEEEEEC-CEEEEeecCCCCCCccCcCc---------ccchhcccccCCCCEEEEEEEEEec
Q 022938           98 ESGFIYEGKIQGFNG--GGLLVRFF-SLVGFLPFPQMSPSHSCKEP---------QKSIHEIAKGLTGSIISVKVIQANE  165 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~--~G~~V~l~-gv~g~ip~sels~~~~~~~p---------~~~~~~~~~~~vG~~V~vkVl~vd~  165 (289)
                      ..|.|+.|+|.++.+  .++||++| |..||+|.++...... .++         ...+      ..||.|-|.|.+-..
T Consensus        37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f-~~~~~~~~~~~i~~~L------k~GqeILVQV~KEa~  109 (1068)
T PRK10811         37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYF-PANYSAHGRPNIKDVL------REGQEVIVQIDKEER  109 (1068)
T ss_pred             CccceEEEEEecccCCcceeEEEecCCcceEEEhhhcccccc-cccccccccccccccc------CCCCEEEEEEeeccc
Confidence            489999999999997  48999999 9999999999854332 111         1123      389999999986443


Q ss_pred             C
Q 022938          166 E  166 (289)
Q Consensus       166 ~  166 (289)
                      .
T Consensus       110 g  110 (1068)
T PRK10811        110 G  110 (1068)
T ss_pred             C
Confidence            3

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

Probab=95.25  E-value=0.13  Score=40.85  Aligned_cols=67  Identities=18%  Similarity=0.087  Sum_probs=44.9

Q ss_pred             CCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcc-----cc-hhcccccCCCCEEEEEEEEEec
Q 022938           99 SGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQ-----KS-IHEIAKGLTGSIISVKVIQANE  165 (289)
Q Consensus        99 ~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~-----~~-~~~~~~~~vG~~V~vkVl~vd~  165 (289)
                      .|+++.|+|++.+..|+.|.++ =-+.|||.+.|..........     +. -...+.+-.|+.|+|||.++.-
T Consensus         3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f   76 (122)
T PF08292_consen    3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF   76 (122)
T ss_dssp             TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred             CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence            6999999999999999999998 578999999997432101000     01 0112334589999999998764

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

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

Probab=95.18  E-value=0.017  Score=56.48  Aligned_cols=68  Identities=19%  Similarity=0.255  Sum_probs=57.1

Q ss_pred             HhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           95 AYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        95 ~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      +..+.|..+.|+|.++.++|+||+++ .+.|+++.++++...             ++.+|+.+-+.+..+.++.+.+.+.
T Consensus       118 ~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~~-------------~~~vgdeiiV~v~~vr~~~geidf~  184 (715)
T COG1107         118 EDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGDP-------------DYAVGDEIIVQVSDVRPEKGEIDFE  184 (715)
T ss_pred             hhcccceeeeccccchhhhcceeecChhhhccccccccCCCC-------------CCCCCCeEEEEeeccCCCCCcccee
Confidence            34689999999999999999999999 899999999998521             1239999999999998877776665


Q ss_pred             ee
Q 022938          174 EK  175 (289)
Q Consensus       174 ~k  175 (289)
                      ..
T Consensus       185 ~~  186 (715)
T COG1107         185 PV  186 (715)
T ss_pred             ec
Confidence            44

>PRK11712 ribonuclease G; Provisional

Probab=94.63  E-value=0.095  Score=51.19  Aligned_cols=60  Identities=23%  Similarity=0.340  Sum_probs=44.5

Q ss_pred             cCCCEEEEEEEEEEcC--cEEEEEC-CEEEEeecCCCCCCc--cCcC---------cccchhcccccCCCCEEEEEEEEE
Q 022938           98 ESGFIYEGKIQGFNGG--GLLVRFF-SLVGFLPFPQMSPSH--SCKE---------PQKSIHEIAKGLTGSIISVKVIQA  163 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~--G~~V~l~-gv~g~ip~sels~~~--~~~~---------p~~~~~~~~~~~vG~~V~vkVl~v  163 (289)
                      ..|.++.|+|.++.++  ++||++| +..||+|.+++....  ...+         ..+.+      ..||.+-|.|.+-
T Consensus        37 ~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l------~~Gq~iLVQV~Ke  110 (489)
T PRK11712         37 IVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELV------RQGQDIMVQVVKD  110 (489)
T ss_pred             ccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhc------cCCCEEEEEEEeC
Confidence            5899999999999984  8999999 999999999873210  0000         11123      3899999999754

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=93.79  E-value=0.27  Score=33.90  Aligned_cols=49  Identities=35%  Similarity=0.541  Sum_probs=30.1

Q ss_pred             eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       195 ~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      +++|+|++-+  .+   -.-++|.+++.        ..+++||.|.|-| ..|. .+|+..|+|
T Consensus        13 ~~~g~fL~~~--~~---~~vlLp~~e~~--------~~~~~Gd~v~VFv-Y~D~-~~rl~AT~k   61 (61)
T PF13509_consen   13 NEFGYFLDDG--EG---KEVLLPKSEVP--------EPLKVGDEVEVFV-YLDK-EGRLVATTK   61 (61)
T ss_dssp             -SSEEEEEET--T----EEEEEEGGG--------------TTSEEEEEE-EE-T-TS-EEEE--
T ss_pred             eCCEEEEECC--CC---CEEEechHHcC--------CCCCCCCEEEEEE-EECC-CCCEEEecC
Confidence            8999999974  32   78999998875        3488999999866 4565 568888775

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=93.50  E-value=0.25  Score=47.30  Aligned_cols=66  Identities=8%  Similarity=0.044  Sum_probs=48.3

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCC---CeEEEEEe
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK---SRITLSIK  258 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~---~ri~lSlK  258 (289)
                      ++|+++.|     ...+++|+++..-|-.++.|++|.++..      +.+.|++||.|+|.|.+|+...   -.|.||..
T Consensus       151 ~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpqIilSRt  224 (449)
T PRK12329        151 LEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQLFVSRA  224 (449)
T ss_pred             hcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCEEEEEcC
Confidence            78999999     5567899883100100289999987764      5588999999999999998652   35777754

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

Probab=92.77  E-value=0.65  Score=38.74  Aligned_cols=74  Identities=18%  Similarity=0.178  Sum_probs=52.2

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEE---C------CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRF---F------SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK  168 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l---~------gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~  168 (289)
                      ..|.+++++|..++..-+-|++   +      ..+|+||..++....  +|--+.++   .|++||.|.++|++.+ .+.
T Consensus        67 ~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tE--kdrv~v~k---sFrPgDiVlAkVis~~-~~~  140 (193)
T KOG3409|consen   67 FVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATE--KDRVKVYK---SFRPGDIVLAKVISLG-DGS  140 (193)
T ss_pred             ccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccc--cchhhhhh---ccCCCcEEEEEEeecC-CCC
Confidence            6899999999999977665554   2      378999999886532  22223332   4569999999999865 345


Q ss_pred             EEEEEeecc
Q 022938          169 KLVFSEKDA  177 (289)
Q Consensus       169 ri~lS~k~~  177 (289)
                      +..||..++
T Consensus       141 ~y~LTtAen  149 (193)
T KOG3409|consen  141 NYLLTTAEN  149 (193)
T ss_pred             cEEEEEecc
Confidence            666665553

>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=90.93  E-value=1.4  Score=33.58  Aligned_cols=53  Identities=21%  Similarity=0.229  Sum_probs=42.9

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN  164 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd  164 (289)
                      ..|.++.|+|..+...-+++++| ...++|+..+....              +|..|.+|.+++.+.+
T Consensus        22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~~--------------~y~~G~rV~lrLkdlE   75 (104)
T PF10246_consen   22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNGE--------------KYVRGSRVRLRLKDLE   75 (104)
T ss_pred             ccCCEEEEEEEEEecCceEEEeCCceeEEEeccccccc--------------ccccCCEEEEEECCHh
Confidence            48999999999999999999999 68999996654321              2348999999997554

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 [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].

>PRK10811 rne ribonuclease E; Reviewed

Probab=90.23  E-value=0.71  Score=48.23  Aligned_cols=60  Identities=27%  Similarity=0.484  Sum_probs=44.8

Q ss_pred             ccccEEEe-------eeeeEEEEEecCCCceeEEEEEEccCcCccccc---------CcccccCCCCEEEEEEEEEeCCC
Q 022938          187 NVEDIFVG-------RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ---------DIRDILNEGDEVRVKVIKIDREK  250 (289)
Q Consensus       187 ~~G~iv~G-------~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~---------~~~~~~~iGd~V~vkV~~id~e~  250 (289)
                      .+|.||.|       .-.++||+|+  .|   ..||+|.+++......         .....+++||.|-|-|.+-...+
T Consensus        37 ~vGnIYkGkVenIvPGInAAFVDIG--~g---knGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gt  111 (1068)
T PRK10811         37 KKANIYKGKITRIEPSLEAAFVDYG--AE---RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGN  111 (1068)
T ss_pred             CccceEEEEEecccCCcceeEEEec--CC---cceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCC
Confidence            58999999       6678999997  55   8999999988533211         23456899999999998754333


Q ss_pred             C
Q 022938          251 S  251 (289)
Q Consensus       251 ~  251 (289)
                      +
T Consensus       112 K  112 (1068)
T PRK10811        112 K  112 (1068)
T ss_pred             C
Confidence            3

>PRK11712 ribonuclease G; Provisional

Probab=88.32  E-value=1.2  Score=43.76  Aligned_cols=59  Identities=24%  Similarity=0.455  Sum_probs=43.2

Q ss_pred             cccccccEEEe-------eeeeEEEEEecCCCceeEEEEEEccCcCcc------------cccCcccccCCCCEEEEEEE
Q 022938          184 SRVNVEDIFVG-------RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKVI  244 (289)
Q Consensus       184 ~~~~~G~iv~G-------~~~G~fV~i~~~~G~~~i~Glv~~sels~~------------~~~~~~~~~~iGd~V~vkV~  244 (289)
                      ....+|.+|.|       .=.++||+|+  .|   -.||+|.+++...            ....+.+.+++||.|-|.|.
T Consensus        34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG--~~---k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~  108 (489)
T PRK11712         34 KRGIVGNIYKGRVSRVLPGMQAAFVDIG--LD---KAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVV  108 (489)
T ss_pred             cccccccEEEEEEeecCCCCceeEEeeC--CC---ccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEE
Confidence            34468889988       5677999997  44   8999999987321            01234556999999999998


Q ss_pred             EEe
Q 022938          245 KID  247 (289)
Q Consensus       245 ~id  247 (289)
                      .=.
T Consensus       109 Ke~  111 (489)
T PRK11712        109 KDP  111 (489)
T ss_pred             eCC
Confidence            753

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

Probab=87.69  E-value=0.9  Score=44.53  Aligned_cols=67  Identities=21%  Similarity=0.294  Sum_probs=49.1

Q ss_pred             cCCCEEEEEEEEEEcC--cEEEEEC-CEEEEeecCCCCCCccCcCcccc-hhcccccCCCCEEEEEEEEEecCCc
Q 022938           98 ESGFIYEGKIQGFNGG--GLLVRFF-SLVGFLPFPQMSPSHSCKEPQKS-IHEIAKGLTGSIISVKVIQANEEMK  168 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~--G~~V~l~-gv~g~ip~sels~~~~~~~p~~~-~~~~~~~~vG~~V~vkVl~vd~~~~  168 (289)
                      ..|.++.|.|+++.+.  .+||++| +-.||+|.++..+ +. ..+... ++  ...+.||.+-|.|..-...++
T Consensus        36 ~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~-~~~~~~~i~--~~lr~~~~~~Vqv~ke~~G~K  106 (487)
T COG1530          36 IVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YF-RAVLEEKIK--VRLRGGQATLVQVVKEPRGTK  106 (487)
T ss_pred             eecCceEEEecccCccchhheeeccCCccceEEecccch-hh-hhcccccce--eeecCCceEEEEEEeecCccc
Confidence            5899999999999985  7999999 8999999999988 32 333220 00  112389998888876654433

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

Probab=85.88  E-value=5.1  Score=33.56  Aligned_cols=78  Identities=24%  Similarity=0.334  Sum_probs=49.7

Q ss_pred             CCCEEEEEEEEEecCCcEEEEEeecchhhhcccccccccEEEeeeeeEEEEEecCCCceeEEEEEEccCcCccc--ccCc
Q 022938          152 TGSIISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL--IQDI  229 (289)
Q Consensus       152 vG~~V~vkVl~vd~~~~ri~lS~k~~~~~~~~~~~~~G~iv~G~~~G~fV~i~~~~G~~~i~Glv~~sels~~~--~~~~  229 (289)
                      +|+.|.+||..++....+..+             +-+|+..          ++  .   ...|++|..++....  .-++
T Consensus        68 ~G~IVtarV~~i~~rfAkv~I-------------~~V~d~~----------lk--~---~FrglirkqdvR~tEkdrv~v  119 (193)
T KOG3409|consen   68 VGAIVTARVSRINLRFAKVDI-------------LSVGDKP----------LK--K---SFRGLIRKQDVRATEKDRVKV  119 (193)
T ss_pred             cCcEEEEEEEeeccceeeEEE-------------EEEcCEE----------hh--h---hhcceeehhhccccccchhhh
Confidence            799999999887643222222             2233322          22  2   277889887775432  2235


Q ss_pred             ccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          230 RDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       230 ~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      .+.|++||.|.|+|++.+. +....||..
T Consensus       120 ~ksFrPgDiVlAkVis~~~-~~~y~LTtA  147 (193)
T KOG3409|consen  120 YKSFRPGDIVLAKVISLGD-GSNYLLTTA  147 (193)
T ss_pred             hhccCCCcEEEEEEeecCC-CCcEEEEEe
Confidence            5679999999999999764 455666653

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

Probab=85.78  E-value=4.4  Score=33.50  Aligned_cols=61  Identities=20%  Similarity=0.249  Sum_probs=40.9

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcc----cccC-------cccccCCCCEEEEEEEEEeCCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQD-------IRDILNEGDEVRVKVIKIDREK  250 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~----~~~~-------~~~~~~iGd~V~vkV~~id~e~  250 (289)
                      -.|++++|     ...|+|++++  +    ++-++..-....+    .-++       -.+..++|..|+++|+......
T Consensus        80 fKGEVvdgvV~~Vnk~G~F~~~G--P----l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~  153 (170)
T KOG3298|consen   80 FKGEVVDGVVTKVNKMGVFARSG--P----LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDE  153 (170)
T ss_pred             cCCcEEEEEEEEEeeeeEEEecc--c----eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEee
Confidence            46889998     8999999997  4    6666654333322    1111       1125888999999999887644


Q ss_pred             CeE
Q 022938          251 SRI  253 (289)
Q Consensus       251 ~ri  253 (289)
                      ..+
T Consensus       154 ~~i  156 (170)
T KOG3298|consen  154 TEI  156 (170)
T ss_pred             eeE
Confidence            443

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=84.73  E-value=8  Score=28.65  Aligned_cols=65  Identities=12%  Similarity=0.089  Sum_probs=46.4

Q ss_pred             CCEEEEEEEEEEcCcEE-EEEC-CEEEEeecCC-CCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938          100 GFIYEGKIQGFNGGGLL-VRFF-SLVGFLPFPQ-MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD  176 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~-V~l~-gv~g~ip~se-ls~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~  176 (289)
                      --.++|+|+.+.+++.| |.+. |..-+.+++- |...+            ....+||.|.|.+...|.++++|+.-.+.
T Consensus         6 ~ie~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~r------------IrIl~GD~V~VE~spYDltkGRIiyR~~~   73 (87)
T PRK12442          6 LIELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHR------------IRILAGDRVTLELSPYDLTKGRINFRHKD   73 (87)
T ss_pred             eEEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeee------------EEecCCCEEEEEECcccCCceeEEEEecC
Confidence            44679999999988876 6887 7554444332 11111            22348999999999999999999987764

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

Probab=82.14  E-value=6  Score=31.29  Aligned_cols=21  Identities=19%  Similarity=0.229  Sum_probs=14.6

Q ss_pred             CcccccCCCCEEEEEEEEEeC
Q 022938          228 DIRDILNEGDEVRVKVIKIDR  248 (289)
Q Consensus       228 ~~~~~~~iGd~V~vkV~~id~  248 (289)
                      ...-.+..|+.|+.||.++.-
T Consensus        56 ~~~l~~d~ge~IRFRV~~~~f   76 (122)
T PF08292_consen   56 EQELFFDIGEEIRFRVESEIF   76 (122)
T ss_dssp             SEEEEE-TT-EEEEEEEEEEE
T ss_pred             CceeEccCCCEEEEEEeEEEE
Confidence            334457899999999999864

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

>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=81.91  E-value=38  Score=31.09  Aligned_cols=114  Identities=11%  Similarity=0.112  Sum_probs=68.9

Q ss_pred             cCCCEEEEEEEEEEc-CcE-EEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           98 ESGFIYEGKIQGFNG-GGL-LVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~-~G~-~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      +.|.++.|+|..-.+ +|+ -+.+++..-.+|.-++                   .+|+.++++|-.-|     +.+.++
T Consensus       230 e~~~vl~~~V~~hd~~y~lt~l~l~~~~l~v~~~~a-------------------~~g~~~R~~I~a~D-----Vslal~  285 (352)
T COG4148         230 EQSSVLEGTVLEHDPRYGLTALALGDQHLWVPKLDA-------------------PVGARLRIRIQARD-----VSLALQ  285 (352)
T ss_pred             ccceEEEEEehhcCCCcceEEEecCceEEEeeccCC-------------------CCCCcEEEEEEccc-----eEEEec
Confidence            568999999999885 565 3555555555654332                   28999999997544     455555


Q ss_pred             cchhhhcccccccccEEEe----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEe
Q 022938          176 DAVWNKYSSRVNVEDIFVG----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID  247 (289)
Q Consensus       176 ~~~~~~~~~~~~~G~iv~G----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id  247 (289)
                      .. -....-++=+|.++.-    ..--+++++   +|   -.-+..++.++.+.     -.+++||.|-|.|.++-
T Consensus       286 ~P-~~~SirNiLp~~v~~i~~~~~~V~v~ld~---~g---~~l~Arit~~srd~-----L~l~~G~~v~AqIKsVs  349 (352)
T COG4148         286 KP-EQTSIRNILPGKVVGIEDDDGQVDVQLDC---GG---KTLWARITPWARDE-----LALKPGQWVYAQIKSVS  349 (352)
T ss_pred             Cc-cccchhhccceeEEEEEcCCCcEEEEEEc---CC---cEEEEEccHhhHHh-----hcCCCCCeEEEEEEEEE
Confidence            43 2233345556655544    222344444   33   33444445554332     23899999999998874

>TIGR00008 infA translation initiation factor IF-1

Probab=81.51  E-value=13  Score=26.27  Aligned_cols=60  Identities=12%  Similarity=0.135  Sum_probs=41.3

Q ss_pred             CEEEEEEEEEEcCcEE-EEEC-CEEEEeecCC-CCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEE
Q 022938          101 FIYEGKIQGFNGGGLL-VRFF-SLVGFLPFPQ-MSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVF  172 (289)
Q Consensus       101 ~iv~g~V~~v~~~G~~-V~l~-gv~g~ip~se-ls~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~l  172 (289)
                      -.+.|+|+...+++.| |.+. |..-..+++- |...+            ....+||.|.+.+...|.++++|+.
T Consensus         5 ie~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~r------------I~I~~GD~V~Ve~spyd~tkgrIi~   67 (68)
T TIGR00008         5 IEMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHY------------IRILPGDKVKVELSPYDLTRGRITY   67 (68)
T ss_pred             EEEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhcc------------EEECCCCEEEEEECcccCCcEeEEe
Confidence            3579999999988876 6877 7555544332 11111            1234899999999999888888763

This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	289
2k4k_A	130	Solution Structure Of Gsp13 From Bacillus Subtilis		1e-09
2aho_B	266	Structure Of The Archaeal Initiation Factor Eif2 Al		8e-06
3aev_A	275	Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex		1e-05
1yz6_A	274	Crystal Structure Of Intact Alpha Subunit Of Aif2 F		1e-05
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		1e-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 =		4e-05

>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis Length = 130

Iteration: 1
 Score = 60.1 bits (144), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 32/87 (36%), Positives = 52/87 (59%), Gaps = 10/87 (11%)
Query: 183 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGD 237
           +++  V  ++ G+      YGAF+ L          GLVH+SEV+   ++DI + L+ GD
Sbjct: 2   AAKFEVGSVYTGKVTGLQAYGAFVALD-----EETQGLVHISEVTHGFVKDINEHLSVGD 56
Query: 238 EVRVKVIKIDREKSRITLSIKQLEEDP 264
           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 = 47.8 bits (112), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 43/68 (63%), Gaps = 3/68 (4%)
Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           DYG+++ L   D    L   +  SEVS   +++IRD+L E  +V VKVI++DR K  + +
Sbjct: 24  DYGSYVSL---DEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDV 80
Query: 256 SIKQLEED 263
           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 = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 3/65 (4%)
Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           +YGAF+ L   D        +H+SEV+   +++IRD L EG +V  KVI++D  K  I L
Sbjct: 24  NYGAFLEL---DEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDL 80
Query: 256 SIKQL 260
           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 = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 3/65 (4%)
Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           +YGAF+ L   D        +H+SEV+   +++IRD L EG +V  KVI++D  K  I L
Sbjct: 23  NYGAFLEL---DEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDL 79
Query: 256 SIKQL 260
           S++++
Sbjct: 80  SLRRV 84

>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase Length = 723

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 49/85 (57%), Gaps = 11/85 (12%)
Query: 183 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGD 237
           ++ + V  ++ G+     D+GAF+ +          GLVH+S+++   ++ + D L  G 
Sbjct: 622 TAEIEVGRVYTGKVTRIVDFGAFVAIGGGK-----EGLVHISQIADKRVEKVTDYLQMGQ 676
Query: 238 EVRVKVIKIDREKSRITLSIKQLEE 262
           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: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           ++GAF+ +       H  GLVH+S +S   ++D  +++  GD V+VKV+++D  ++R+ L
Sbjct: 667 NFGAFVDIGV-----HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGL 721
Query: 256 SIK 258
           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: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           ++GAF+ +       H  GLVH+S +S   ++D  +++  GD V+VKV+++D  ++R+ L
Sbjct: 668 NFGAFVDIGV-----HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGL 722
Query: 256 SIK 258
           S++
Sbjct: 723 SMR 725

>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures Length = 76

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/81 (33%), Positives = 47/81 (58%), Gaps = 11/81 (13%)
Query: 184 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 238
           + + V  ++ G+     D+GAF+ +          GLVH+S+++   ++ + D L  G E
Sbjct: 1   AEIEVGRVYTGKVTRIVDFGAFVAIGGGK-----EGLVHISQIADKRVEKVTDYLQMGQE 55
Query: 239 VRVKVIKIDREKSRITLSIKQ 259
           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	289
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	1e-23
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	9e-04
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	2e-23
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	6e-23
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	7e-05
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	7e-23
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	8e-08
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	2e-20
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	3e-04
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	4e-20
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	5e-20
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	2e-18
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	7e-18
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	1e-16
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	2e-16
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	5e-16
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	8e-16
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	3e-13
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	5e-12
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	1e-08
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	2e-08
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	6e-08
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	1e-07
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	2e-07
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-05
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	4e-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	8e-05
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	8e-04

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

 Score = 92.5 bits (230), Expect = 1e-23
 Identities = 32/87 (36%), Positives = 52/87 (59%), Gaps = 10/87 (11%)

Query: 183 SSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGD 237
           +++  V  ++ G+      YGAF+ L          GLVH+SEV+   ++DI + L+ GD
Sbjct: 2   AAKFEVGSVYTGKVTGLQAYGAFVAL-----DEETQGLVHISEVTHGFVKDINEHLSVGD 56

Query: 238 EVRVKVIKIDREKSRITLSIKQLEEDP 264
           EV+VKV+ +D EK +I+LSI+  +  P
Sbjct: 57  EVQVKVLAVDEEKGKISLSIRATQAAP 83

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

 Score = 37.8 bits (88), Expect = 9e-04
 Identities = 25/133 (18%), Positives = 40/133 (30%), Gaps = 19/133 (14%)

Query: 98  ESGFIYEGKIQGFNGGGLLVRFFSLV-GFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSII 156
           E G +Y GK+ G    G  V       G +   +++         K I+E      G  +
Sbjct: 6   EVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFV-----KDINEHLS--VGDEV 58

Query: 157 SVKVIQANEEMKKLVFSEKDAVWN------KYSSRVNVEDIFVGRDYGAFIHLRFPDGLY 210
            VKV+  +EE  K+  S +           K       +          F      D L 
Sbjct: 59  QVKVLAVDEEKGKISLSIRATQAAPEKKESKPRKPKAAQVSEEASTPQGFN--TLKDKL- 115

Query: 211 HLTGLVHVSEVSW 223
                + +S    
Sbjct: 116 --EEWIEMSNRKD 126

>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 = 93.3 bits (232), Expect = 2e-23
 Identities = 23/90 (25%), Positives = 47/90 (52%), Gaps = 8/90 (8%)

Query: 187 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 241
            VED+ +       + GA++ L   + +    G++ +SE+S   I+ I  ++  G    V
Sbjct: 14  EVEDVVMVNVRSIAEMGAYVSLLEYNNI---EGMILLSELSRRRIRSINKLIRIGRNECV 70

Query: 242 KVIKIDREKSRITLSIKQLEEDPLLETLEK 271
            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 = 89.9 bits (224), Expect = 6e-23
 Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 10/91 (10%)

Query: 179 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDIL 233
           +N + +      I  G+       GA + L   DG+    G +  SE S D ++D   +L
Sbjct: 22  FNNWVALNKKGAIVTGKVTAVDAKGATVELA--DGV---EGYLRASEASRDRVEDATLVL 76

Query: 234 NEGDEVRVKVIKIDREKSRITLSIKQLEEDP 264
           + 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 = 40.3 bits (95), Expect = 7e-05
 Identities = 0/29 (0%), Positives = 4/29 (13%)

Query: 244 IKIDREKSRITLSIKQLEEDPLLETLEKV 272
           +         +  +           +   
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMFNNWVALN 29

>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 = 91.7 bits (228), Expect = 7e-23
 Identities = 22/90 (24%), Positives = 48/90 (53%), Gaps = 8/90 (8%)

Query: 187 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 241
            ++DI +       + GA++ L   D +    G++ +SE+S   I+ I+ ++  G     
Sbjct: 14  EIDDIVMVNVQQIAEMGAYVKLLEYDNI---EGMILLSELSRRRIRSIQKLIRVGKNDVA 70

Query: 242 KVIKIDREKSRITLSIKQLEEDPLLETLEK 271
            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 = 50.1 bits (120), Expect = 8e-08
 Identities = 21/172 (12%), Positives = 46/172 (26%), Gaps = 21/172 (12%)

Query: 96  YKESGFIYEGKIQGFNGGGL---LVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLT 152
           Y E   I    +Q     G    L+ + ++ G +   ++S         +SI ++ +   
Sbjct: 12  YPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRI-----RSIQKLIR--V 64

Query: 153 GSIISVKVIQANEEMKKLVFSEKDAV---WNKYSSRVNVEDIFVGR-DYGAFIHLRFPDG 208
           G      V++ ++E   +  S++        K   +            Y A       + 
Sbjct: 65  GKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEE 124

Query: 209 LYHLTGLVHVSEVSW-DLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 259
           LY                     +              I+     +   +K 
Sbjct: 125 LYK------TIAWPLSRKFGHAYEAFKLSIIDETVWEGIEPPSKDVLDELKN 170

>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 = 88.1 bits (218), Expect = 2e-20
 Identities = 25/90 (27%), Positives = 49/90 (54%), Gaps = 8/90 (8%)

Query: 187 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 241
            VED+ +       + GA++ L   + +    G++H+SE+S   I+ I  ++  G    V
Sbjct: 12  EVEDVVMVNVRSIQEMGAYVSLLEYNNI---EGMIHLSELSRRRIRSINKLIRIGRNECV 68

Query: 242 KVIKIDREKSRITLSIKQLEEDPLLETLEK 271
           KVI++D+EK  I LS +++  +  ++  +K
Sbjct: 69  KVIRVDKEKGYIDLSKRRVSPEEAIKCEDK 98

>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 = 40.3 bits (94), Expect = 3e-04
 Identities = 18/153 (11%), Positives = 48/153 (31%), Gaps = 18/153 (11%)

Query: 124 GFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAV---WN 180
           G +   ++S         +SI+++ +   G    VKVI+ ++E   +  S++        
Sbjct: 41  GMIHLSELSRRRI-----RSINKLIR--IGRNECVKVIRVDKEKGYIDLSKRRVSPEEAI 93

Query: 181 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLV---HVSEVSWDLIQDIRDI 232
           K   +               +   +      + L+  T  V         +      +  
Sbjct: 94  KCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHA 153

Query: 233 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPL 265
           +++   +    +  D  +  I    ++L    +
Sbjct: 154 VSDPSILDSLDLNEDEREVLINNINRRLTPQAV 186

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115

 Score = 82.7 bits (205), Expect = 4e-20
 Identities = 32/92 (34%), Positives = 46/92 (50%), Gaps = 11/92 (11%)

Query: 179 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDI 232
           W   + R        GR     DYG F+ +   +G+    GLVHVSE+ W         +
Sbjct: 21  WVAIAKRYPEGTKLTGRVTNLTDYGCFVEIE--EGV---EGLVHVSEMDWTNKNIHPSKV 75

Query: 233 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 264
           +N GD V V V+ ID E+ RI+L +KQ + +P
Sbjct: 76  VNVGDVVEVMVLDIDEERRRISLGLKQCKANP 107

>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 = 86.2 bits (213), Expect = 5e-20
 Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 8/90 (8%)

Query: 187 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 241
           +  +I +       DYG+++ L    GL      +  SEVS   +++IRD+L E  +V V
Sbjct: 10  SEGEILIATVKQVFDYGSYVSLDEYGGL---QAFLPWSEVSSKWVKNIRDVLKENRKVIV 66

Query: 242 KVIKIDREKSRITLSIKQLEEDPLLETLEK 271
           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 = 78.6 bits (194), Expect = 2e-18
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 6/71 (8%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID--REKSRI 253
           DYGAFI +          GLVH + +S   +    +I++ GD+V VK+I  +   ++ ++
Sbjct: 35  DYGAFIKI----PGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKV 90

Query: 254 TLSIKQLEEDP 264
           +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 = 76.2 bits (188), Expect = 7e-18
 Identities = 20/92 (21%), Positives = 45/92 (48%), Gaps = 10/92 (10%)

Query: 179 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDI 232
                    + DI+ G+      +G F+  +         GLVH+SE+  +  + ++ D+
Sbjct: 3   SGSSGEEPTIGDIYNGKVTSIMQFGCFV--QLEGLRKRWEGLVHISELRREGRVANVADV 60

Query: 233 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDP 264
           +++G  V+VKV+       + +LS+K ++++ 
Sbjct: 61  VSKGQRVKVKVLSFTGT--KTSLSMKDVDQET 90

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80

 Score = 71.9 bits (177), Expect = 1e-16
 Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 9/68 (13%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
            YGAFI+L        + GL+   ++    +++    LN GDE+ V+ I +  EK  I  
Sbjct: 18  KYGAFINL-----NEQVRGLLRPRDMISLRLEN----LNVGDEIIVQAIDVRPEKREIDF 68

Query: 256 SIKQLEED 263
               LE  
Sbjct: 69  KYIPLEHH 76

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Length = 275

 Score = 76.2 bits (187), Expect = 2e-16
 Identities = 27/90 (30%), Positives = 46/90 (51%), Gaps = 8/90 (8%)

Query: 187 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 241
              +  V       +YGAF+ L    G       +H+SEV+   +++IRD L EG +V  
Sbjct: 10  EEGEFVVATVKRIHNYGAFLELDEYPGK---EAFMHISEVASTWVRNIRDYLKEGQKVVA 66

Query: 242 KVIKIDREKSRITLSIKQLEEDPLLETLEK 271
           KVI++D  K  I LS++++ +      L++
Sbjct: 67  KVIRVDPRKGHIDLSLRRVTQQQRKAKLQE 96

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 77.2 bits (191), Expect = 5e-16
 Identities = 27/86 (31%), Positives = 47/86 (54%), Gaps = 15/86 (17%)

Query: 186 VNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 238
             V  I+ G+     D+GAF++  F   DGL      VHVS++S + +    D+L EG  
Sbjct: 635 AEVGKIYDGKVVKVVDFGAFVNF-FGAKDGL------VHVSQISNERVAKPSDVLKEGQM 687

Query: 239 VRVKVIKIDREKSRITLSIKQLEEDP 264
           V+VK++  D  + +  LS+K ++++ 
Sbjct: 688 VKVKLLGFDD-RGKTKLSMKVVDQET 712

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

 Score = 76.4 bits (189), Expect = 8e-16
 Identities = 28/86 (32%), Positives = 48/86 (55%), Gaps = 15/86 (17%)

Query: 186 VNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 238
           + V  ++ G+     D+GAF+ +     +GL      VH+S+++   ++ + D L  G E
Sbjct: 625 IEVGRVYTGKVTRIVDFGAFVAI-GGGKEGL------VHISQIADKRVEKVTDYLQMGQE 677

Query: 239 VRVKVIKIDREKSRITLSIKQLEEDP 264
           V VKV+++DR + RI LSIK+  E  
Sbjct: 678 VPVKVLEVDR-QGRIRLSIKEATEQS 702

>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 = 68.4 bits (168), Expect = 3e-13
 Identities = 21/90 (23%), Positives = 44/90 (48%), Gaps = 19/90 (21%)

Query: 186 VNVEDIFVGR-----DYGAFIHLRFP--DGLYHLTGLVHVSEVSWDL----IQDIRDILN 234
             V +  +G       +GAF+ L  P  DGL      +H+S++        ++++ D+L 
Sbjct: 665 PEVGERILGSVVKTTTFGAFVSL-LPGKDGL------LHISQIRKLAGGKRVENVEDVLG 717

Query: 235 EGDEVRVKVIKIDREKSRITLSIKQLEEDP 264
            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 = 64.9 bits (159), Expect = 5e-12
 Identities = 22/69 (31%), Positives = 44/69 (63%), Gaps = 5/69 (7%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL 255
           ++GAF+ +    G+ H  GLVH+S +S   ++D  +++  GD V+VKV+++D  ++R+ L
Sbjct: 667 NFGAFVDI----GV-HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGL 721

Query: 256 SIKQLEEDP 264
           S++  +   
Sbjct: 722 SMRMSDTPG 730

>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 = 52.6 bits (126), Expect = 1e-08
 Identities = 28/155 (18%), Positives = 65/155 (41%), Gaps = 25/155 (16%)

Query: 130 QMSPSHSCKEPQKSIHEIAK-----------GLTGSIISVKVIQANEEMKKLVFSEKDAV 178
           ++ P+   K   +      +           GL  +I++VK  +    +     +  +  
Sbjct: 12  RIPPNEFGKPLNEIALNELRQQYQEKILKDLGLVLAILNVKTSEEGMLVFGDGATYHEVE 71

Query: 179 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL----VHVSEVSWDLI-QD 228
           ++  +    V+++  G      +YG F++L   DGL H++ +    +    V   +  + 
Sbjct: 72  FDMITYVPVVQEVVEGEVLQVDNYGVFVNLGPMDGLVHISQITDDTLKYDNVRGIIFGEK 131

Query: 229 IRDILNEGDEVRVKVIKIDREK----SRITLSIKQ 259
            + ++ +GD+VR +VI +         RI L+++Q
Sbjct: 132 SKKVIQKGDKVRARVISVASTVTGRLPRIALTMRQ 166

>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 = 52.6 bits (126), Expect = 2e-08
 Identities = 30/156 (19%), Positives = 64/156 (41%), Gaps = 26/156 (16%)

Query: 130 QMSPSHSCKEPQKSIHEIAK-----------GLTGSIISVKVIQANEEMKKLVFSEKDAV 178
           ++ P    K+ ++++ +I             G   SI+ VK I   + +     +    V
Sbjct: 12  KVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVV 71

Query: 179 WNKYSSRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGL----VHVSEVSWDLI-QD 228
           +        + ++  G      ++G+F+ L   DGL H++ +    V        +I ++
Sbjct: 72  FETLVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKE 131

Query: 229 IRDILNEGDEVRVKVIKIDREKSR-----ITLSIKQ 259
              +L  GD VR +++ I  +  R     I L+++Q
Sbjct: 132 TGKVLEIGDYVRARIVAISLKAERKRGSKIALTMRQ 167

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

 Score = 52.6 bits (126), Expect = 6e-08
 Identities = 9/65 (13%), Positives = 18/65 (27%), Gaps = 6/65 (9%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-IRDILNEGDEVRVKVIKIDREKSRIT 254
                           +  +V+    +   ++    +I   G     KVI ID       
Sbjct: 918 HNDIICTTNS-----EVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAE 972

Query: 255 LSIKQ 259
           +S+  
Sbjct: 973 VSLLD 977

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

 Score = 51.8 bits (124), Expect = 1e-07
 Identities = 9/65 (13%), Positives = 18/65 (27%), Gaps = 6/65 (9%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQD-IRDILNEGDEVRVKVIKIDREKSRIT 254
                           +  +V+    +   ++    +I   G     KVI ID       
Sbjct: 915 HNDIICTTNS-----EVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAE 969

Query: 255 LSIKQ 259
           +S+  
Sbjct: 970 VSLLD 974

>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 = 50.3 bits (120), Expect = 2e-07
 Identities = 19/124 (15%), Positives = 40/124 (32%), Gaps = 17/124 (13%)

Query: 155 IISVKVIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGL 209
            I ++V + +     L + E      + +        +       +  G F++L  P+  
Sbjct: 119 YIRLEVDKKDRIWGLLAYQEDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYL--PENN 176

Query: 210 YHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETL 269
               G +H SE               G  +  +VI        + LS+K    + L    
Sbjct: 177 ML--GFIHPSE--------RYAEPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDA 226

Query: 270 EKVI 273
           + ++
Sbjct: 227 QMIL 230

>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 = 41.1 bits (96), Expect = 2e-04
 Identities = 24/175 (13%), Positives = 53/175 (30%), Gaps = 29/175 (16%)

Query: 100 GFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVK 159
                G I   N     V+       L   +              H +     G  +   
Sbjct: 7   ASFIVGLIIDENDRFYFVQKDGQTYALAKEEGQ------------HTV-----GDTVKGF 49

Query: 160 VIQANEEMKKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVS 219
                ++  +L   E  A  +++     V +  V +D G F+      GL     +V + 
Sbjct: 50  AYTDMKQKLRLTTLEVTATQDQFG-WGRVTE--VRKDLGVFVDT----GLPDKEIVVSLD 102

Query: 220 EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKVIP 274
            +        +    +GD++ ++ +++D++     L   Q +   L       + 
Sbjct: 103 ILPELKELWPK----KGDQLYIR-LEVDKKDRIWGLLAYQEDFQRLARPAYNNMQ 152

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 47.5 bits (112), Expect = 3e-06
 Identities = 47/303 (15%), Positives = 93/303 (30%), Gaps = 74/303 (24%)

Query: 1   MLSLSSRIGSNTCLDASSCTHSSLSLSLSLSSLVC-VNPLIIERICQRNLCPVGKFSTNA 59
           +  L  +I  N     S   HSS ++ L + S+   +  L+  +  +  L          
Sbjct: 202 LQKLLYQIDPNWT---SRSDHSS-NIKLRIHSIQAELRRLLKSKPYENCLL--------- 248

Query: 60  AKITPTTVNPILDDSSDAN-----NRQSQ----SRSSADWKAARAYKESGFIYEGKIQGF 110
                     +L +  +A      N   +    +R         A   +    +      
Sbjct: 249 ----------VLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTL 298

Query: 111 NGG---GLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM 167
                  LL+++         PQ  P           +     +    I   +    +  
Sbjct: 299 TPDEVKSLLLKYLDCR-----PQDLPREVLT-----TNPRRLSIIAESIRDGLAT-WDNW 347

Query: 168 KKLVFSEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLR-FPDGLYHLTGLVHVS----EVS 222
           K +     D +     S +NV +    R    F  L  FP          H+      + 
Sbjct: 348 KHV---NCDKLTTIIESSLNVLEPAEYRKM--FDRLSVFPPS-------AHIPTILLSLI 395

Query: 223 W-DLI-QDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLE---TLEKVIPQGL 277
           W D+I  D+  ++N+    +  +++   ++S I++    LE    LE    L + I   +
Sbjct: 396 WFDVIKSDVMVVVNK--LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI---V 450

Query: 278 EPY 280
           + Y
Sbjct: 451 DHY 453

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.7 bits (102), Expect = 5e-05
 Identities = 34/228 (14%), Positives = 70/228 (30%), Gaps = 48/228 (21%)

Query: 107 IQGFNGGG------LLVRFFSLVGFLPFPQ--MSPSHSCKEP-------QKSIHEIAKGL 151
           I G  G G       +   + +   + F    ++  + C  P       QK +++I    
Sbjct: 155 IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKN-CNSPETVLEMLQKLLYQIDPNW 213

Query: 152 T-----GSIISVKVIQANEEMKKLVFSEK--------DAVWNK-------YSSRV----- 186
           T      S I +++     E+++L+ S+           V N         S ++     
Sbjct: 214 TSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTR 273

Query: 187 --NVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVI 244
              V D                  L        + +      QD+   +   +  R+ +I
Sbjct: 274 FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSII 333

Query: 245 --KIDREKSRITLSIKQLEEDPLLETLEKVIPQGLEPY-LKSFYKKMV 289
              I    +    + K +  D L   +E  +   LEP   +  + ++ 
Sbjct: 334 AESIRDGLATWD-NWKHVNCDKLTTIIESSLNV-LEPAEYRKMFDRLS 379

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A Length = 179

 Score = 42.7 bits (100), Expect = 4e-05
 Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 15/91 (16%)

Query: 181 KYSSRVNVEDIFVGR-----DYGAFIHLRFPDGL-----YHLTGLVHVSEVSWDLIQDIR 230
                +   D+ +GR     +  A I +    G          G++HVS V    +++I 
Sbjct: 50  SPIPEIVKGDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEIS 109

Query: 231 DILNEGDEVRVKVIKIDREKSRITLSIKQLE 261
           + +   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 = 41.2 bits (96), Expect = 5e-05
 Identities = 11/79 (13%), Positives = 29/79 (36%), Gaps = 5/79 (6%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRIT 254
           D+G  + +    G+      + + +    +  ++    L  G  +   V K+      ++
Sbjct: 34  DHGYLVDI----GVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVS 89

Query: 255 LSIKQLEEDPLLETLEKVI 273
           LS+   E    + T ++  
Sbjct: 90  LSVGHSEVSTAIATEQQSW 108

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

 Score = 41.5 bits (97), Expect = 8e-05
 Identities = 21/154 (13%), Positives = 44/154 (28%), Gaps = 24/154 (15%)

Query: 130 QMSPSHSCKEPQKSIHEIAK--------GLTGSIISVKVIQANEEMKKLVFSEKDAVWNK 181
            + PS+     Q  +             G  G II V      +  K  V   +     +
Sbjct: 13  SLHPSYFGPRMQDYLKAKLLADVEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFE 72

Query: 182 YSSRVNVEDIFVG----------RDYGAFIHLRFPDGLYHLTGL----VHVSEVSWDLIQ 227
              R  +   F G             G F ++   +       +          +     
Sbjct: 73  VKYRAVLWRPFRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYS 132

Query: 228 DIRDILNEGDEVRVKVI--KIDREKSRITLSIKQ 259
               ++ +G  VR+K++  + D  +     ++K+
Sbjct: 133 GEDQVIEKGSNVRLKIVGTRTDATEIFAIATMKE 166

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

 Score = 38.4 bits (89), Expect = 8e-04
 Identities = 21/154 (13%), Positives = 42/154 (27%), Gaps = 24/154 (15%)

Query: 130 QMSPSHSCKEPQKSIHEIAKGLT--------GSIISVKVIQANEEMKKLVFSEKDAVWNK 181
            + PS      ++ +                G I+ V      +  +  +     +    
Sbjct: 12  TLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFN 71

Query: 182 YSSRVNVEDIFVG----------RDYGAFIHLRFPDGLYHLTGL---VHVSEVSWDLI-Q 227
              R  V   F G            +G  + +           +   +  +  S     Q
Sbjct: 72  VKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQ 131

Query: 228 DIRDILNEGDEVRVKVIKIDREKSRI--TLSIKQ 259
              D++     +RVK+     + S I    SIK+
Sbjct: 132 SSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKE 165

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	289
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.96
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.79
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.71
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.69
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.68
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.65
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.58
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.57
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.56
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.56
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.54
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.54
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.54
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.53
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.5
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.5
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.5
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.43
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	99.42
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.41
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.4
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.4
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.38
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.38
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.32
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.31
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.3
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.22
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.14
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.14
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.07
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.07
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.07
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.03
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.03
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.01
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.99
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.96
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.96
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.92
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	98.92
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.92
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.89
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.84
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.83
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	98.83
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.81
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.8
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.79
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.77
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	98.77
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	98.72
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.69
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.62
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.61
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.61
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.6
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.6
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.53
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	98.51
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.48
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.46
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.45
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.42
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.4
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.39
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.37
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.25
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.04
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	97.96
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	97.89
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.88
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.81
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	97.79
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	97.75
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	97.68
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	97.52
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.49
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.43
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.43
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	97.43
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	97.34
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.34
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.33
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.31
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	96.95
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	95.41
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	95.17
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	94.7
2r7d_A	469	Ribonuclease II family protein; structural genomic	93.6
2r7d_A	469	Ribonuclease II family protein; structural genomic	90.7
2eqj_A	66	Metal-response element-binding transcription facto	90.62
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	87.99
1jjg_A	102	M156R; beta barrel, S1 motif, OB fold, MYXV156R, N	85.21
3h8z_A	128	FragIle X mental retardation syndrome-related Pro;	81.3

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

Probab=99.96  E-value=1.3e-28  Score=221.27  Aligned_cols=203  Identities=10%  Similarity=0.044  Sum_probs=169.5

Q ss_pred             ccccccceeEeCCCCCCccceeEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhh
Q 022938            5 SSRIGSNTCLDASSCTHSSLSLSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQS   84 (289)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~   84 (289)
                      ..++-.++++++..    |...+++.+..    |+   ++||++++.|+. |. ++|+.+|++.+.              
T Consensus        14 V~~~~~~G~fv~~~----g~egllp~se~----~~---~vGdevev~v~~-d~-~~r~iat~~~p~--------------   66 (285)
T 3go5_A           14 IIDENDRFYFVQKD----GQTYALAKEEG----QH---TVGDTVKGFAYT-DM-KQKLRLTTLEVT--------------   66 (285)
T ss_dssp             EEEECSSEEEEEET----TEEEEEEGGGC----CC---CTTSEEEEEEEE-CT-TSCEEEECSCCC--------------
T ss_pred             EEEEECCEEEEEcC----CeEEEEEHHHC----cc---ccCCEEEEEEEE-CC-CCCEEEeccccc--------------
Confidence            45777899999873    56666777766    33   999999999973 54 567778865321              


Q ss_pred             hhhhHHHHHHHhhcCCCEEEEEEEEEE-cCcEEEEECC--EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938           85 RSSADWKAARAYKESGFIYEGKIQGFN-GGGLLVRFFS--LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI  161 (289)
Q Consensus        85 ~~~~~~~~l~~~~~~G~iv~g~V~~v~-~~G~~V~l~g--v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl  161 (289)
                                  ++.|++++|+|++++ ++|+||++|.  .+||||.+|++|... .+          ..+||.+.|+ +
T Consensus        67 ------------~~~G~~~~g~V~~v~~~~GaFVdiG~~~~d~lvp~sel~~~~~-~~----------~~~Gd~v~v~-l  122 (285)
T 3go5_A           67 ------------ATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKE-LW----------PKKGDQLYIR-L  122 (285)
T ss_dssp             ------------SCSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGGSCSSGG-GS----------CCTTCEEEEE-E
T ss_pred             ------------ccCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHHCCcccc-cc----------cCCCCEEEEE-E
Confidence                        479999999999999 7999999984  899999999988542 22          2399999877 5


Q ss_pred             EEecCCcEEEEEeec----chhhhcccccccccEEEe-----eeeeEEE-EEecCCCceeEEEEEEccCcCcccccCccc
Q 022938          162 QANEEMKKLVFSEKD----AVWNKYSSRVNVEDIFVG-----RDYGAFI-HLRFPDGLYHLTGLVHVSEVSWDLIQDIRD  231 (289)
Q Consensus       162 ~vd~~~~ri~lS~k~----~~~~~~~~~~~~G~iv~G-----~~~G~fV-~i~~~~G~~~i~Glv~~sels~~~~~~~~~  231 (289)
                      .+|+ ++|+.+|+|+    .+|......+++|++|+|     +++|+|| .++  +|   +.||||.||++        +
T Consensus       123 ~iD~-~~Ri~ls~k~~~~~~~~~~~~~~~~~G~~V~g~V~~i~~~G~fV~~i~--~g---~~Glih~SEl~--------~  188 (285)
T 3go5_A          123 EVDK-KDRIWGLLAYQEDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYLPE--NN---MLGFIHPSERY--------A  188 (285)
T ss_dssp             EECT-TSCEEEEECCHHHHHHHCCCCCSCCTTCEEEEEEEEEETTEEEEEETT--TT---EEEEECGGGCS--------S
T ss_pred             EECC-CCcEEEEehhhhhcchhhhhhhhCCCCCEEEEEEEEEeCCcEEEEEeC--CC---eEEEEEHHHcc--------c
Confidence            8998 7899999973    478888899999999999     8999999 985  55   99999999997        3


Q ss_pred             ccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHhhhh
Q 022938          232 ILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETLEKV  272 (289)
Q Consensus       232 ~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~~~~  272 (289)
                      .+++||.|+|+|+++|++++||+||+|+...+++++..+..
T Consensus       189 ~l~~Gd~v~~~V~~id~~d~kI~LSlk~~~~~~~~~~a~~i  229 (285)
T 3go5_A          189 EPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDAQMI  229 (285)
T ss_dssp             CCCTTCEEEEEEEEEETTTTEEEEECSCCCCCCCCHHHHHH
T ss_pred             cCCCCCEEEEEEEEEECCCCeEEEEeChhhhhccchHHHHH
Confidence            58999999999999999999999999999999998876554

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

Probab=99.79  E-value=4.7e-19  Score=159.01  Aligned_cols=145  Identities=15%  Similarity=0.090  Sum_probs=121.5

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeecc
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDA  177 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~~  177 (289)
                      ..|++++|+|++++++|+||+++|.+||+|.++++.           .      +||.|+|.|. .|. .+|+++|.+. 
T Consensus         5 ~~G~~v~g~V~~~~~~G~fv~~~g~egllp~se~~~-----------~------vGdevev~v~-~d~-~~r~iat~~~-   64 (285)
T 3go5_A            5 NLASFIVGLIIDENDRFYFVQKDGQTYALAKEEGQH-----------T------VGDTVKGFAY-TDM-KQKLRLTTLE-   64 (285)
T ss_dssp             TTTEEEEEEEEEECSSEEEEEETTEEEEEEGGGCCC-----------C------TTSEEEEEEE-ECT-TSCEEEECSC-
T ss_pred             cCCCEEEEEEEEEECCEEEEEcCCeEEEEEHHHCcc-----------c------cCCEEEEEEE-ECC-CCCEEEeccc-
Confidence            479999999999999999999999999999999853           1      9999999998 464 5677777654 


Q ss_pred             hhhhcccccccccEEEe-----e-eeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCC
Q 022938          178 VWNKYSSRVNVEDIFVG-----R-DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS  251 (289)
Q Consensus       178 ~~~~~~~~~~~G~iv~G-----~-~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~  251 (289)
                      |      .+++|+++.|     + ++|+||+++. +|   +.||||.|+++|.+..    .+++||.+.++ +.+|+ ++
T Consensus        65 p------~~~~G~~~~g~V~~v~~~~GaFVdiG~-~~---~d~lvp~sel~~~~~~----~~~~Gd~v~v~-l~iD~-~~  128 (285)
T 3go5_A           65 V------TATQDQFGWGRVTEVRKDLGVFVDTGL-PD---KEIVVSLDILPELKEL----WPKKGDQLYIR-LEVDK-KD  128 (285)
T ss_dssp             C------CSCSSSCEEEEEEEEETTTEEEEECSC-TT---CCEEEEGGGSCSSGGG----SCCTTCEEEEE-EEECT-TS
T ss_pred             c------cccCCCEEEEEEEEEccCceEEEEECC-CC---cEEEEEHHHCCccccc----ccCCCCEEEEE-EEECC-CC
Confidence            2      3689999998     6 6999999961 14   7999999999986532    46899999766 68998 78


Q ss_pred             eEEEEEecC-CCCchhHHhhhhCCCChH
Q 022938          252 RITLSIKQL-EEDPLLETLEKVIPQGLE  278 (289)
Q Consensus       252 ri~lSlK~~-~~~p~~~~~~~~~~g~~~  278 (289)
                      ||.+|+|+. ..+||.....++..|+..
T Consensus       129 Ri~ls~k~~~~~~~~~~~~~~~~~G~~V  156 (285)
T 3go5_A          129 RIWGLLAYQEDFQRLARPAYNNMQNQNW  156 (285)
T ss_dssp             CEEEEECCHHHHHHHCCCCCSCCTTCEE
T ss_pred             cEEEEehhhhhcchhhhhhhhCCCCCEE
Confidence            999999976 578999988999998864

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

Probab=99.71  E-value=9.2e-18  Score=131.19  Aligned_cols=91  Identities=35%  Similarity=0.634  Sum_probs=81.8

Q ss_pred             chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcc-cccCcccccCCCCEEEEEEEEEeCCC
Q 022938          177 AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREK  250 (289)
Q Consensus       177 ~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~-~~~~~~~~~~iGd~V~vkV~~id~e~  250 (289)
                      .||+....++++|+++.|     +++|+||+|+  +|   +.||+|+++++++ +..++.+.|++||.|+|+|+++|+++
T Consensus        19 ~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~--~~---~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~~~   93 (115)
T 2khi_A           19 SHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIE--EG---VEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEER   93 (115)
T ss_dssp             --CCCSSCSSCSSCEEEEEEEEEETTEEEEECS--TT---CEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEETTT
T ss_pred             CCHHHHhhcCCCCCEEEEEEEEEECCEEEEEEC--CC---CEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEECCC
Confidence            588888889999999999     8999999996  55   9999999999984 67888899999999999999999999


Q ss_pred             CeEEEEEecCCCCchhHHhhhh
Q 022938          251 SRITLSIKQLEEDPLLETLEKV  272 (289)
Q Consensus       251 ~ri~lSlK~~~~~p~~~~~~~~  272 (289)
                      ++|.||+|++.+|||+++.++|
T Consensus        94 ~rI~lslk~~~~~p~~~~~~~~  115 (115)
T 2khi_A           94 RRISLGLKQCKANPWQQFAETH  115 (115)
T ss_dssp             TEEEECCCCCCSSCCCCCCCCC
T ss_pred             CEEEEEEEecCcCHHHHHHhhC
Confidence            9999999999999999887654

>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=99.69  E-value=4.6e-19  Score=148.99  Aligned_cols=113  Identities=15%  Similarity=0.175  Sum_probs=92.2

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEE---CCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRF---FSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l---~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      +.|+++.|+|++++++|+||++   +|++|+||+|++++.+. .+|.+.++      +||.|+|+|+++|.+++++.||+
T Consensus        14 ~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v-~~~~~~~~------vGd~V~VkVl~vD~~~~rI~LSl   86 (182)
T 1kl9_A           14 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRI-RSINKLIR------IGRNECVVVIRVDKEKGYIDLSK   86 (182)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC-------------C------TTCEEEEEEEEEETTTTEEEEES
T ss_pred             CCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCccc-CCHHHhcC------CCCEEEEEEEEEECCCCEEEEEE
Confidence            6899999999999999999999   48999999999999886 88888887      99999999999999999999999


Q ss_pred             ec---chhhhcccccccccEEEe-----ee-eeEEEEEecCCCceeEEEEEEccCcCcc
Q 022938          175 KD---AVWNKYSSRVNVEDIFVG-----RD-YGAFIHLRFPDGLYHLTGLVHVSEVSWD  224 (289)
Q Consensus       175 k~---~~~~~~~~~~~~G~iv~G-----~~-~G~fV~i~~~~G~~~i~Glv~~sels~~  224 (289)
                      |+   .||......++.|+.+.|     ++ +|  +++.  +|   +.|++|.++++|.
T Consensus        87 k~~~~~p~~~~~~~~~~g~~v~g~v~~i~~~~g--v~l~--~g---iegl~h~s~~~~~  138 (182)
T 1kl9_A           87 RRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLE--YTKD--EQ---LESLFQRTAWVFD  138 (182)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--CCSH--HH---HHHHHHHTHHHHH
T ss_pred             eecCcChHHHHHHhccCCCEEEEEEEEchhhcC--Cccc--CC---hhheEEeeecchh
Confidence            96   479888899999999998     55 99  7775  54   9999999988775

>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=99.68  E-value=3.2e-17  Score=137.69  Aligned_cols=90  Identities=26%  Similarity=0.405  Sum_probs=71.0

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  261 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~  261 (289)
                      ++|+++.|     ++||+||+|...+|   +.||+|+|+++|.++.++++.|++||.|+|+|+++|+++++|.||+|++.
T Consensus        14 ~~G~iv~G~V~~I~~fGaFV~L~e~~g---~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~~~   90 (182)
T 1kl9_A           14 EVEDVVMVNVRSIAEMGAYVSLLEYNN---IEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVS   90 (182)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTTTT---EEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTTCC
T ss_pred             CCCCEEEEEEEEEeccEEEEEEccCCC---cEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeecC
Confidence            78999999     89999999931144   99999999999999999999999999999999999999999999999999


Q ss_pred             CCchhHHhhhhCCCChHH
Q 022938          262 EDPLLETLEKVIPQGLEP  279 (289)
Q Consensus       262 ~~p~~~~~~~~~~g~~~~  279 (289)
                      ++||....+++..|+...
T Consensus        91 ~~p~~~~~~~~~~g~~v~  108 (182)
T 1kl9_A           91 PEEAIKCEDKFTKSKTVY  108 (182)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             cChHHHHHHhccCCCEEE
Confidence            999999999999887754

>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=99.65  E-value=1.1e-16  Score=133.84  Aligned_cols=91  Identities=24%  Similarity=0.414  Sum_probs=74.3

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  261 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~  261 (289)
                      ++|+++.|     ++||+||+|...+|   +.||||+|+++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++.
T Consensus        14 ~~G~iv~G~V~~i~~fGaFV~L~e~~g---veGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~~~   90 (175)
T 2a19_A           14 EIDDIVMVNVQQIAEMGAYVKLLEYDN---IEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVS   90 (175)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTTTT---CEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTTCC
T ss_pred             CCCCEEEEEEEEEecceEEEEEcCCCC---cEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEecC
Confidence            38999988     89999999931134   99999999999999999999999999999999999999999999999999


Q ss_pred             CCchhHHhhhhCCCChHHH
Q 022938          262 EDPLLETLEKVIPQGLEPY  280 (289)
Q Consensus       262 ~~p~~~~~~~~~~g~~~~~  280 (289)
                      ++||....+++..|+....
T Consensus        91 ~~~~~~~~~~~~~g~~v~g  109 (175)
T 2a19_A           91 SEDIIKCEEKYQKSKTVHS  109 (175)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             cChHHHHHHhccCCCcceE
Confidence            9999999999998876544

>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=99.58  E-value=6.5e-16  Score=121.30  Aligned_cols=90  Identities=28%  Similarity=0.406  Sum_probs=79.5

Q ss_pred             cchhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCC
Q 022938          176 DAVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK  250 (289)
Q Consensus       176 ~~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~  250 (289)
                      +.+|+.....+++|+++.|     .+||+||+|.   | +++.||||++++++.++.++.+.|++||.|+|+|+++|+++
T Consensus        10 ~~~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~---g-~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~   85 (119)
T 2cqo_A           10 SGRPETMENLPALYTIFQGEVAMVTDYGAFIKIP---G-CRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKN   85 (119)
T ss_dssp             CCCCCCSCCSCCTTCEEEEEEEEEETTEEEEECT---T-CSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECS
T ss_pred             ccchhhhhcccCCCCEEEEEEEEEeCceEEEEEC---C-CcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEeccc
Confidence            3467778888999999999     8999999993   2 02699999999999999999999999999999999999864


Q ss_pred             --CeEEEEEecCCCCchhHHh
Q 022938          251 --SRITLSIKQLEEDPLLETL  269 (289)
Q Consensus       251 --~ri~lSlK~~~~~p~~~~~  269 (289)
                        ++|.||+|++.++||+.+.
T Consensus        86 ~~~~i~LSlk~~~~~~~~~~~  106 (119)
T 2cqo_A           86 DRIKVSLSMKVVNQGTGKDLD  106 (119)
T ss_dssp             SCEEEEEESTTBCSSSCCBSC
T ss_pred             cCceEEEEEeecccCCccccC
Confidence              6999999999999998764

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

Probab=99.57  E-value=4.8e-15  Score=118.14  Aligned_cols=79  Identities=41%  Similarity=0.755  Sum_probs=73.4

Q ss_pred             cccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          184 SRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       184 ~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      .++++|+++.|     +++|+||+|.  +|   +.||||++++++.++.++.+.|++||.|+|+|+++|+++++|.||+|
T Consensus         3 ~~~~vG~iv~G~V~~i~~~G~FV~l~--~~---~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk   77 (130)
T 2k4k_A            3 AKFEVGSVYTGKVTGLQAYGAFVALD--EE---TQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIR   77 (130)
T ss_dssp             CCCCTTCEEEEEEEEEETTEEEEEEE--TT---EEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESH
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEEC--CC---cEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence            46889999999     8999999996  55   99999999999999999999999999999999999999999999999


Q ss_pred             cCCCCchhH
Q 022938          259 QLEEDPLLE  267 (289)
Q Consensus       259 ~~~~~p~~~  267 (289)
                      ++.++||..
T Consensus        78 ~~~~~p~~~   86 (130)
T 2k4k_A           78 ATQAAPEKK   86 (130)
T ss_dssp             HHHHSCCCC
T ss_pred             ecccCcccc
Confidence            999999763

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

Probab=99.56  E-value=8.2e-15  Score=113.25  Aligned_cols=86  Identities=17%  Similarity=0.293  Sum_probs=76.1

Q ss_pred             hhhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938           85 RSSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA  163 (289)
Q Consensus        85 ~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v  163 (289)
                      ..+.+|+.+...++.|++++|+|+++.++|+||+++ |++||||.+++++.+. .+|.+.++      +||.|+|+|+++
T Consensus        17 ~~~~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~-~~~~~~~~------vGd~V~v~V~~v   89 (109)
T 2khj_A           17 RGSHMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRV-EDATLVLS------VGDEVEAKFTGV   89 (109)
T ss_dssp             ----CHHHHTTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSS-SSGGGSCC------TTCEEEEEEEEE
T ss_pred             cccCHHHHHhhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccc-cChhhccC------CCCEEEEEEEEE
Confidence            456689998888999999999999999999999999 9999999999998876 77777776      999999999999


Q ss_pred             ecCCcEEEEEeecc
Q 022938          164 NEEMKKLVFSEKDA  177 (289)
Q Consensus       164 d~~~~ri~lS~k~~  177 (289)
                      |.+++++.||++..
T Consensus        90 d~~~~ki~LS~k~~  103 (109)
T 2khj_A           90 DRKNRAISLSVRAK  103 (109)
T ss_dssp             ETTTTEEEEETTSS
T ss_pred             ECCCCEEEEEEeec
Confidence            99889999999873

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

Probab=99.56  E-value=3.5e-15  Score=115.33  Aligned_cols=81  Identities=32%  Similarity=0.519  Sum_probs=75.1

Q ss_pred             chhhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCC
Q 022938          177 AVWNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS  251 (289)
Q Consensus       177 ~~~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~  251 (289)
                      +||+....++++|+++.|     .++|+||+|+  +|   +.||+|++++++.++.++.+.|++||.|+|+|+++|++++
T Consensus        20 ~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~--~~---~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~~~~   94 (109)
T 2khj_A           20 HMFNNWVALNKKGAIVTGKVTAVDAKGATVELA--DG---VEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDRKNR   94 (109)
T ss_dssp             -CHHHHTTTCCSSSEEEEEEEEECSSCEEEECS--TT---CBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEETTTT
T ss_pred             CHHHHHhhcCCCCCEEEEEEEEEECCeEEEEEC--CC---CEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEECCCC
Confidence            589999999999999999     8999999995  55   9999999999999999999999999999999999999889


Q ss_pred             eEEEEEecCCC
Q 022938          252 RITLSIKQLEE  262 (289)
Q Consensus       252 ri~lSlK~~~~  262 (289)
                      +|.||+|++++
T Consensus        95 ki~LS~k~~~~  105 (109)
T 2khj_A           95 AISLSVRAKDE  105 (109)
T ss_dssp             EEEEETTSSSS
T ss_pred             EEEEEEeecCh
Confidence            99999999764

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

Probab=99.54  E-value=8.3e-15  Score=108.82  Aligned_cols=77  Identities=30%  Similarity=0.409  Sum_probs=68.7

Q ss_pred             ccccccccEEEe----eeeeEEEEEecCCCceeEEEEEEcc-CcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          183 SSRVNVEDIFVG----RDYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       183 ~~~~~~G~iv~G----~~~G~fV~i~~~~G~~~i~Glv~~s-els~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      +...++|+++.|    ++||+||+|...+|   ++||+|+| +++++++.++++.+ +||.|+|+|+++|+++++|.||+
T Consensus         6 y~~~~vG~~~~G~V~v~~fG~FVel~~~~~---~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lsl   81 (88)
T 1luz_A            6 YSLPNAGDVIKGRVYEKDYALYIYLFDYPH---FEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNY   81 (88)
T ss_dssp             SCCCCTTCEEEEEEEEETTEEEEEETTCTT---SEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEE
T ss_pred             ecCCCCCCEEEEEEEEEccEEEEEECCCCC---eEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEE
Confidence            455688999999    89999999952124   99999999 99999999999999 99999999999999999999999


Q ss_pred             ecCCCC
Q 022938          258 KQLEED  263 (289)
Q Consensus       258 K~~~~~  263 (289)
                      |++.+|
T Consensus        82 k~~~~~   87 (88)
T 1luz_A           82 KRMCRH   87 (88)
T ss_dssp             EEECSC
T ss_pred             eecCCC
Confidence            998775

>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=99.54  E-value=7.7e-15  Score=112.29  Aligned_cols=82  Identities=26%  Similarity=0.521  Sum_probs=71.7

Q ss_pred             cccccccccEEEe-----eeeeEEEEEecC-CCceeEEEEEEccCc-CcccccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 022938          182 YSSRVNVEDIFVG-----RDYGAFIHLRFP-DGLYHLTGLVHVSEV-SWDLIQDIRDILNEGDEVRVKVIKIDREKSRIT  254 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~-~G~~~i~Glv~~sel-s~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~  254 (289)
                      ....+++|+++.|     .+||+||+|+.. +|   +.||+|+|++ ++.++.++.+.|++||.|+|+|+++|+  ++|.
T Consensus         6 ~~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~---~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~--~~i~   80 (103)
T 2eqs_A            6 SGEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKR---WEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG--TKTS   80 (103)
T ss_dssp             CCSSCCTTCEEEEEEEEECSSCEEEEECSSSSC---CEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET--TEEE
T ss_pred             ccccCCCCCEEEEEEEEEeccEEEEEEcCCCCC---eEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC--CeeE
Confidence            3456899999999     899999999621 14   9999999999 666788899999999999999999997  6999


Q ss_pred             EEEecCCCCchhHH
Q 022938          255 LSIKQLEEDPLLET  268 (289)
Q Consensus       255 lSlK~~~~~p~~~~  268 (289)
                      ||+|++.++||+.+
T Consensus        81 LSlk~~~~~~~~~~   94 (103)
T 2eqs_A           81 LSMKDVDQETGEDL   94 (103)
T ss_dssp             EESTTBCTTTCCBC
T ss_pred             EEEeecccCCchhc
Confidence            99999999999865

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

Probab=99.54  E-value=9.9e-15  Score=113.90  Aligned_cols=93  Identities=18%  Similarity=0.426  Sum_probs=75.9

Q ss_pred             hhhHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEe
Q 022938           86 SSADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQAN  164 (289)
Q Consensus        86 ~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd  164 (289)
                      ...+|+.+...++.|+++.|+|+++.++|+||+++ |++||+|.+++++.....++.+.++      +||.|+|+|+++|
T Consensus        17 ~~~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~------vGd~V~vkV~~vd   90 (115)
T 2khi_A           17 RGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVN------VGDVVEVMVLDID   90 (115)
T ss_dssp             ----CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCC------TTCEEEEEEEEEE
T ss_pred             ccCCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccEEC------CCCEEEEEEEEEE
Confidence            34466665566899999999999999999999998 8999999999987422266776665      9999999999999


Q ss_pred             cCCcEEEEEeec---chhhhccc
Q 022938          165 EEMKKLVFSEKD---AVWNKYSS  184 (289)
Q Consensus       165 ~~~~ri~lS~k~---~~~~~~~~  184 (289)
                      .+++++.||++.   +||+...+
T Consensus        91 ~~~~rI~lslk~~~~~p~~~~~~  113 (115)
T 2khi_A           91 EERRRISLGLKQCKANPWQQFAE  113 (115)
T ss_dssp             TTTTEEEECCCCCCSSCCCCCCC
T ss_pred             CCCCEEEEEEEecCcCHHHHHHh
Confidence            989999999996   57776544

>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=99.53  E-value=7.6e-15  Score=122.59  Aligned_cols=90  Identities=17%  Similarity=0.158  Sum_probs=76.3

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEE---CCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRF---FSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l---~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      +.|+++.|+|+++.++|+||++   +|++|+||.+++++.+. .+|.+.++      +||.|+|+|+++|++++++.||+
T Consensus        14 ~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v-~~~~~~~~------vGd~V~vkVl~vd~~~~~I~LSl   86 (175)
T 2a19_A           14 EIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRI-RSIQKLIR------VGKNDVAVVLRVDKEKGYIDLSK   86 (175)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC---------CCCCCCC------TTSEEEEEEEEEETTTTEEEEES
T ss_pred             CCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCccc-CCHHHcCC------CCCEEEEEEEEEECCCCeEEEEE
Confidence            4899999999999999999999   58999999999999886 88888887      99999999999999999999999


Q ss_pred             ec---chhhhcccccccccEEEe
Q 022938          175 KD---AVWNKYSSRVNVEDIFVG  194 (289)
Q Consensus       175 k~---~~~~~~~~~~~~G~iv~G  194 (289)
                      +.   .+|....+.+++|+.+.|
T Consensus        87 k~~~~~~~~~~~~~~~~g~~v~g  109 (175)
T 2a19_A           87 RRVSSEDIIKCEEKYQKSKTVHS  109 (175)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             EecCcChHHHHHHhccCCCcceE
Confidence            96   488888889999998888

>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=99.50  E-value=1.1e-14  Score=131.42  Aligned_cols=89  Identities=28%  Similarity=0.480  Sum_probs=80.9

Q ss_pred             cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  260 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~  260 (289)
                      .++|+++.|     ++||+||+|+..+   ++.||+|+|+++|.++.++.+.|++||.|.|+|+++|+++++|.||+|++
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            358999999     8999999994112   39999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhHHhhhhCCCCh
Q 022938          261 EEDPLLETLEKVIPQGL  277 (289)
Q Consensus       261 ~~~p~~~~~~~~~~g~~  277 (289)
                      .++||....+++..|+.
T Consensus        88 ~~~p~~~~~~~~~~G~~  104 (308)
T 1q8k_A           88 SPEEAIKCEDKFTKSKT  104 (308)
T ss_dssp             CHHHHHHHHHHHHHHHH
T ss_pred             ccChHHHHHHHccCCCe
Confidence            99999999999988865

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

Probab=99.50  E-value=2e-14  Score=128.17  Aligned_cols=89  Identities=30%  Similarity=0.511  Sum_probs=80.6

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLE  261 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~  261 (289)
                      ++|+++.|     .+||+||+|+..+|   +.||||+|+++++++.++.+.|++||.|.|+|+++|+++++|.||+|++.
T Consensus        10 ~~Gdiv~G~V~~I~~fGaFV~L~e~~g---ieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~~   86 (275)
T 3aev_A           10 EEGEFVVATVKRIHNYGAFLELDEYPG---KEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVT   86 (275)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTSTT---CEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESTTCC
T ss_pred             CCCCEEEEEEEEEECcEEEEEECCCCC---eEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEEeecC
Confidence            58999999     89999999952134   99999999999999999999999999999999999999999999999999


Q ss_pred             CCchhHHhhhhCCCChH
Q 022938          262 EDPLLETLEKVIPQGLE  278 (289)
Q Consensus       262 ~~p~~~~~~~~~~g~~~  278 (289)
                      ++||....+++..|...
T Consensus        87 ~~~~~~~~~~~~~g~~v  103 (275)
T 3aev_A           87 QQQRKAKLQEFKRAQKA  103 (275)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             cchhHHHHHhccCCCeE
Confidence            99999998888877653

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

Probab=99.50  E-value=1.3e-13  Score=100.56  Aligned_cols=69  Identities=32%  Similarity=0.523  Sum_probs=62.0

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  259 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~  259 (289)
                      ++++|+++.|     +++|+||+++  +|   +.||+|+|++++.++    +.|++||.|+|+|+++|+++++|.||+|+
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--EQ---VRGLLRPRDMISLRL----ENLNVGDEIIVQAIDVRPEKREIDFKYIP   72 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEE--TT---EEEEECGGGCSSCCG----GGCCTTCEEEEEEEEEETTTTEEEEEECS
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEEC--CC---CEEEEEHHHCCcccc----eeeCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            4688999999     8999999997  55   999999999998765    67999999999999999989999999999


Q ss_pred             CCC
Q 022938          260 LEE  262 (289)
Q Consensus       260 ~~~  262 (289)
                      +.+
T Consensus        73 ~~~   75 (80)
T 2k52_A           73 LEH   75 (80)
T ss_dssp             CC-
T ss_pred             ccc
Confidence            875

>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=99.43  E-value=3.7e-14  Score=128.07  Aligned_cols=98  Identities=15%  Similarity=0.181  Sum_probs=88.9

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      +.|+++.|+|+++.++|+||+++   |++||||.++++|.+. .+|.+.++      +||.|.|+|+++|++++++.||+
T Consensus        12 ~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i-~~~~~~~k------vGd~V~VkVl~vD~~~~rI~LSl   84 (308)
T 1q8k_A           12 EVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRI-RSINKLIR------IGRNECVKVIRVDKEKGYIDLSK   84 (308)
T ss_dssp             SSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSC-SCCTTTCS------SSCEEEEEEEEEETTTTEEEEEC
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccc-cCHHHhcC------CCCEEEEEEEEEeCCCCEEEEEE
Confidence            58999999999999999999994   7999999999999886 78888887      99999999999999999999999


Q ss_pred             ec---chhhhcccccccccEEEe-----ee-eeEEEE
Q 022938          175 KD---AVWNKYSSRVNVEDIFVG-----RD-YGAFIH  202 (289)
Q Consensus       175 k~---~~~~~~~~~~~~G~iv~G-----~~-~G~fV~  202 (289)
                      |.   .||......+++|+++.|     .+ +|+|++
T Consensus        85 K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~~G~fi~  121 (308)
T 1q8k_A           85 RRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKD  121 (308)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSS
T ss_pred             EecccChHHHHHHHccCCCeeEEEEEEcccccCCccC
Confidence            96   589888889999999988     55 698764

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

Probab=99.42  E-value=2.6e-14  Score=130.47  Aligned_cols=144  Identities=15%  Similarity=0.184  Sum_probs=109.3

Q ss_pred             eEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHHHHhhcCCCEEEE
Q 022938           26 LSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAARAYKESGFIYEG  105 (289)
Q Consensus        26 ~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~G~iv~g  105 (289)
                      ..++|+++.-.+|.  +.+|+.+++.|...+.  +|+.+...+      ..+.+.++++++...|+++.  .+.|++++|
T Consensus        73 ~~Isl~ea~~~d~~--~~vGd~ie~~I~~~df--gR~aa~~aK------qvi~qkireaere~i~~e~~--~~~GeIV~G  140 (344)
T 1hh2_P           73 TQISLEEAKKIDPL--AEVGSIVKKELNVKNF--GRIAAQTAK------QVLIQRIRELEKEKQFEKYS--ELKGTVTTA  140 (344)
T ss_dssp             SCEEHHHHHHHCTT--CCTTCEEEEECCCCCS--SSCSGGGHH------HHHHHHHHHHTTCCSSCCTT--CCTTCEEEE
T ss_pred             cEEeHHHHhhhCcc--ccCCCEEEEEEccccC--ccHHHHHHH------HHHHHHHHHHHHHHHHHHHh--hcCCCEEEE
Confidence            35777888777774  8999999999966654  555555322      22445566666555554431  248999999


Q ss_pred             EEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc--EEEEEeecchhhhcc
Q 022938          106 KIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK--KLVFSEKDAVWNKYS  183 (289)
Q Consensus       106 ~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~--ri~lS~k~~~~~~~~  183 (289)
                      +|.+++++|+||++|+.+|+||.+|++       |.+.++      +||+|+|+|++++.+.+  ++.||++.+.+.+.+
T Consensus       141 ~V~ri~~~~v~VDlGk~EgiLp~sE~i-------p~E~~~------vGD~Vkv~V~~V~~~~kg~~I~LSRt~p~~lk~L  207 (344)
T 1hh2_P          141 EVIRVMGEWADIRIGKLETRLPKKEWI-------PGEEIK------AGDLVKVYIIDVVKTTKGPKILVSRRVPEFVIGL  207 (344)
T ss_dssp             EEEEECSSEEEEEETTEEEEEEGGGSC-------TTCCCC------TTCEEEEEEEEEEEETTEEEEEEESSSHHHHHHH
T ss_pred             EEEEEecCcEEEEeCCeEEEEeHHHcC-------CCcCCC------CCCEEEEEEEEEEcCCCCcEEEEEeeccHHHHHH
Confidence            999999999999999999999999986       344454      99999999999997654  899999988777777


Q ss_pred             cccccccEEEe
Q 022938          184 SRVNVEDIFVG  194 (289)
Q Consensus       184 ~~~~~G~iv~G  194 (289)
                      .++++.++.+|
T Consensus       208 felEVPEI~dG  218 (344)
T 1hh2_P          208 MKLEIPEVENG  218 (344)
T ss_dssp             HHHHCHHHHHS
T ss_pred             HHhhcccceee
Confidence            77777666655

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

Probab=99.41  E-value=1.1e-12  Score=104.51  Aligned_cols=74  Identities=24%  Similarity=0.433  Sum_probs=68.4

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      ++.|+++.|+|+++.++|+||+++ +++||||.+++++.+. .++.+.++      +||.|.|+|+++|.+.+++.||++
T Consensus         5 ~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~-~~~~~~~~------vGd~V~vkV~~vd~~~~kI~LSlk   77 (130)
T 2k4k_A            5 FEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFV-KDINEHLS------VGDEVQVKVLAVDEEKGKISLSIR   77 (130)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCC-SCGGGTCC------TTCEEEEEEEEEETTTTEEEEESH
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccc-cCccccCC------CCCEEEEEEEEEeCCCCEEEEEEe
Confidence            579999999999999999999997 9999999999999886 77777776      999999999999998999999999


Q ss_pred             cc
Q 022938          176 DA  177 (289)
Q Consensus       176 ~~  177 (289)
                      ..
T Consensus        78 ~~   79 (130)
T 2k4k_A           78 AT   79 (130)
T ss_dssp             HH
T ss_pred             ec
Confidence            64

>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=99.40  E-value=4.7e-14  Score=125.33  Aligned_cols=90  Identities=29%  Similarity=0.415  Sum_probs=81.3

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  259 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~  259 (289)
                      .+++|+++.|     .++|+||+++..+   ++.||+|+|+++++++.++.+.|++||.|.|+|+++|+++++|.||+|+
T Consensus         8 ~~~vG~iv~G~V~~I~~~GaFV~l~e~~---~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~   84 (266)
T 3cw2_C            8 LPSEGEILIATVKQVFDYGSYVSLDEYG---GLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (266)
T ss_dssp             SCCTTCEEEEEEEECCSSSBEEEETTTT---SEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEESTT
T ss_pred             cCCCCCEEEEEEEEEeccEEEEEEcCCC---CeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            4688999999     8999999994113   3999999999999999999999999999999999999999999999999


Q ss_pred             CCCCchhHHhhhhCCCCh
Q 022938          260 LEEDPLLETLEKVIPQGL  277 (289)
Q Consensus       260 ~~~~p~~~~~~~~~~g~~  277 (289)
                      +.++||....+++..|+.
T Consensus        85 ~~~~~~~~~~~~~~~~~~  102 (266)
T 3cw2_C           85 VTDDERRKKNLQWKKIQR  102 (266)
T ss_dssp             SCTTHHHHHHHHHHHHHH
T ss_pred             cchhhHHHHHHhccccCc
Confidence            999999999988888753

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

Probab=99.40  E-value=1.8e-12  Score=94.40  Aligned_cols=70  Identities=20%  Similarity=0.292  Sum_probs=62.6

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      ++.|+++.|+|+++.++|+||+++ +++|++|.+++++.+.     +.+      .+||.|+|+|+++|++++++.||++
T Consensus         3 ~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel~~~~~-----~~~------~~Gd~V~v~V~~vd~~~~~i~lsl~   71 (80)
T 2k52_A            3 VEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRL-----ENL------NVGDEIIVQAIDVRPEKREIDFKYI   71 (80)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSCCG-----GGC------CTTCEEEEEEEEEETTTTEEEEEEC
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCcccc-----eee------CCCCEEEEEEEEEECCCCEEEEEEe
Confidence            478999999999999999999999 9999999999987542     333      3999999999999999999999998


Q ss_pred             cc
Q 022938          176 DA  177 (289)
Q Consensus       176 ~~  177 (289)
                      +.
T Consensus        72 ~~   73 (80)
T 2k52_A           72 PL   73 (80)
T ss_dssp             SC
T ss_pred             ec
Confidence            64

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

Probab=99.38  E-value=6.2e-13  Score=98.64  Aligned_cols=72  Identities=18%  Similarity=0.252  Sum_probs=63.0

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecC-CCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFP-QMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVF  172 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~s-els~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~l  172 (289)
                      .+.|+++.|+|+ ++++|+||+++   |++|++|.| ++++.+. .++.+.+       +||.|+|+|+++|.+++++.|
T Consensus         9 ~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~-~~~~~~~-------~Gd~V~VkV~~vd~~~~kI~l   79 (88)
T 1luz_A            9 PNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRY-VEYRDKL-------VGKTVKVKVIRVDYTKGYIDV   79 (88)
T ss_dssp             CCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHH-HHHHHHH-------TTCEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccc-cCHhHEe-------CCCEEEEEEEEEECCCCEEEE
Confidence            378999999999 99999999994   699999999 9998765 4444332       899999999999999999999


Q ss_pred             Eeecc
Q 022938          173 SEKDA  177 (289)
Q Consensus       173 S~k~~  177 (289)
                      |+|+.
T Consensus        80 slk~~   84 (88)
T 1luz_A           80 NYKRM   84 (88)
T ss_dssp             EEEEE
T ss_pred             EEeec
Confidence            99874

>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=99.38  E-value=1.4e-13  Score=107.84  Aligned_cols=82  Identities=17%  Similarity=0.218  Sum_probs=69.9

Q ss_pred             HHHHHHHhhcCCCEEEEEEEEEEcCcEEEEECC--EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecC
Q 022938           89 DWKAARAYKESGFIYEGKIQGFNGGGLLVRFFS--LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEE  166 (289)
Q Consensus        89 ~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~g--v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~  166 (289)
                      .|+.+...++.|+++.|+|+++.++|+||++++  .+||||.+++++.+. .++.+.++      +||.|+|+|+++|.+
T Consensus        12 ~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~-~~~~~~~~------~Gd~V~VkV~~vd~~   84 (119)
T 2cqo_A           12 RPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRV-DKPSEIVD------VGDKVWVKLIGREMK   84 (119)
T ss_dssp             CCCCSCCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCC-SCHHHHCC------TTCEEEEEEEEEEEC
T ss_pred             chhhhhcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccc-cChhhcCC------CCCEEEEEEEEEecc
Confidence            344444456899999999999999999999975  599999999999876 77777776      999999999999986


Q ss_pred             C--cEEEEEeecc
Q 022938          167 M--KKLVFSEKDA  177 (289)
Q Consensus       167 ~--~ri~lS~k~~  177 (289)
                      +  +++.||++..
T Consensus        85 ~~~~~i~LSlk~~   97 (119)
T 2cqo_A           85 NDRIKVSLSMKVV   97 (119)
T ss_dssp             SSCEEEEEESTTB
T ss_pred             ccCceEEEEEeec
Confidence            4  6999999974

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

Probab=99.32  E-value=1.4e-12  Score=116.12  Aligned_cols=98  Identities=10%  Similarity=0.151  Sum_probs=86.0

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      +.|+++.|+|+++.++|+||+++   |++||||.+++++.+. .+|.+.++      +||.|.|+|+++|++++++.||+
T Consensus        10 ~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v-~~~~~~~k------vGd~V~vkVi~vD~~~~~I~LSl   82 (275)
T 3aev_A           10 EEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWV-RNIRDYLK------EGQKVVAKVIRVDPRKGHIDLSL   82 (275)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCC-SCGGGTCC------TTCEEEEEEEEEETTTTEEEEES
T ss_pred             CCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccc-cCHHhccC------CCCEEEEEEEEEECCCCEEEEEE
Confidence            58999999999999999999995   7999999999999886 77887776      99999999999999999999999


Q ss_pred             ec---chhhhcccccccccEEEe-----e-eeeEEEE
Q 022938          175 KD---AVWNKYSSRVNVEDIFVG-----R-DYGAFIH  202 (289)
Q Consensus       175 k~---~~~~~~~~~~~~G~iv~G-----~-~~G~fV~  202 (289)
                      +.   .+|......++.|+.+.|     . ++|++++
T Consensus        83 k~~~~~~~~~~~~~~~~g~~v~g~v~~v~~~~G~~~e  119 (275)
T 3aev_A           83 RRVTQQQRKAKLQEFKRAQKAENLLRLAAEKLGKDFE  119 (275)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCHH
T ss_pred             eecCcchhHHHHHhccCCCeEEEEEEEchhhcCCCHH
Confidence            97   478777788888888877     3 6666544

>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=99.31  E-value=5.9e-12  Score=96.12  Aligned_cols=72  Identities=22%  Similarity=0.326  Sum_probs=63.6

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC----CEEEEeecCCC-CCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF----SLVGFLPFPQM-SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLV  171 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~----gv~g~ip~sel-s~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~  171 (289)
                      ++.|+++.|+|+++.++|+||+++    +++||||.+++ ++.+. .++.+.++      +||.|+|+|+++|.  +++.
T Consensus        10 ~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~-~~~~~~~~------~Gd~V~VkV~~vd~--~~i~   80 (103)
T 2eqs_A           10 PTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRV-ANVADVVS------KGQRVKVKVLSFTG--TKTS   80 (103)
T ss_dssp             CCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCC-CCHHHHCC------TTCEEEEEEEEEET--TEEE
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCccc-CCcccEeC------CCCEEEEEEEEEEC--CeeE
Confidence            579999999999999999999998    69999999999 55554 66777666      99999999999996  6999


Q ss_pred             EEeecc
Q 022938          172 FSEKDA  177 (289)
Q Consensus       172 lS~k~~  177 (289)
                      ||+|..
T Consensus        81 LSlk~~   86 (103)
T 2eqs_A           81 LSMKDV   86 (103)
T ss_dssp             EESTTB
T ss_pred             EEEeec
Confidence            999973

>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=99.30  E-value=2.4e-14  Score=143.20  Aligned_cols=128  Identities=17%  Similarity=0.323  Sum_probs=46.0

Q ss_pred             EEEEE--EEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeecchhhhc
Q 022938          105 GKIQG--FNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKDAVWNKY  182 (289)
Q Consensus       105 g~V~~--v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~~~~~~~  182 (289)
                      |++.+  ..++|++|++++ +|.++++..++... ..            .-+    +|..       +    . .|    
T Consensus       617 Gk~Ik~I~~~~G~~IdI~~-dG~v~Is~~~~~~~-~~------------a~~----~i~~-------i----~-~p----  662 (757)
T 1e3p_A          617 RQMINQIQEDTGAEITIED-DGTIYIGAADGPAA-EA------------ARA----TING-------I----A-NP----  662 (757)
T ss_dssp             ----CTTCCCCCSCC---------CCCBSSHHHH-CC-------------------------------------------
T ss_pred             ceeeehhhHhhCCEEEecC-CceEEEecCCHHHH-HH------------HHH----HHHH-------h----c-ch----
Confidence            44555  457899999986 89999888664321 00            000    0000       0    0 11    


Q ss_pred             ccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCc----CcccccCcccccCCCCEEEEEEEEEeCCCCeE
Q 022938          183 SSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEV----SWDLIQDIRDILNEGDEVRVKVIKIDREKSRI  253 (289)
Q Consensus       183 ~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sel----s~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri  253 (289)
                       .++++|+++.|     .+||+||+|.  +|   +.||+|+|++    +|+++.++.+.|++||.|+|+|+++|+ ++||
T Consensus       663 -~~~~vG~i~~G~V~~i~~fGaFV~l~--~g---~eGLvHiSel~~~~s~~rv~~~~~~~~vGd~V~VkVi~vd~-~grI  735 (757)
T 1e3p_A          663 -TSPEVGERILGSVVKTTTFGAFVSLL--PG---KDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDS-RGKL  735 (757)
T ss_dssp             -----------CBEEECC-CSCEECCC--------CCCCC-------------------CCSSCBCCCCCCCCCS-SCC-
T ss_pred             -hhcccccEEEEEEEEccccEEEEEEc--CC---cEEEEEhHHhccccCCCcccCcccccCCCCEEEEEEEEECC-CCCE
Confidence             56799999999     8999999995  55   9999999999    999999999999999999999999998 9999


Q ss_pred             EEEEecCCCCchhHHhhhhC
Q 022938          254 TLSIKQLEEDPLLETLEKVI  273 (289)
Q Consensus       254 ~lSlK~~~~~p~~~~~~~~~  273 (289)
                      .||+|++.++||....+++.
T Consensus       736 ~LS~k~~~~~pw~~~~~~~~  755 (757)
T 1e3p_A          736 SLIPVIEGEEAASDEKKDDA  755 (757)
T ss_dssp             --------------------
T ss_pred             EEEEecCCCCchhhhhhccc
Confidence            99999999999998877664

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

Probab=99.22  E-value=9.4e-13  Score=130.79  Aligned_cols=88  Identities=30%  Similarity=0.515  Sum_probs=0.0

Q ss_pred             hhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeE
Q 022938          179 WNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRI  253 (289)
Q Consensus       179 ~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri  253 (289)
                      ++....++++|++|.|     .+||+||+|.  +|   +.||+|+|+++|+++.++.+.|++||.|+|+|+++|+ ++||
T Consensus       628 i~~i~~~~~vG~v~~G~V~~I~~fGaFVel~--~g---~eGLvHiSels~~rv~~~~d~~kvGD~V~VkVi~iD~-~grI  701 (726)
T 4aid_A          628 IKSITDEAEVGKIYDGKVVKVVDFGAFVNFF--GA---KDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDD-RGKT  701 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHhhhhcCCcEEEEEEEEEeccEEEEEEC--CC---cEEEEEHHHcCcccccCccccCCCCCEEEEEEEEECC-CCcE
Confidence            4556788999999999     9999999996  55   9999999999999999999999999999999999998 8999


Q ss_pred             EEEEecCCCCchhHHhhhh
Q 022938          254 TLSIKQLEEDPLLETLEKV  272 (289)
Q Consensus       254 ~lSlK~~~~~p~~~~~~~~  272 (289)
                      .||+|++.++||.++.++.
T Consensus       702 ~LS~K~~~~~~G~~~~~k~  720 (726)
T 4aid_A          702 KLSMKVVDQETGEDLSKKE  720 (726)
T ss_dssp             -------------------
T ss_pred             EEEEeecccCcchhhhhhh
Confidence            9999999999999875543

>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=99.14  E-value=1.2e-11  Score=109.82  Aligned_cols=86  Identities=20%  Similarity=0.200  Sum_probs=72.7

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEE---CCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRF---FSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l---~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      ++.|+++.|+|+++.++|+||++   +|.+||||.+++++.+. .++.+.++      +||.|.|+|+++|.+++++.||
T Consensus         9 ~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v-~~~~~~~~------vGd~V~VkVi~vd~~~g~I~LS   81 (266)
T 3cw2_C            9 PSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWV-KNIRDVLK------ENRKVIVKVIRVDRRKGTVDVS   81 (266)
T ss_dssp             CCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSC-CCHHHHSC------TTCEEEEEECCCCSSSCCCBEE
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccc-cCHHHhCc------CCCEEEEEEEEEeCCCCEEEEE
Confidence            47999999999999999999999   57999999999999886 77777776      9999999999999889999999


Q ss_pred             eec---chhhhcccccccc
Q 022938          174 EKD---AVWNKYSSRVNVE  189 (289)
Q Consensus       174 ~k~---~~~~~~~~~~~~G  189 (289)
                      ++.   .+|......++.|
T Consensus        82 lk~~~~~~~~~~~~~~~~~  100 (266)
T 3cw2_C           82 LKKVTDDERRKKNLQWKKI  100 (266)
T ss_dssp             STTSCTTHHHHHHHHHHHH
T ss_pred             EEecchhhHHHHHHhcccc
Confidence            986   3554433333333

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

Probab=99.14  E-value=4.5e-12  Score=126.31  Aligned_cols=85  Identities=34%  Similarity=0.628  Sum_probs=0.0

Q ss_pred             hhhcccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeE
Q 022938          179 WNKYSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRI  253 (289)
Q Consensus       179 ~~~~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri  253 (289)
                      ++....++++|+++.|     .+||+||++.  +|   +.||+|+|+++|+++.++.+.|++||.|+|+|+++|+ ++||
T Consensus       618 i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~--~g---~eGLvHiSel~~~~v~~~~~~~~vGd~V~VkVi~vd~-~grI  691 (723)
T 3cdi_A          618 IEEITAEIEVGRVYTGKVTRIVDFGAFVAIG--GG---KEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRI  691 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHhhhhhcCcEEEEEEEEEecceEEEEeC--CC---ceEEEEHHHcCCccccCcccccCCCCEEEEEEEEECC-CCcE
Confidence            3445678899999999     9999999996  55   9999999999999999999999999999999999998 9999


Q ss_pred             EEEEecCCCCchhHHh
Q 022938          254 TLSIKQLEEDPLLETL  269 (289)
Q Consensus       254 ~lSlK~~~~~p~~~~~  269 (289)
                      .||+|++.++||....
T Consensus       692 ~LS~k~~~~~~g~~~~  707 (723)
T 3cdi_A          692 RLSIKEATEQSQPAAA  707 (723)
T ss_dssp             ----------------
T ss_pred             EEEEEeccCCCCcccC
Confidence            9999999999998754

>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=99.07  E-value=1.1e-10  Score=91.38  Aligned_cols=76  Identities=16%  Similarity=0.250  Sum_probs=61.9

Q ss_pred             cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCc-CcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 022938          182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEV-SWDLIQDIRDILNEGDEVRVKVIKIDREKSRITL  255 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sel-s~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~l  255 (289)
                      .+.++++|+++.|     .+||+||+|+ .++   ..|++|.++. +|.+..++.+.|++||.|+|+|+++|+++++|.|
T Consensus        15 ~~~~l~~G~i~~G~V~~v~~fG~fV~l~-~~~---~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~L   90 (119)
T 1wi5_A           15 SAEALKPGMLLTGTVSSLEDHGYLVDIG-VDG---TRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSL   90 (119)
T ss_dssp             CTTTCCTTCEEEEEEEEECSSEEEEECC-CSS---CEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEE
T ss_pred             cHhcCCCCCEEEEEEEEEeCceEEEEEC-CCC---eEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCCCCEEEE
Confidence            3568899999999     8999999995 223   6677666554 2444567889999999999999999999999999


Q ss_pred             EEecCC
Q 022938          256 SIKQLE  261 (289)
Q Consensus       256 SlK~~~  261 (289)
                      |+|+..
T Consensus        91 slk~~~   96 (119)
T 1wi5_A           91 SVGHSE   96 (119)
T ss_dssp             ECCCCC
T ss_pred             EEchhh
Confidence            999754

>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=99.07  E-value=7.4e-11  Score=92.33  Aligned_cols=74  Identities=16%  Similarity=0.265  Sum_probs=62.1

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCC-CCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMS-PSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels-~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      ++.|++++|+|++++++|+||+++  +..|++|.+++. +... .+|.+.++      +||.|+|+|+++|.+++++.||
T Consensus        19 l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~~~~~-~~~~~~~~------~Gd~V~vkV~~vd~~~~~i~Ls   91 (119)
T 1wi5_A           19 LKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQ-KNKGAKLK------VGQYLNCIVEKVKGNGGVVSLS   91 (119)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHH-HSSSCCCC------TTCEEEEEEEECCTTSCEEEEE
T ss_pred             CCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccccccc-cCccCEeC------CCCEEEEEEEEEeCCCCEEEEE
Confidence            689999999999999999999998  688888877652 2221 35666665      9999999999999989999999


Q ss_pred             eecc
Q 022938          174 EKDA  177 (289)
Q Consensus       174 ~k~~  177 (289)
                      +++.
T Consensus        92 lk~~   95 (119)
T 1wi5_A           92 VGHS   95 (119)
T ss_dssp             CCCC
T ss_pred             Echh
Confidence            9975

>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=99.07  E-value=5e-10  Score=94.35  Aligned_cols=75  Identities=19%  Similarity=0.287  Sum_probs=64.3

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccC----------cCcccchhcccccCCCCEEEEEEEEEecC
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSC----------KEPQKSIHEIAKGLTGSIISVKVIQANEE  166 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~----------~~p~~~~~~~~~~~vG~~V~vkVl~vd~~  166 (289)
                      ...|++++|+|++++++|+||++++.+|++|.+++++.+..          .++.+.++      +||.|+|+|+++|.+
T Consensus        79 ~~~Gev~~G~V~~v~~~G~fV~l~~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~------~Gd~V~vkV~~vd~~  152 (187)
T 1go3_E           79 PEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLE------IGDYVRARIVAISLK  152 (187)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC--CEEETTTCCEEC------TTCEEEEEEEEEECC
T ss_pred             cCCCCEEEEEEEEEeCcEEEEEEcCccEEEEhHHhCCCcceECCccceEEecCCCeEEc------CCCEEEEEEEEEEcc
Confidence            37899999999999999999999999999999999877642          14555555      999999999999987


Q ss_pred             Cc-----EEEEEeecc
Q 022938          167 MK-----KLVFSEKDA  177 (289)
Q Consensus       167 ~~-----ri~lS~k~~  177 (289)
                      .+     ++.+|++..
T Consensus       153 ~~~p~~~~I~lS~k~~  168 (187)
T 1go3_E          153 AERKRGSKIALTMRQP  168 (187)
T ss_dssp             C-----CEEEEECCST
T ss_pred             cCCCCccEEEEEEcCC
Confidence            55     999999984

>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=99.03  E-value=4.3e-10  Score=94.77  Aligned_cols=76  Identities=26%  Similarity=0.522  Sum_probs=64.2

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccccc-----------CcccccCCCCEEEEEEEEEeC
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ-----------DIRDILNEGDEVRVKVIKIDR  248 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~-----------~~~~~~~iGd~V~vkV~~id~  248 (289)
                      ...+|+++.|     +++|+||+++  +    .+|++|+|+++++++.           ++.+.|++||.|+|+|+++|.
T Consensus        78 ~~~~Gev~~G~V~~v~~~G~fV~l~--~----~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~  151 (187)
T 1go3_E           78 IPEMYELIEGEVVDVVEFGSFVRLG--P----LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISL  151 (187)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECS--S----SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEEC
T ss_pred             ccCCCCEEEEEEEEEeCcEEEEEEc--C----ccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEc
Confidence            4678999999     8999999995  2    8999999999988765           778899999999999999998


Q ss_pred             CCC-----eEEEEEecCC--CCchh
Q 022938          249 EKS-----RITLSIKQLE--EDPLL  266 (289)
Q Consensus       249 e~~-----ri~lSlK~~~--~~p~~  266 (289)
                      +++     +|.||+|+..  +.+|-
T Consensus       152 ~~~~p~~~~I~lS~k~~~LG~~~w~  176 (187)
T 1go3_E          152 KAERKRGSKIALTMRQPYLGKLEWI  176 (187)
T ss_dssp             CC-----CEEEEECCSTTCEEHHHH
T ss_pred             ccCCCCccEEEEEEcCCCCCcHHHH
Confidence            755     9999999954  44443

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

Probab=99.03  E-value=2.2e-10  Score=119.38  Aligned_cols=75  Identities=13%  Similarity=0.072  Sum_probs=69.1

Q ss_pred             cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccc-ccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 022938          182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITL  255 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~-~~~~~~~~~iGd~V~vkV~~id~e~~ri~l  255 (289)
                      ...++++|+++.|     ++||+||+|+  .|   +.|+||+|++++.+ +.++.+.|++||.|+|+|+++|+++++|.|
T Consensus       896 t~~~l~~G~iv~G~V~~V~~fGaFV~L~--~g---veGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~L  970 (1219)
T 3psi_A          896 SEKTFFKGSIIPVRVERFWHNDIICTTN--SE---VECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEV  970 (1219)
T ss_dssp             CTTTSCTTCEEEEEEEEECSSCEEEECT--TS---CEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEE
T ss_pred             cHhhCCCCCEEEEEEEEEecceEEEEeC--CC---ceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEE
Confidence            4588999999999     8999999995  55   99999999999998 789999999999999999999999999999


Q ss_pred             EEecCC
Q 022938          256 SIKQLE  261 (289)
Q Consensus       256 SlK~~~  261 (289)
                      |+|...
T Consensus       971 Slk~~d  976 (1219)
T 3psi_A          971 SLLDHD  976 (1219)
T ss_dssp             ECCHHH
T ss_pred             EecHHH
Confidence            999653

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

Probab=99.01  E-value=5.7e-10  Score=116.31  Aligned_cols=77  Identities=12%  Similarity=0.031  Sum_probs=71.0

Q ss_pred             HhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           95 AYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        95 ~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      +.+++|++++|+|++|.++|+||+++ |++|+||++++++.+...+|.+.++      +||.|+|+|+++|.+++++.||
T Consensus       898 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~p~~v~k------vGd~V~vkVl~VD~~~~rI~LS  971 (1219)
T 3psi_A          898 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYE------IGKTYPAKVIYIDYANITAEVS  971 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTTSCSCSTTTSC------TTCEEEEEEEEEEGGGTEEEEE
T ss_pred             hhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCcccCCHHHcCC------CCCEEEEEEEEEECCCCEEEEE
Confidence            56789999999999999999999999 9999999999999873378888887      9999999999999999999999


Q ss_pred             eecc
Q 022938          174 EKDA  177 (289)
Q Consensus       174 ~k~~  177 (289)
                      ++..
T Consensus       972 lk~~  975 (1219)
T 3psi_A          972 LLDH  975 (1219)
T ss_dssp             CCHH
T ss_pred             ecHH
Confidence            9863

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

Probab=98.99  E-value=3.7e-10  Score=94.60  Aligned_cols=80  Identities=29%  Similarity=0.594  Sum_probs=64.3

Q ss_pred             ccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-----------cCcccccCCCCEEEEEEEEE
Q 022938          183 SSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKI  246 (289)
Q Consensus       183 ~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-----------~~~~~~~~iGd~V~vkV~~i  246 (289)
                      .....+|+++.|     +++|+||+++  +    .+|++|++++++++.           ++....|++||.|++||+++
T Consensus        76 v~~p~~Gev~~G~V~~v~~~G~fv~l~--~----~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v  149 (180)
T 4ayb_E           76 TYVPVVQEVVEGEVLQVDNYGVFVNLG--P----MDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISV  149 (180)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECS--S----SEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEE
T ss_pred             eeeccCCCEEEEEEeeeccceEEEEEC--C----ccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEE
Confidence            345688999999     9999999995  2    899999999998866           46777899999999999999


Q ss_pred             eCC----CCeEEEEEec--CCCCchhHH
Q 022938          247 DRE----KSRITLSIKQ--LEEDPLLET  268 (289)
Q Consensus       247 d~e----~~ri~lSlK~--~~~~p~~~~  268 (289)
                      |++    ..||.||+|+  +-+.+|-+.
T Consensus       150 ~~~~~~~~~rI~ls~k~~gLG~~~W~~~  177 (180)
T 4ayb_E          150 ASTVTGRLPRIALTMRQPYLGKLEWITQ  177 (180)
T ss_dssp             CC-------CEEEECCSTTCEEHHHHTT
T ss_pred             eCCCCcccCcEEEEcCCCCCCCChhHhh
Confidence            864    4589999998  445555543

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

Probab=98.96  E-value=1.9e-10  Score=115.45  Aligned_cols=75  Identities=28%  Similarity=0.536  Sum_probs=68.7

Q ss_pred             cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      .+.++++|+++.|     ++||+||+++  .|   ++||||+|++++.++.++.+.|++||.|+|+|+++|+++++|.||
T Consensus       648 ~~~~l~vG~iv~G~V~~V~~fGaFV~l~--~~---~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~LS  722 (785)
T 3bzc_A          648 SLKDLKPGMVLEGVVTNVTNFGAFVDIG--VH---QDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLS  722 (785)
T ss_dssp             SSTTCCTTCBCCCEEEEEETTEEEEECS--SS---SEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEEC
T ss_pred             chhhcCCCCEEEEEEEEEecCCeEEEeC--CC---cEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEE
Confidence            3567899999988     8999999996  44   899999999999999999999999999999999999999999999


Q ss_pred             EecCC
Q 022938          257 IKQLE  261 (289)
Q Consensus       257 lK~~~  261 (289)
                      +|...
T Consensus       723 lk~~~  727 (785)
T 3bzc_A          723 MRMSD  727 (785)
T ss_dssp             CSSCC
T ss_pred             EecCC
Confidence            99754

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

Probab=98.96  E-value=1.9e-09  Score=90.24  Aligned_cols=75  Identities=15%  Similarity=0.310  Sum_probs=62.1

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccC----------cCcccchhcccccCCCCEEEEEEEEEecC
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSC----------KEPQKSIHEIAKGLTGSIISVKVIQANEE  166 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~----------~~p~~~~~~~~~~~vG~~V~vkVl~vd~~  166 (289)
                      ...|++++|+|++++++|+||+++.++|++|.+++++.+..          +++.+.++      +||.|+|||+++|.+
T Consensus        79 p~~Gev~~G~V~~v~~~G~fv~l~~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~------~Gd~VrvkV~~v~~~  152 (180)
T 4ayb_E           79 PVVQEVVEGEVLQVDNYGVFVNLGPMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQ------KGDKVRARVISVAST  152 (180)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCC------TTCEEEEEEEEECC-
T ss_pred             ccCCCEEEEEEeeeccceEEEEECCccceEEeeecCCCccccchhcceEEEeccCeEEC------CCCEEEEEEEEEeCC
Confidence            36999999999999999999999999999999999987652          23444444      999999999999864


Q ss_pred             C----cEEEEEeecc
Q 022938          167 M----KKLVFSEKDA  177 (289)
Q Consensus       167 ~----~ri~lS~k~~  177 (289)
                      .    .+|.+|+|++
T Consensus       153 ~~~~~~rI~ls~k~~  167 (180)
T 4ayb_E          153 VTGRLPRIALTMRQP  167 (180)
T ss_dssp             ------CEEEECCST
T ss_pred             CCcccCcEEEEcCCC
Confidence            3    4899999984

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

Probab=98.92  E-value=3.6e-10  Score=113.39  Aligned_cols=74  Identities=20%  Similarity=0.368  Sum_probs=69.2

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      +++|++++|+|++|.++|+||+++ +++|+||++++++.+. .+|.+.++      +||.|+|+|+++|.+++++.||++
T Consensus       652 l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v-~d~~~~~~------vGd~V~VkVi~VD~~~~rI~LSlk  724 (785)
T 3bzc_A          652 LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFV-KDPYEVVK------AGDIVKVKVMEVDIPRNRVGLSMR  724 (785)
T ss_dssp             CCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCC-SCHHHHCC------TTCCCCCBEEEEETTTTEEEECCS
T ss_pred             cCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCcccc-CChhheeC------CCCEEEEEEEEEECCCCEEEEEEe
Confidence            689999999999999999999999 8999999999999876 78888876      999999999999999999999998


Q ss_pred             cc
Q 022938          176 DA  177 (289)
Q Consensus       176 ~~  177 (289)
                      ..
T Consensus       725 ~~  726 (785)
T 3bzc_A          725 MS  726 (785)
T ss_dssp             SC
T ss_pred             cC
Confidence            64

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

Probab=98.92  E-value=1.1e-10  Score=119.86  Aligned_cols=75  Identities=13%  Similarity=0.072  Sum_probs=0.4

Q ss_pred             cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccc-ccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 022938          182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITL  255 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~-~~~~~~~~~iGd~V~vkV~~id~e~~ri~l  255 (289)
                      ...++++|+++.|     ++||+||+|+  .|   +.|+||+|++++.+ +.++.+.|++||.|+|+|+++|+++++|.|
T Consensus       899 t~~~l~~G~iv~G~V~~V~~fGaFV~L~--~g---veGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~L  973 (1030)
T 3psf_A          899 SEKTFFKGSIIPVRVERFWHNDIICTTN--SE---VECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEV  973 (1030)
T ss_dssp             C-------------------------------------------------------------------------------
T ss_pred             cHHHhcCCCEEEEEEEEEccCeEEEEeC--CC---cEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEE
Confidence            3478999999999     9999999996  55   99999999999998 799999999999999999999999999999


Q ss_pred             EEecCC
Q 022938          256 SIKQLE  261 (289)
Q Consensus       256 SlK~~~  261 (289)
                      |+|...
T Consensus       974 Slk~~d  979 (1030)
T 3psf_A          974 SLLDHD  979 (1030)
T ss_dssp             ------
T ss_pred             EechHH
Confidence            999854

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

Probab=98.92  E-value=1.2e-10  Score=115.72  Aligned_cols=82  Identities=26%  Similarity=0.368  Sum_probs=1.0

Q ss_pred             hHHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecC
Q 022938           88 ADWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEE  166 (289)
Q Consensus        88 ~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~  166 (289)
                      ..|+.+...++.|++++|+|+++.++|+||++. |++|+||+|++++.++ .++.+.++      +||.|+|+|+++|+ 
T Consensus       626 ~~i~~i~~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~~rv-~~~~d~~k------vGD~V~VkVi~iD~-  697 (726)
T 4aid_A          626 DWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERV-AKPSDVLK------EGQMVKVKLLGFDD-  697 (726)
T ss_dssp             HC------------------------------------------------------------------------------
T ss_pred             HHHHHHhhhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCcccc-cCccccCC------CCCEEEEEEEEECC-
Confidence            457777778899999999999999999999998 8999999999999887 78888887      99999999999997 


Q ss_pred             CcEEEEEeecc
Q 022938          167 MKKLVFSEKDA  177 (289)
Q Consensus       167 ~~ri~lS~k~~  177 (289)
                      ++|+.||+|..
T Consensus       698 ~grI~LS~K~~  708 (726)
T 4aid_A          698 RGKTKLSMKVV  708 (726)
T ss_dssp             -----------
T ss_pred             CCcEEEEEeec
Confidence            78999999974

>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=98.89  E-value=2.3e-09  Score=91.78  Aligned_cols=78  Identities=21%  Similarity=0.208  Sum_probs=65.3

Q ss_pred             cccccccEEEe-----eeeeEEEEEecCCC---ceeEEEEEEccCcCccccc--CcccccCCCCEEEEEEEEEeCCCCeE
Q 022938          184 SRVNVEDIFVG-----RDYGAFIHLRFPDG---LYHLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRI  253 (289)
Q Consensus       184 ~~~~~G~iv~G-----~~~G~fV~i~~~~G---~~~i~Glv~~sels~~~~~--~~~~~~~iGd~V~vkV~~id~e~~ri  253 (289)
                      ...++|++|.|     .++|+||+|....+   ..+..|++|++++++.+.+  ++.+.|++||.|+|+|++++.+++++
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            36799999999     89999999852100   0037899999999998887  89999999999999999999877899


Q ss_pred             EEEEecCC
Q 022938          254 TLSIKQLE  261 (289)
Q Consensus       254 ~lSlK~~~  261 (289)
                      .||+|+..
T Consensus       157 ~LS~k~~~  164 (209)
T 2nn6_I          157 LLTTAENE  164 (209)
T ss_dssp             EEECCSSS
T ss_pred             EEEEecCC
Confidence            99999853

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

Probab=98.84  E-value=3.2e-10  Score=113.09  Aligned_cols=81  Identities=21%  Similarity=0.311  Sum_probs=0.0

Q ss_pred             HHHHHHHhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC
Q 022938           89 DWKAARAYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM  167 (289)
Q Consensus        89 ~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~  167 (289)
                      .++.+...++.|++++|+|+++.++|+||++. |.+||+|+|++++.++ .++.+.++      +||.|+|+|+++|. +
T Consensus       617 ~i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~~~~v-~~~~~~~~------vGd~V~VkVi~vd~-~  688 (723)
T 3cdi_A          617 RIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRV-EKVTDYLQ------MGQEVPVKVLEVDR-Q  688 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHhhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCccc-cCcccccC------CCCEEEEEEEEECC-C
Confidence            45556667899999999999999999999998 9999999999999886 88888887      99999999999997 8


Q ss_pred             cEEEEEeecc
Q 022938          168 KKLVFSEKDA  177 (289)
Q Consensus       168 ~ri~lS~k~~  177 (289)
                      +++.||+|..
T Consensus       689 grI~LS~k~~  698 (723)
T 3cdi_A          689 GRIRLSIKEA  698 (723)
T ss_dssp             ----------
T ss_pred             CcEEEEEEec
Confidence            9999999963

>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=98.83  E-value=1.1e-08  Score=84.90  Aligned_cols=78  Identities=14%  Similarity=0.110  Sum_probs=57.4

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCccc----chh--cccccCCCCEEEEEEEEEecCCc--E
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQK----SIH--EIAKGLTGSIISVKVIQANEEMK--K  169 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~----~~~--~~~~~~vG~~V~vkVl~vd~~~~--r  169 (289)
                      ..|++++|+|++++++|+||+++..+|++|.+++++.+. .+|.+    ...  ...-+.+||.|+|+|.++|.+.+  .
T Consensus        80 ~~Gev~~G~V~~v~~fG~fV~l~~~~glvhis~l~~~~~-~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~~~  158 (172)
T 2c35_B           80 FKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEME-FDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIF  158 (172)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEE-EESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEEE
T ss_pred             CCCCEEEEEEEEEeCCEEEEEECCEEEEEEHHHCCCCcE-ECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCCCCcE
Confidence            689999999999999999999997889999999986533 22221    000  00123499999999999998765  2


Q ss_pred             EEEEeec
Q 022938          170 LVFSEKD  176 (289)
Q Consensus       170 i~lS~k~  176 (289)
                      .+.|+++
T Consensus       159 ~igsm~~  165 (172)
T 2c35_B          159 AIGSLMD  165 (172)
T ss_dssp             EEEECCS
T ss_pred             EEEEecC
Confidence            3337765

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

Probab=98.83  E-value=3.6e-10  Score=116.14  Aligned_cols=78  Identities=12%  Similarity=0.018  Sum_probs=0.0

Q ss_pred             HhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           95 AYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        95 ~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      +.+++|++++|+|++|.++|+||+++ |++|+||++++++.+...+|.+.++      +||.|+|+|+++|.+++++.||
T Consensus       901 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~~~~v~k------vGd~V~vkVl~VD~~~~rI~LS  974 (1030)
T 3psf_A          901 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYE------IGKTYPAKVIYIDYANITAEVS  974 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCCcccCCHHHcCC------CCCEEEEEEEEEECCCCEEEEE
Confidence            56789999999999999999999999 9999999999999873378888887      9999999999999999999999


Q ss_pred             eecch
Q 022938          174 EKDAV  178 (289)
Q Consensus       174 ~k~~~  178 (289)
                      +|...
T Consensus       975 lk~~d  979 (1030)
T 3psf_A          975 LLDHD  979 (1030)
T ss_dssp             -----
T ss_pred             echHH
Confidence            99753

>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=98.81  E-value=8.1e-09  Score=88.39  Aligned_cols=75  Identities=20%  Similarity=0.278  Sum_probs=66.0

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC---------CEEEEeecCCCCCCccCc--CcccchhcccccCCCCEEEEEEEEEec
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF---------SLVGFLPFPQMSPSHSCK--EPQKSIHEIAKGLTGSIISVKVIQANE  165 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~---------gv~g~ip~sels~~~~~~--~p~~~~~~~~~~~vG~~V~vkVl~vd~  165 (289)
                      .+.|+++.|+|+++.++|+||+++         +.+|+||.+|+++.+. .  ++.+.|+      +||.|+|+|++++.
T Consensus        79 p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~-~~~~~~~~l~------~GD~V~akVisi~~  151 (209)
T 2nn6_I           79 PDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEK-DKVEIYKSFR------PGDIVLAKVISLGD  151 (209)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSS-CCCCGGGTCC------SSSEEEEEEEEEET
T ss_pred             CCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccc-cccchhhhcC------CCCEEEEEEEEEeC
Confidence            589999999999999999999984         5789999999998775 4  5666666      99999999999997


Q ss_pred             CCcEEEEEeecch
Q 022938          166 EMKKLVFSEKDAV  178 (289)
Q Consensus       166 ~~~ri~lS~k~~~  178 (289)
                      +++++.||.+...
T Consensus       152 ~~~~i~LS~k~~~  164 (209)
T 2nn6_I          152 AQSNYLLTTAENE  164 (209)
T ss_dssp             TTTEEEEECCSSS
T ss_pred             CCCeEEEEEecCC
Confidence            7789999999853

>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=98.80  E-value=2e-08  Score=83.29  Aligned_cols=78  Identities=15%  Similarity=0.080  Sum_probs=57.0

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccc----hhcccccCCCCEEEEEEEEEecCCcE--EE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKS----IHEIAKGLTGSIISVKVIQANEEMKK--LV  171 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~----~~~~~~~~vG~~V~vkVl~vd~~~~r--i~  171 (289)
                      ..|++++|+|++++++|+||+++..+||+|.+++++.+. .+|...    ..+..-+.+||.|+|+|+++|.+.+.  .+
T Consensus        82 ~~Gev~~G~V~~v~~fG~FV~l~~~dglvhis~l~~~~~-~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~~~~i  160 (171)
T 1y14_B           82 FKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT-FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI  160 (171)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTCE-ECC-----CEECSSCEECTTCEEEEEEEEEEEETTEEEEE
T ss_pred             CCCCEEEEEEEEEecCEEEEEecCeEEEEEHHHCCCCce-ECcccCceEEeccceEECCCCEEEEEEEEEEcCCCCcEEE
Confidence            689999999999999999999988999999999986543 233211    00001144999999999999987642  22


Q ss_pred             EEeec
Q 022938          172 FSEKD  176 (289)
Q Consensus       172 lS~k~  176 (289)
                      .|+++
T Consensus       161 gsm~~  165 (171)
T 1y14_B          161 GSIKE  165 (171)
T ss_dssp             EECCS
T ss_pred             EEcCC
Confidence            35554

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

Probab=98.79  E-value=8.8e-09  Score=86.15  Aligned_cols=67  Identities=28%  Similarity=0.425  Sum_probs=59.0

Q ss_pred             cccccEEEe-----eeeeEEEEEecC--------CCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCe
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFP--------DGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR  252 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~--------~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~r  252 (289)
                      .+ |++|.|     .++|+||+|...        .+   ..|++|++++++.+..++.+.|++||.|+|+|++     ++
T Consensus        56 p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~---~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~-----~~  126 (179)
T 3m7n_A           56 VK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNR---GIGILHVSNVDEGYVKEISEAVGYLDILKARVIG-----DN  126 (179)
T ss_dssp             CT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTC---EEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE-----TT
T ss_pred             CC-CCEEEEEEEEEeCCcEEEEEccccCcccccccC---eeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC-----Ce
Confidence            46 999999     899999999720        03   8999999999999999999999999999999998     78


Q ss_pred             EEEEEecCC
Q 022938          253 ITLSIKQLE  261 (289)
Q Consensus       253 i~lSlK~~~  261 (289)
                      +.||+|..+
T Consensus       127 i~LS~k~~~  135 (179)
T 3m7n_A          127 LRLSTKEEE  135 (179)
T ss_dssp             TEEECCSTT
T ss_pred             EEEEEecCC
Confidence            999998853

>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=98.77  E-value=1.9e-08  Score=86.31  Aligned_cols=78  Identities=15%  Similarity=0.089  Sum_probs=59.3

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccc----hhcccccCCCCEEEEEEEEEecCCc---EE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKS----IHEIAKGLTGSIISVKVIQANEEMK---KL  170 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~----~~~~~~~~vG~~V~vkVl~vd~~~~---ri  170 (289)
                      +.|++++|+|++++++|+||+++..+||+|.++|++.+. -+|...    ..+..-+.+||.|+|+|+++|.+.+   ++
T Consensus        82 ~vGev~~G~V~~vt~fG~FVelg~~dGlVhiS~l~d~~~-~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~~i~~I  160 (215)
T 2b8k_G           82 FKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT-FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI  160 (215)
T ss_dssp             CTTEEEEEEEEEEETTEEEEECTTSEEEEEGGGSCSSCC-CBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETTEEEEE
T ss_pred             CCCCEEEEEEEEEecceEEEEecCcEEEEEHHHCCccce-eccccccceeeccccEECCCCEEEEEEEEEEcCCCccEEE
Confidence            699999999999999999999988999999999986543 333311    0000113499999999999998765   44


Q ss_pred             EEEeecc
Q 022938          171 VFSEKDA  177 (289)
Q Consensus       171 ~lS~k~~  177 (289)
                      - |++++
T Consensus       161 g-Smk~~  166 (215)
T 2b8k_G          161 G-SIKED  166 (215)
T ss_dssp             E-ECCST
T ss_pred             E-EcCCC
Confidence            4 77763

>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=98.77  E-value=3.1e-09  Score=97.38  Aligned_cols=151  Identities=14%  Similarity=0.115  Sum_probs=95.8

Q ss_pred             eEeecccccccCCcccccCCCeEEEEEEEEeCCCCeEeeeeecc---------------------cccCCcchhhhhhhh
Q 022938           26 LSLSLSSLVCVNPLIIERICQRNLCPVGKFSTNAAKITPTTVNP---------------------ILDDSSDANNRQSQS   84 (289)
Q Consensus        26 ~~~~l~~~~~~~p~~~~~vG~~v~~~Vl~~d~~~~~i~ls~k~~---------------------l~~~~~~~~~~~~~~   84 (289)
                      ++-.++++++....+.|...+.+.+.   +|++++.+.+-....                     ...++..+.+.++++
T Consensus        41 v~~aie~al~~a~kk~~~~~~~~~V~---id~~tg~~~v~~~~~~~d~~e~~~~~~~~~~fgRiaaqtaKQvI~QkiREa  117 (366)
T 1k0r_A           41 LLETIKSALLTAYRHTQGHQTDARIE---IDRKTGVVRVIARETDEAGNLISEWDDTPEGFGRIAATTARQVMLQRFRDA  117 (366)
T ss_dssp             TTTSSTTTTTSSGGGSSSCCSSCCCC---CCSSSCCCCCCEECCCSSSSCCCEECCCCTTSTTTTTTTTTHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHhcCCCCcEEEE---EECCCCeEEEEEEEEecCCCEEEEEeCCHHHhCHHHHHHHHHHHHHHHHHH
Confidence            34455666666666666544444443   366666544432211                     011122234445555


Q ss_pred             hhhhHHHHHHHhhcCCCEEEEEEEE----EEcCcEEEEECC----EEEEeecCCCCCCccCcCcccchhcccccCCCCEE
Q 022938           85 RSSADWKAARAYKESGFIYEGKIQG----FNGGGLLVRFFS----LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSII  156 (289)
Q Consensus        85 ~~~~~~~~l~~~~~~G~iv~g~V~~----v~~~G~~V~l~g----v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V  156 (289)
                      ++...|+++..  +.|++++|+|.+    +.+++++|++|+    ++|+||.+|+.       |.+.|+      +||+|
T Consensus       118 Er~~i~~ef~~--r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi-------P~E~~~------~GDrV  182 (366)
T 1k0r_A          118 ENERTYGEFST--REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV-------PGESYE------HGNRL  182 (366)
T ss_dssp             C--------CC--CTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC-------TTCCCC------TTCEE
T ss_pred             HHHHHHHHHHh--cCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC-------CCccCC------CCCEE
Confidence            55555555332  499999999999    999999999996    99999999976       445554      99999


Q ss_pred             EEEEEEEecCC--cEEEEEeecchhhhcccccccccEEEe
Q 022938          157 SVKVIQANEEM--KKLVFSEKDAVWNKYSSRVNVEDIFVG  194 (289)
Q Consensus       157 ~vkVl~vd~~~--~ri~lS~k~~~~~~~~~~~~~G~iv~G  194 (289)
                      +|.|++++.+.  .++.||+....+...+.++++-++.+|
T Consensus       183 kvyV~~V~~~~kgpqI~LSRT~p~lv~~Lfe~EVPEI~dG  222 (366)
T 1k0r_A          183 RCYVVGVTRGAREPLITLSRTHPNLVRKLFSLEVPEIADG  222 (366)
T ss_dssp             EEEEEEEECCSSSCEEEEESSCHHHHHHHHHHHCHHHHTT
T ss_pred             EEEEEEEecCCCccEEEEEeCChHHHHHHHHhcchhhcCC
Confidence            99999999864  489999998766655555555555444

>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=98.72  E-value=4.5e-10  Score=112.43  Aligned_cols=80  Identities=15%  Similarity=0.157  Sum_probs=37.7

Q ss_pred             HhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCC----CCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcE
Q 022938           95 AYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQM----SPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKK  169 (289)
Q Consensus        95 ~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sel----s~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~r  169 (289)
                      ..++.|++++|+|+++.++|+||++. |++||+|+|++    ++.++ .+|.+.++      +||.|+|+|+++|. +++
T Consensus       663 ~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s~~rv-~~~~~~~~------vGd~V~VkVi~vd~-~gr  734 (757)
T 1e3p_A          663 TSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRV-ENVEDVLG------VGQKVQVEIAEIDS-RGK  734 (757)
T ss_dssp             ----------CBEEECC-CSCEECCC---CCCCC--------------------CC------SSCBCCCCCCCCCS-SCC
T ss_pred             hhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccCCCcc-cCcccccC------CCCEEEEEEEEECC-CCC
Confidence            45789999999999999999999997 99999999999    88886 88888887      99999999999998 899


Q ss_pred             EEEEeec---chhhhc
Q 022938          170 LVFSEKD---AVWNKY  182 (289)
Q Consensus       170 i~lS~k~---~~~~~~  182 (289)
                      +.||++.   .||...
T Consensus       735 I~LS~k~~~~~pw~~~  750 (757)
T 1e3p_A          735 LSLIPVIEGEEAASDE  750 (757)
T ss_dssp             ----------------
T ss_pred             EEEEEecCCCCchhhh
Confidence            9999986   466544

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

Probab=98.69  E-value=1.3e-08  Score=84.60  Aligned_cols=77  Identities=16%  Similarity=0.212  Sum_probs=58.1

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCccc---chh-cccccCCCCEEEEEEEEEecCCc---EE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQK---SIH-EIAKGLTGSIISVKVIQANEEMK---KL  170 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~---~~~-~~~~~~vG~~V~vkVl~vd~~~~---ri  170 (289)
                      ..|++++|+|++++++|+||+++.++||+|.++|++.+. -++.+   .+. ....+.+||.|+|+|.++|.+.+   ++
T Consensus        83 ~~Gev~~G~V~~v~~fG~FV~l~~~~glVh~s~l~~~~~-~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~~~~~~~~I  161 (172)
T 3h0g_G           83 FRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMK-FDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDATEIFAI  161 (172)
T ss_dssp             CTTCEEECCCCEEETTEEECCBTTBCCEEEGGGSCTTCC-CBSSSSSCBEESSSCEECSSCCEEEEEEEEEESSSCEEEE
T ss_pred             CCCCEEEEEEEEEEcceEEEEeCCeEEEEEHHHCCCccc-cCcccccceEecCCcEECCCCEEEEEEEEEECCCCCceEE
Confidence            689999999999999999999998889999999986653 33310   000 01123499999999999998764   34


Q ss_pred             EEEeec
Q 022938          171 VFSEKD  176 (289)
Q Consensus       171 ~lS~k~  176 (289)
                      - |+++
T Consensus       162 g-tm~~  166 (172)
T 3h0g_G          162 A-TMKE  166 (172)
T ss_dssp             E-ECCS
T ss_pred             E-EcCC
Confidence            3 6654

>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=98.62  E-value=4.6e-08  Score=81.19  Aligned_cols=66  Identities=15%  Similarity=0.317  Sum_probs=52.6

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc----c--------CcccccCCCCEEEEEEEEEeCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----Q--------DIRDILNEGDEVRVKVIKIDRE  249 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~----~--------~~~~~~~iGd~V~vkV~~id~e  249 (289)
                      .+|+++.|     +++|+||+++  +    ..||+|+|+|++.+.    .        +....+++||.|+|+|+++|.+
T Consensus        80 ~~Gev~~G~V~~v~~fG~fV~l~--~----~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~  153 (172)
T 2c35_B           80 FKGEVVDAVVTQVNKVGLFTEIG--P----MSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVD  153 (172)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEET--T----EEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEE
T ss_pred             CCCCEEEEEEEEEeCCEEEEEEC--C----EEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcC
Confidence            58999999     9999999995  3    679999999975532    2        1145799999999999999987


Q ss_pred             CC---eEEEEEec
Q 022938          250 KS---RITLSIKQ  259 (289)
Q Consensus       250 ~~---ri~lSlK~  259 (289)
                      .+   ++. |||+
T Consensus       154 ~~~~~~ig-sm~~  165 (172)
T 2c35_B          154 KNDIFAIG-SLMD  165 (172)
T ss_dssp             TTEEEEEE-ECCS
T ss_pred             CCCcEEEE-EecC
Confidence            66   455 7765

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

Probab=98.61  E-value=7.8e-08  Score=80.34  Aligned_cols=69  Identities=19%  Similarity=0.262  Sum_probs=61.4

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-----------CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecC
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-----------SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEE  166 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-----------gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~  166 (289)
                      + |+++.|+|+++.++|+||+++           +.+|+||.+++++.+. .++.+.|+      +||.|.|+|++    
T Consensus        57 ~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~-~~~~~~~~------~GD~V~akVi~----  124 (179)
T 3m7n_A           57 K-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYV-KEISEAVG------YLDILKARVIG----  124 (179)
T ss_dssp             T-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCC-SSGGGTCC------TTCEEEEEEEE----
T ss_pred             C-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchh-hCHhhcCC------CCCEEEEEEEC----
Confidence            7 999999999999999999986           5899999999999876 67777776      99999999996    


Q ss_pred             CcEEEEEeecchh
Q 022938          167 MKKLVFSEKDAVW  179 (289)
Q Consensus       167 ~~ri~lS~k~~~~  179 (289)
                       +++.||.+...+
T Consensus       125 -~~i~LS~k~~~l  136 (179)
T 3m7n_A          125 -DNLRLSTKEEEM  136 (179)
T ss_dssp             -TTTEEECCSTTC
T ss_pred             -CeEEEEEecCCC
Confidence             789999987543

>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=98.61  E-value=3.7e-08  Score=84.55  Aligned_cols=76  Identities=18%  Similarity=0.174  Sum_probs=58.9

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc----------ccccCCCCEEEEEEEEEeCC
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI----------RDILNEGDEVRVKVIKIDRE  249 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~----------~~~~~iGd~V~vkV~~id~e  249 (289)
                      ..++|+++.|     +++|+||+++  +    .+||+|+|+|++.+.-++          ++.+++||.|+|+|+++|.+
T Consensus        80 ~p~vGev~~G~V~~vt~fG~FVelg--~----~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~  153 (215)
T 2b8k_G           80 KPFKGEVVDGTVVSCSQHGFEVQVG--P----MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQ  153 (215)
T ss_dssp             CCCTTEEEEEEEEEEETTEEEEECT--T----SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEE
T ss_pred             ccCCCCEEEEEEEEEecceEEEEec--C----cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcC
Confidence            3489999999     8999999995  2    799999999986533222          26699999999999999987


Q ss_pred             CC---eEEEEEecCCCCchhH
Q 022938          250 KS---RITLSIKQLEEDPLLE  267 (289)
Q Consensus       250 ~~---ri~lSlK~~~~~p~~~  267 (289)
                      .+   +|. |||+.-.-||..
T Consensus       154 ~~~i~~Ig-Smk~~~LG~~~~  173 (215)
T 2b8k_G          154 VSSIHAIG-SIKEDYLGAISH  173 (215)
T ss_dssp             TTEEEEEE-ECCSTTCEEC--
T ss_pred             CCccEEEE-EcCCCCCCCcch
Confidence            64   667 888765555553

>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=98.60  E-value=7.2e-08  Score=79.94  Aligned_cols=61  Identities=16%  Similarity=0.187  Sum_probs=49.5

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCc----------ccccCCCCEEEEEEEEEeCC
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI----------RDILNEGDEVRVKVIKIDRE  249 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~----------~~~~~iGd~V~vkV~~id~e  249 (289)
                      ...+|+++.|     +++|+||+++  +    .+||+|+|++++.+.-++          ++.+++||.|+++|+++|.+
T Consensus        80 ~~~~Gev~~G~V~~v~~fG~FV~l~--~----~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~  153 (171)
T 1y14_B           80 KPFKGEVVDGTVVSCSQHGFEVQVG--P----MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQ  153 (171)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEET--T----EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEE
T ss_pred             cCCCCCEEEEEEEEEecCEEEEEec--C----eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEEcC
Confidence            3469999999     9999999995  2    899999999976533111          26799999999999999987


Q ss_pred             CC
Q 022938          250 KS  251 (289)
Q Consensus       250 ~~  251 (289)
                      .+
T Consensus       154 ~~  155 (171)
T 1y14_B          154 VS  155 (171)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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=98.60  E-value=3.6e-08  Score=89.99  Aligned_cols=108  Identities=14%  Similarity=0.083  Sum_probs=78.0

Q ss_pred             ccCCCCEEEEEEEEEecCCcEEEEEeec--------chhhhcccccc--cccEEEe-----eeeeEEEEEecCCCceeEE
Q 022938          149 KGLTGSIISVKVIQANEEMKKLVFSEKD--------AVWNKYSSRVN--VEDIFVG-----RDYGAFIHLRFPDGLYHLT  213 (289)
Q Consensus       149 ~~~vG~~V~vkVl~vd~~~~ri~lS~k~--------~~~~~~~~~~~--~G~iv~G-----~~~G~fV~i~~~~G~~~i~  213 (289)
                      ++.+|+.+++.|...|.. +....+.|+        +..+..+++++  .|++++|     .++|+||+++   +   +.
T Consensus        86 ~~~vGd~ie~~I~~~dfg-R~aa~~aKqvi~qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~v~VDlG---k---~E  158 (344)
T 1hh2_P           86 LAEVGSIVKKELNVKNFG-RIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIG---K---LE  158 (344)
T ss_dssp             TCCTTCEEEEECCCCCSS-SCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEET---T---EE
T ss_pred             cccCCCEEEEEEccccCc-cHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCcEEEEeC---C---eE
Confidence            456999999999877642 222223232        23344566666  8999999     8889999994   3   99


Q ss_pred             EEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecCCCCchhHHh
Q 022938          214 GLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQLEEDPLLETL  269 (289)
Q Consensus       214 Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~~~~p~~~~~  269 (289)
                      |++|.++++      +.+.|++||.|+|.|++++++++...+++-...++....+.
T Consensus       159 giLp~sE~i------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p~~lk~Lf  208 (344)
T 1hh2_P          159 TRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVIGLM  208 (344)
T ss_dssp             EEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESSSHHHHHHHH
T ss_pred             EEEeHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEeeccHHHHHHH
Confidence            999999986      45789999999999999998766555555555555544443

>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=98.53  E-value=6.3e-08  Score=85.06  Aligned_cols=70  Identities=26%  Similarity=0.392  Sum_probs=61.9

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc---cCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI---QDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~---~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      ..++||+|.|     .++|+||+|+  .+   ..|++|++++++.+.   .++++.|++||.|.|+|++++. .+++.||
T Consensus        71 ~p~~GDiV~G~V~~v~~~ga~VdI~--~~---~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~-~~~i~LS  144 (251)
T 2je6_I           71 YPKINDIVIGLVEDVEIYGWVVDIK--AP---YKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVLS  144 (251)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS--SS---SCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEEE
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEcC--CC---eEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECC-CCcEEEE
Confidence            5699999999     8999999996  33   899999999998776   7888999999999999999997 4799999


Q ss_pred             EecC
Q 022938          257 IKQL  260 (289)
Q Consensus       257 lK~~  260 (289)
                      +|+.
T Consensus       145 ~r~~  148 (251)
T 2je6_I          145 VKGK  148 (251)
T ss_dssp             CCST
T ss_pred             Eccc
Confidence            9874

>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=98.51  E-value=5.6e-08  Score=84.52  Aligned_cols=84  Identities=21%  Similarity=0.256  Sum_probs=69.8

Q ss_pred             cCCCEEEEEEEE----EEcCcEEEEECC----EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCC--
Q 022938           98 ESGFIYEGKIQG----FNGGGLLVRFFS----LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEM--  167 (289)
Q Consensus        98 ~~G~iv~g~V~~----v~~~G~~V~l~g----v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~--  167 (289)
                      +.|++++|+|.+    +.+..++|++|.    .+|+||.+|+.       |.+.|+      +||+++|.|++++.+.  
T Consensus         6 r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqi-------p~E~~~------~GDrIkayV~~V~~~~~g   72 (251)
T 2asb_A            6 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV-------PGESYE------HGNRLRCYVVGVTRGARE   72 (251)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC-------TTCCCC------TTCEEEEEEEEEECCSSS
T ss_pred             cCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcC-------CCccCC------CCCEEEEEEEEEEcCCCC
Confidence            689999999999    899999999995    99999999975       445554      9999999999999764  


Q ss_pred             cEEEEEeecchhhhcccccccccEEEe
Q 022938          168 KKLVFSEKDAVWNKYSSRVNVEDIFVG  194 (289)
Q Consensus       168 ~ri~lS~k~~~~~~~~~~~~~G~iv~G  194 (289)
                      .++.||+....+.+.+.++++-++.+|
T Consensus        73 pqIiLSRt~p~lvk~Lfe~EVPEI~dG   99 (251)
T 2asb_A           73 PLITLSRTHPNLVRKLFSLEVPEIADG   99 (251)
T ss_dssp             CEEEEESSCHHHHHHHHHHHCHHHHTT
T ss_pred             CEEEEEeccHHHHHHHHHhcchHhhcC
Confidence            599999998777666666666665555

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

Probab=98.48  E-value=5.4e-08  Score=80.80  Aligned_cols=65  Identities=18%  Similarity=0.267  Sum_probs=52.4

Q ss_pred             ccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccccc----------CcccccCCCCEEEEEEEEEe
Q 022938          183 SSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----------DIRDILNEGDEVRVKVIKID  247 (289)
Q Consensus       183 ~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~----------~~~~~~~iGd~V~vkV~~id  247 (289)
                      .....+|++++|     +++|+||+++  +    ++||+|+++|++.+.-          +....+++||.|+++|+++|
T Consensus        79 vf~p~~Gev~~G~V~~v~~fG~FV~l~--~----~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd  152 (172)
T 3h0g_G           79 LWRPFRGEVVDAIVTTVNKMGFFANIG--P----LNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTR  152 (172)
T ss_dssp             EECCCTTCEEECCCCEEETTEEECCBT--T----BCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEE
T ss_pred             eeccCCCCEEEEEEEEEEcceEEEEeC--C----eEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEE
Confidence            335578999999     9999999995  3    6799999999765433          33568999999999999999


Q ss_pred             CCCCeE
Q 022938          248 REKSRI  253 (289)
Q Consensus       248 ~e~~ri  253 (289)
                      .+.+++
T Consensus       153 ~~~~~~  158 (172)
T 3h0g_G          153 TDATEI  158 (172)
T ss_dssp             ESSSCE
T ss_pred             CCCCCc
Confidence            877443

>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=98.46  E-value=2.8e-07  Score=79.95  Aligned_cols=70  Identities=26%  Similarity=0.376  Sum_probs=61.4

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcc-cccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~-~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      ..++||+|.|     .++|+||+|+  .   ...|++|+++++.. ...++++.|++||.|.|+|++++. .+++.||+|
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--S---PYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMK  127 (229)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECS--S---SSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECC
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC--C---CeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECC-CCcEEEEEc
Confidence            4699999999     8899999996  2   28899999999964 567889999999999999999997 579999998


Q ss_pred             cC
Q 022938          259 QL  260 (289)
Q Consensus       259 ~~  260 (289)
                      +.
T Consensus       128 ~~  129 (229)
T 2ba0_A          128 DR  129 (229)
T ss_dssp             SS
T ss_pred             cc
Confidence            75

>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=98.45  E-value=5.1e-07  Score=78.24  Aligned_cols=74  Identities=23%  Similarity=0.387  Sum_probs=62.5

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      .+.|+++.|+|+++.++|++|+++ ..+|++|.++++......+..+.++      +||.|.|+|++++. .+++.||.+
T Consensus        55 p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~~~~~~~~~~l~------~GD~V~arVi~v~~-~~~i~LS~r  127 (229)
T 2ba0_A           55 PSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLD------IGDAIIAKVLNIDP-KMKVTLTMK  127 (229)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCC------TTCEEEEEEEEECT-TCCEEEECC
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHccccccccchhcccC------CCCEEEEEEEEECC-CCcEEEEEc
Confidence            479999999999999999999999 7999999999985322245555665      99999999999986 468999987


Q ss_pred             cc
Q 022938          176 DA  177 (289)
Q Consensus       176 ~~  177 (289)
                      ..
T Consensus       128 ~~  129 (229)
T 2ba0_A          128 DR  129 (229)
T ss_dssp             SS
T ss_pred             cc
Confidence            64

>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=98.42  E-value=3.3e-07  Score=80.49  Aligned_cols=74  Identities=14%  Similarity=0.178  Sum_probs=62.0

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccC--cCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSC--KEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~--~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      .+.|+++.|+|+++.++|+||+++ +.+|+||.++++..+..  .++.+.|+      +||.|.|+|++++.+ +++.||
T Consensus        72 p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei~~~~~~~~~~~~~~l~------vGD~V~arVi~v~~~-~~i~LS  144 (251)
T 2je6_I           72 PKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLD------VGDYVIARIENFDRS-IDPVLS  144 (251)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCC------TTCEEEEEEEEEETT-EEEEEE
T ss_pred             CCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCccccccchhhcCC------CCCEEEEEEEEECCC-CcEEEE
Confidence            489999999999999999999999 79999999999865420  23344454      999999999999954 699999


Q ss_pred             eecc
Q 022938          174 EKDA  177 (289)
Q Consensus       174 ~k~~  177 (289)
                      .+..
T Consensus       145 ~r~~  148 (251)
T 2je6_I          145 VKGK  148 (251)
T ss_dssp             CCST
T ss_pred             Eccc
Confidence            9874

>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=98.40  E-value=1.8e-07  Score=81.46  Aligned_cols=70  Identities=17%  Similarity=0.354  Sum_probs=60.4

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcc----cccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQDIRDILNEGDEVRVKVIKIDREKSRITL  255 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~----~~~~~~~~~~iGd~V~vkV~~id~e~~ri~l  255 (289)
                      ..++||+|.|     .++|+||+|+  .+   ..|++|+++++..    +..++.+.|++||.|.|+|++++. .+++.|
T Consensus        63 ~p~~GDiV~G~V~~v~~~~~~V~I~--~~---~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~-~~~i~L  136 (235)
T 2z0s_A           63 VPQAGDVVIGLIQSVGIMNWFVDIN--SP---YVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPLL  136 (235)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECS--SS---SCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEEE
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeC--CC---eEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECC-CCcEEE
Confidence            5699999999     8899999996  33   8999999999863    356788899999999999999997 468999


Q ss_pred             EEecC
Q 022938          256 SIKQL  260 (289)
Q Consensus       256 SlK~~  260 (289)
                      |+|+.
T Consensus       137 S~k~~  141 (235)
T 2z0s_A          137 TVQGE  141 (235)
T ss_dssp             ECCSS
T ss_pred             EEecc
Confidence            99874

>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=98.39  E-value=3.2e-07  Score=79.91  Aligned_cols=74  Identities=16%  Similarity=0.206  Sum_probs=61.5

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCcc---CcCcccchhcccccCCCCEEEEEEEEEecCCcEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHS---CKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVF  172 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~---~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~l  172 (289)
                      .+.|+++.|+|+++.++|+||+++ +.+|++|.++++..+.   ..++.+.|+      +||.|.++|++++.+ +++.|
T Consensus        64 p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~~~~~~~~~~~~~l~------~GD~V~a~Vi~v~~~-~~i~L  136 (235)
T 2z0s_A           64 PQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLK------VGDYIKAKVVAFDKT-RSPLL  136 (235)
T ss_dssp             CCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSC------TTCEEEEEEEEECTT-SCEEE
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCccccchhhHhhcCC------CCCEEEEEEEEECCC-CcEEE
Confidence            489999999999999999999999 7999999999976321   134455555      999999999999854 58999


Q ss_pred             Eeecc
Q 022938          173 SEKDA  177 (289)
Q Consensus       173 S~k~~  177 (289)
                      |.+..
T Consensus       137 S~k~~  141 (235)
T 2z0s_A          137 TVQGE  141 (235)
T ss_dssp             ECCSS
T ss_pred             EEecc
Confidence            98753

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

Probab=98.37  E-value=8.5e-07  Score=67.05  Aligned_cols=83  Identities=29%  Similarity=0.425  Sum_probs=56.8

Q ss_pred             cCCCEEEEEEEEEE---cCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEE
Q 022938           98 ESGFIYEGKIQGFN---GGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVF  172 (289)
Q Consensus        98 ~~G~iv~g~V~~v~---~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~l  172 (289)
                      +.++..+|+|+..+   .+| |+.-+  |.+.|+|++++.+...   +.+.      ..+|+.|++.|..+         
T Consensus        12 ~~~~~~~G~Vk~fn~~kGfG-FI~~~~gg~dvfvH~s~l~~~~~---~~~~------l~~Ge~V~g~V~~i---------   72 (101)
T 2bh8_A           12 LQSGKMTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAGSSGAA---VRGN------PQQGDRVEGKIKSI---------   72 (101)
T ss_dssp             ----CEEEEEEEEEGGGTEE-EEEESSSSCEEEEECCCSCSSSC---CCCC------CCTTCEEEEEEEEC---------
T ss_pred             cccccceeEEEEEECCCCCE-EEEeCCCCcEEEEEEEEEecCCc---cccC------CCCCCEEEEEEEEe---------
Confidence            46778899999986   467 66654  6999999999976421   0011      12566666655433         


Q ss_pred             EeecchhhhcccccccccEEEeeeeeEEEEEecCCCceeEEEEEEccCcCcccc
Q 022938          173 SEKDAVWNKYSSRVNVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI  226 (289)
Q Consensus       173 S~k~~~~~~~~~~~~~G~iv~G~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~  226 (289)
                                            .++|+||+|.  +|   ++||+|+|+++|.++
T Consensus        73 ----------------------~~fG~fv~l~--~~---~eGlvhis~i~~~~~   99 (101)
T 2bh8_A           73 ----------------------TDFGIFIGLD--GG---IDGLVHLSDISWAQA   99 (101)
T ss_dssp             ----------------------CSEEEEECTT--SC---EEEEEEEEEEEECCC
T ss_pred             ----------------------CCcEEEEEcC--CC---ceEEEEHHHCccCcC
Confidence                                  6799999995  44   999999999998764

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

Probab=98.25  E-value=3.7e-06  Score=83.32  Aligned_cols=81  Identities=15%  Similarity=0.300  Sum_probs=60.3

Q ss_pred             HhhcCCC--EEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCC--CccCcCcc-cch--hcccccCCCCEEEEEEEEEec
Q 022938           95 AYKESGF--IYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSP--SHSCKEPQ-KSI--HEIAKGLTGSIISVKVIQANE  165 (289)
Q Consensus        95 ~~~~~G~--iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~--~~~~~~p~-~~~--~~~~~~~vG~~V~vkVl~vd~  165 (289)
                      -..+.|+  +++|+|++++++|+||++.  |++|+||.+++++  .+..-+.. ..+  +....+.+||.|+|+|.++|.
T Consensus       554 l~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~vd~  633 (644)
T 2id0_A          554 LKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRM  633 (644)
T ss_dssp             HGGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEET
T ss_pred             hhhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEEEEEeC
Confidence            3457899  9999999999999999993  8999999999973  22101100 000  001124499999999999999


Q ss_pred             CCcEEEEEee
Q 022938          166 EMKKLVFSEK  175 (289)
Q Consensus       166 ~~~ri~lS~k  175 (289)
                      ++++|.+++.
T Consensus       634 ~~~~I~~~l~  643 (644)
T 2id0_A          634 ETRSIIARPV  643 (644)
T ss_dssp             TTTEEEEEEC
T ss_pred             CCCEEEEEEc
Confidence            9999999863

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

Probab=98.04  E-value=1.4e-05  Score=67.99  Aligned_cols=70  Identities=13%  Similarity=0.012  Sum_probs=52.5

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccc--h----------hcccccCCCCEEEEEEEEEec
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKS--I----------HEIAKGLTGSIISVKVIQANE  165 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~--~----------~~~~~~~vG~~V~vkVl~vd~  165 (289)
                      ..|+++.|+|++++++|+||+++.++|+++.+++.+.+..-++...  +          .....+.+|+.|+|||.+++.
T Consensus        80 ~~GEv~~G~Vs~vt~~GifV~lg~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~  159 (203)
T 3ayh_B           80 FRGEVMLGKIKSCSEEGIRVTISFFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQIESEDF  159 (203)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEEEEEEE
T ss_pred             CCCCEEEEEEEEEeccEEEEEEeCceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEEEEEEc
Confidence            6899999999999999999999888999999999765431111110  0          011235599999999999986


Q ss_pred             CC
Q 022938          166 EM  167 (289)
Q Consensus       166 ~~  167 (289)
                      ..
T Consensus       160 ~~  161 (203)
T 3ayh_B          160 VD  161 (203)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

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

Probab=97.96  E-value=1.2e-05  Score=79.65  Aligned_cols=69  Identities=13%  Similarity=0.143  Sum_probs=56.0

Q ss_pred             cccccc--EEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCc--cc--cc--------CcccccCCCCEEEEEEEE
Q 022938          185 RVNVED--IFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSW--DL--IQ--------DIRDILNEGDEVRVKVIK  245 (289)
Q Consensus       185 ~~~~G~--iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~--~~--~~--------~~~~~~~iGd~V~vkV~~  245 (289)
                      .-++|+  ++.|     +++|+||+|. ..|   ++|+||++++++  ++  ..        +....|++||.|+|+|.+
T Consensus       555 ~~~vGe~~~f~g~V~~V~~~G~fV~L~-~~g---ieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~  630 (644)
T 2id0_A          555 KDKAGTDTRFAAEIVDISRGGMRVRLV-DNG---AIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAE  630 (644)
T ss_dssp             GGGTTSCCCEEEEEEEEETTEEEEEET-TTC---CEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEE
T ss_pred             hhccCCCceEEEEEEEEeCCceEEEEc-CCc---EEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEEEE
Confidence            447788  8888     8999999994 134   999999999973  22  11        345679999999999999


Q ss_pred             EeCCCCeEEEEE
Q 022938          246 IDREKSRITLSI  257 (289)
Q Consensus       246 id~e~~ri~lSl  257 (289)
                      +|+++++|.+++
T Consensus       631 vd~~~~~I~~~l  642 (644)
T 2id0_A          631 VRMETRSIIARP  642 (644)
T ss_dssp             EETTTTEEEEEE
T ss_pred             EeCCCCEEEEEE
Confidence            999999999986

>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=97.89  E-value=2e-05  Score=75.56  Aligned_cols=72  Identities=18%  Similarity=0.284  Sum_probs=56.8

Q ss_pred             cCCCEEEEEEEEEEcC--cEEEEEC-CEEEEeecCCCCCCccC--------cCcccchhcccccCCCCEEEEEEEEEecC
Q 022938           98 ESGFIYEGKIQGFNGG--GLLVRFF-SLVGFLPFPQMSPSHSC--------KEPQKSIHEIAKGLTGSIISVKVIQANEE  166 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~--G~~V~l~-gv~g~ip~sels~~~~~--------~~p~~~~~~~~~~~vG~~V~vkVl~vd~~  166 (289)
                      ..|.++.|+|+++.++  |+||+++ |..||+|.+++++.+..        .+..+.++      +||.|.|+|.+....
T Consensus        44 ~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk------~Gq~VlVQV~Ke~~g  117 (517)
T 2bx2_L           44 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLR------EGQEVIVQIDKEERG  117 (517)
T ss_dssp             CTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC-------CCCGGGTCC------TTCEEEEEEEECCCT
T ss_pred             CCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcChhhhccccccccccchhhhcc------CCCEEEEEEEeeccc
Confidence            6899999999999999  9999999 99999999999866531        11223343      999999999987766


Q ss_pred             CcEEEEEee
Q 022938          167 MKKLVFSEK  175 (289)
Q Consensus       167 ~~ri~lS~k  175 (289)
                      ++...||..
T Consensus       118 ~KGa~lTt~  126 (517)
T 2bx2_L          118 NKGAALTTF  126 (517)
T ss_dssp             TCCCEEESS
T ss_pred             cCCceEEee
Confidence            555555543

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

Probab=97.88  E-value=3e-05  Score=66.53  Aligned_cols=71  Identities=15%  Similarity=0.022  Sum_probs=53.1

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccc--hh-----cccccCCCCEEEEEEEEEecCCc
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKS--IH-----EIAKGLTGSIISVKVIQANEEMK  168 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~--~~-----~~~~~~vG~~V~vkVl~vd~~~~  168 (289)
                      ..|+++.|+|++++++|+||++. .++|+++.+++.+.+..-++...  +-     ....+.+|+.|+|||.++|...+
T Consensus        80 ~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~~~~  158 (218)
T 2ckz_B           80 FLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVDV  158 (218)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEECCC
T ss_pred             CCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEcccC
Confidence            68999999999999999999994 68999999999665431122110  00     11235699999999999997654

>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=97.81  E-value=3.3e-05  Score=70.70  Aligned_cols=85  Identities=9%  Similarity=0.159  Sum_probs=61.0

Q ss_pred             hhhcccccc--cccEEEe--e-------eeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEe
Q 022938          179 WNKYSSRVN--VEDIFVG--R-------DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKID  247 (289)
Q Consensus       179 ~~~~~~~~~--~G~iv~G--~-------~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id  247 (289)
                      .+..+++++  +|++++|  .       +.++||+++  .|..++.|++|.+++.      |.+.|++||.|+|.|.+++
T Consensus       119 r~~i~~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG--~~~~k~EgiLP~~Eqi------P~E~~~~GDrVkvyV~~V~  190 (366)
T 1k0r_A          119 NERTYGEFSTREGEIVAGVIQRDSRANARGLVVVRIG--TETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVT  190 (366)
T ss_dssp             --------CCCTTCEEEEEEECCHHHHHTTCEEEEEC--CSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEE
T ss_pred             HHHHHHHHHhcCCCEEEEEEEEccccccCCeEEEEeC--CCccceEEEEcHHHcC------CCccCCCCCEEEEEEEEEe
Confidence            445566776  9999999  2       258999996  2101299999999986      4588999999999999999


Q ss_pred             CCCCeEEEEEecCCCCchhHHhhh
Q 022938          248 REKSRITLSIKQLEEDPLLETLEK  271 (289)
Q Consensus       248 ~e~~ri~lSlK~~~~~p~~~~~~~  271 (289)
                      .+.+...+.+....|++...+.+.
T Consensus       191 ~~~kgpqI~LSRT~p~lv~~Lfe~  214 (366)
T 1k0r_A          191 RGAREPLITLSRTHPNLVRKLFSL  214 (366)
T ss_dssp             CCSSSCEEEEESSCHHHHHHHHHH
T ss_pred             cCCCccEEEEEeCChHHHHHHHHh
Confidence            987777777777777777666654

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

Probab=97.79  E-value=2.9e-05  Score=65.96  Aligned_cols=58  Identities=10%  Similarity=0.181  Sum_probs=47.9

Q ss_pred             cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-------------------cCcccccCCCCEEEE
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-------------------QDIRDILNEGDEVRV  241 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-------------------~~~~~~~~iGd~V~v  241 (289)
                      -.+|+++.|     +++|+||+++  .    ++|++|.+++.+++.                   ++....|++||.|++
T Consensus        79 p~~GEv~~G~Vs~vt~~GifV~lg--~----~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~Vrv  152 (203)
T 3ayh_B           79 PFRGEVMLGKIKSCSEEGIRVTIS--F----FDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRF  152 (203)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS--S----CCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEE
T ss_pred             cCCCCEEEEEEEEEeccEEEEEEe--C----ceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEE
Confidence            377888888     9999999995  2    789999999976643                   445567999999999


Q ss_pred             EEEEEeCC
Q 022938          242 KVIKIDRE  249 (289)
Q Consensus       242 kV~~id~e  249 (289)
                      ||.+++..
T Consensus       153 rV~~v~~~  160 (203)
T 3ayh_B          153 QIESEDFV  160 (203)
T ss_dssp             EEEEEEEC
T ss_pred             EEEEEEcc
Confidence            99999863

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

Probab=97.75  E-value=4e-05  Score=77.22  Aligned_cols=70  Identities=13%  Similarity=0.156  Sum_probs=49.4

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCC--CCccC----------cC----cccchhcccccCCCCEEEEEEE
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMS--PSHSC----------KE----PQKSIHEIAKGLTGSIISVKVI  161 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels--~~~~~----------~~----p~~~~~~~~~~~vG~~V~vkVl  161 (289)
                      .++++|+|+++.++|+||.+.  |++|+||.++++  ..++.          .+    +...      +.+||.|+|+|.
T Consensus       670 ~~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~------~~lGD~V~VkV~  743 (760)
T 2vnu_D          670 ESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRD------VYVFDKVEVQVR  743 (760)
T ss_dssp             CSEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEE------EETTCEEEEEEC
T ss_pred             ceEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcE------EecCCEEEEEEE
Confidence            389999999999999999997  899999999995  32210          11    1233      449999999999


Q ss_pred             EEecC---CcEEEEEee
Q 022938          162 QANEE---MKKLVFSEK  175 (289)
Q Consensus       162 ~vd~~---~~ri~lS~k  175 (289)
                      .+|.+   +++|.+|+|
T Consensus       744 ~vd~~~~~~~kI~lslk  760 (760)
T 2vnu_D          744 SVMDPITSKRKAELLLK  760 (760)
T ss_dssp             --------CCEEEC---
T ss_pred             EEECccccCCcEEEEeC
Confidence            99987   589999875

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

Probab=97.68  E-value=5.9e-05  Score=77.76  Aligned_cols=70  Identities=13%  Similarity=0.156  Sum_probs=56.0

Q ss_pred             CCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCC--CCccC----------cC----cccchhcccccCCCCEEEEEEE
Q 022938          100 GFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMS--PSHSC----------KE----PQKSIHEIAKGLTGSIISVKVI  161 (289)
Q Consensus       100 G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels--~~~~~----------~~----p~~~~~~~~~~~vG~~V~vkVl  161 (289)
                      |++++|+|+++.++|+||.+.  |++|+||.++++  +.+..          .+    +...      +.+||+|+|+|.
T Consensus       887 ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~------~~lGD~V~VkV~  960 (977)
T 2wp8_J          887 ESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRD------VYVFDKVEVQVR  960 (977)
T ss_dssp             TCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEE------EETTCEEEEEEC
T ss_pred             ceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcE------EccCCEEEEEEE
Confidence            999999999999999999997  899999999996  33210          11    1233      449999999999


Q ss_pred             EEecC---CcEEEEEee
Q 022938          162 QANEE---MKKLVFSEK  175 (289)
Q Consensus       162 ~vd~~---~~ri~lS~k  175 (289)
                      .+|.+   ++||.||+|
T Consensus       961 ~vd~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          961 SVMDPITSKRKAELLLK  977 (977)
T ss_dssp             CCCCSSSCCCCCCEEEC
T ss_pred             EEcCcccCCCceEEEeC
Confidence            99863   378999886

>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=97.52  E-value=8.7e-05  Score=71.16  Aligned_cols=74  Identities=23%  Similarity=0.380  Sum_probs=59.7

Q ss_pred             cccccccccEEEe-----eee--eEEEEEecCCCceeEEEEEEccCcCcccc---------cCcccccCCCCEEEEEEEE
Q 022938          182 YSSRVNVEDIFVG-----RDY--GAFIHLRFPDGLYHLTGLVHVSEVSWDLI---------QDIRDILNEGDEVRVKVIK  245 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~--G~fV~i~~~~G~~~i~Glv~~sels~~~~---------~~~~~~~~iGd~V~vkV~~  245 (289)
                      ......+|.+|.|     .++  |+||+++  +|   ..||+|++++++.+.         .++.+.+++||.|.|.|.+
T Consensus        39 ~~~~~~vGnIY~GkV~rv~p~~~aAFVdiG--~g---k~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~K  113 (517)
T 2bx2_L           39 PGHEQKKANIYKGKITRIEPSLEAAFVDYG--AE---RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDK  113 (517)
T ss_dssp             SSSCCCTTCEEEEEEEEEETTTTEEEEESS--SS---SCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEE
T ss_pred             CCCcCCCCCEEEEEEEEeccCCceEEEEeC--CC---cEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEe
Confidence            3345689999999     677  9999997  55   889999999987763         3466789999999999999


Q ss_pred             EeCCCCeEEEEEecC
Q 022938          246 IDREKSRITLSIKQL  260 (289)
Q Consensus       246 id~e~~ri~lSlK~~  260 (289)
                      ....++.-.||..-+
T Consensus       114 e~~g~KGa~lTt~is  128 (517)
T 2bx2_L          114 EERGNKGAALTTFIS  128 (517)
T ss_dssp             CCCTTCCCEEESSCC
T ss_pred             eccccCCceEEeeEE
Confidence            987777777776544

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

Probab=97.49  E-value=0.00011  Score=63.06  Aligned_cols=62  Identities=10%  Similarity=0.184  Sum_probs=48.2

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc--------------cCcccccCCCCEEEEEEEE
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI--------------QDIRDILNEGDEVRVKVIK  245 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~--------------~~~~~~~~iGd~V~vkV~~  245 (289)
                      .-.+|+++.|     +++|+||++.   |  .++|++|.+++..++.              ++....|++||.|++||.+
T Consensus        78 ~p~vGEv~~G~Is~Vt~fGifVeL~---g--~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~  152 (218)
T 2ckz_B           78 KPFLGEIVTGWISKCTAEGIKVSLL---G--IFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIER  152 (218)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECT---T--SCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEE
T ss_pred             cCCCCCEEEEEEEEEccCcEEEEcc---C--ccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEE
Confidence            3467888888     9999999993   2  2789999999976542              3345669999999999999


Q ss_pred             EeCCCC
Q 022938          246 IDREKS  251 (289)
Q Consensus       246 id~e~~  251 (289)
                      +|.+.+
T Consensus       153 v~~~~~  158 (218)
T 2ckz_B          153 EVFVDV  158 (218)
T ss_dssp             EEECCC
T ss_pred             EEcccC
Confidence            997553

>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=97.43  E-value=6.6e-05  Score=67.58  Aligned_cols=69  Identities=20%  Similarity=0.255  Sum_probs=54.8

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcc----cc------cCcccccCCCCEEEEEEEEEeCC
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LI------QDIRDILNEGDEVRVKVIKIDRE  249 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~----~~------~~~~~~~~iGd~V~vkV~~id~e  249 (289)
                      ..++|++|.|     .++|+||+|+.+     ..|++|++++++.    +.      .+.++.|++||.|.|+|++++. 
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 IGEVGDIVVGRITEVQQKRWKVETNSR-----LDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-  165 (308)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECSSS-----SCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEECCC-----cCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCC-
Confidence            5689999888     899999999622     5789999998652    22      2355789999999999999995 


Q ss_pred             CCeEEEEEec
Q 022938          250 KSRITLSIKQ  259 (289)
Q Consensus       250 ~~ri~lSlK~  259 (289)
                      ...+.||+|+
T Consensus       166 ~~~i~LStr~  175 (308)
T 2nn6_H          166 DGAVSLHTRS  175 (308)
T ss_dssp             TTEEEEECCS
T ss_pred             CCCEEEEecC
Confidence            6789999985

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

Probab=97.43  E-value=4.3e-05  Score=57.55  Aligned_cols=87  Identities=21%  Similarity=0.156  Sum_probs=53.1

Q ss_pred             ccCCCeEEEEEEEEeCCCCeEeeeeecccccCCcchhhhhhhhhhhhHHHHH-HHhhcCCCEEEEEEEEEEcCcEEEEEC
Q 022938           42 ERICQRNLCPVGKFSTNAAKITPTTVNPILDDSSDANNRQSQSRSSADWKAA-RAYKESGFIYEGKIQGFNGGGLLVRFF  120 (289)
Q Consensus        42 ~~vG~~v~~~Vl~~d~~~~~i~ls~k~~l~~~~~~~~~~~~~~~~~~~~~~l-~~~~~~G~iv~g~V~~v~~~G~~V~l~  120 (289)
                      -..++....+|..++..++-=-++..    +...+++-.+....    |+.+ ...++.|++++++|+.+.++|+||++.
T Consensus        11 ~~~~~~~~G~Vk~fn~~kGfGFI~~~----~gg~dvfvH~s~l~----~~~~~~~~l~~Ge~V~g~V~~i~~fG~fv~l~   82 (101)
T 2bh8_A           11 RLQSGKMTGIVKWFNADKGFGFITPD----DGSKDVFVHFSAGS----SGAAVRGNPQQGDRVEGKIKSITDFGIFIGLD   82 (101)
T ss_dssp             -----CEEEEEEEEEGGGTEEEEEES----SSSCEEEEECCCSC----SSSCCCCCCCTTCEEEEEEEECCSEEEEECTT
T ss_pred             ccccccceeEEEEEECCCCCEEEEeC----CCCcEEEEEEEEEe----cCCccccCCCCCCEEEEEEEEeCCcEEEEEcC
Confidence            44677788889888877663222211    00111111111110    0000 123689999999999999999999997


Q ss_pred             -CEEEEeecCCCCCCcc
Q 022938          121 -SLVGFLPFPQMSPSHS  136 (289)
Q Consensus       121 -gv~g~ip~sels~~~~  136 (289)
                       +++|++|+++++|.+.
T Consensus        83 ~~~eGlvhis~i~~~~~   99 (101)
T 2bh8_A           83 GGIDGLVHLSDISWAQA   99 (101)
T ss_dssp             SCEEEEEEEEEEEECCC
T ss_pred             CCceEEEEHHHCccCcC
Confidence             9999999999998653

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

Probab=97.43  E-value=8.1e-05  Score=75.01  Aligned_cols=65  Identities=18%  Similarity=0.198  Sum_probs=44.9

Q ss_pred             cEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcC--cccc-----------cC----cccccCCCCEEEEEEEEEe
Q 022938          190 DIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVS--WDLI-----------QD----IRDILNEGDEVRVKVIKID  247 (289)
Q Consensus       190 ~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels--~~~~-----------~~----~~~~~~iGd~V~vkV~~id  247 (289)
                      +++.|     +++|+||.|. ..|   ++|+||+++++  .++.           .+    ....|++||.|+|+|..+|
T Consensus       671 ~~~~g~V~~V~~~G~fV~l~-~~g---iEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV~~vd  746 (760)
T 2vnu_D          671 STETGYVIKVFNNGIVVLVP-KFG---VEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVM  746 (760)
T ss_dssp             SEEEEEEEEEETTEEEEEET-TTT---EEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC---
T ss_pred             eEEEEEEEEEECCeEEEEEe-CCC---cEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCCEEEEEEEEEE
Confidence            46666     9999999995 125   99999999996  3321           12    2578999999999999999


Q ss_pred             CC---CCeEEEEEe
Q 022938          248 RE---KSRITLSIK  258 (289)
Q Consensus       248 ~e---~~ri~lSlK  258 (289)
                      .+   ++||.||+|
T Consensus       747 ~~~~~~~kI~lslk  760 (760)
T 2vnu_D          747 DPITSKRKAELLLK  760 (760)
T ss_dssp             -----CCEEEC---
T ss_pred             CccccCCcEEEEeC
Confidence            87   699999987

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

Probab=97.34  E-value=0.00012  Score=75.46  Aligned_cols=66  Identities=20%  Similarity=0.213  Sum_probs=52.8

Q ss_pred             ccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcC--cccc-----------cC----cccccCCCCEEEEEEEEE
Q 022938          189 EDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVS--WDLI-----------QD----IRDILNEGDEVRVKVIKI  246 (289)
Q Consensus       189 G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels--~~~~-----------~~----~~~~~~iGd~V~vkV~~i  246 (289)
                      |+++.|     +++|+||.|. ..|   ++|+||+++++  .++.           .+    ....|++||.|+|+|..+
T Consensus       887 ge~~~g~V~~V~~~G~fV~L~-~~g---iEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~VkV~~v  962 (977)
T 2wp8_J          887 ESTETGYVIKVFNNGIVVLVP-KFG---VEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSV  962 (977)
T ss_dssp             TCEEEEEEEEECSSEEEEECT-TTC---CEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEEECCC
T ss_pred             ceEEEEEEEEEcCCeEEEEEc-CCC---eEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCCEEEEEEEEE
Confidence            778887     8999999994 125   99999999997  3321           12    347899999999999999


Q ss_pred             eCC---CCeEEEEEe
Q 022938          247 DRE---KSRITLSIK  258 (289)
Q Consensus       247 d~e---~~ri~lSlK  258 (289)
                      |.+   ++||.||+|
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   389999987

>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=97.34  E-value=0.00028  Score=58.37  Aligned_cols=65  Identities=15%  Similarity=0.155  Sum_probs=53.6

Q ss_pred             cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      .++||+|.|     ...+++|+|+.. .   ..|++|.+++. ...+..+..|++||.|.|+|.+++. ...+.||
T Consensus         5 P~~gDvViG~V~~v~~~~~~VdI~~~-~---~~a~L~~s~~~-g~~k~~r~~l~~GDlV~ArV~~~~~-~~~~~Lt   74 (175)
T 2ja9_A            5 PSVNDFVIGVIIGTFSDSYKVSLQNF-S---SSVSLSYMAFP-NASKKNRPTLQVGDLVYARVCTAEK-ELEAEIE   74 (175)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEESSTT-S---CCEEEETTSST-TCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEE
T ss_pred             CCCcCEEEEEEEEEECcEEEEEECCC-C---ccEEEEHHHCC-chhhhhhccCCCCCEEEEEEEEecC-CCceEEE
Confidence            368899988     789999999730 2   78999999886 3346677889999999999999997 5678999

>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=97.33  E-value=0.00086  Score=55.39  Aligned_cols=68  Identities=15%  Similarity=0.154  Sum_probs=54.9

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECC--EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFS--LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~g--v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      +.|+++.|.|+.+...+++|+++.  ..|++|.+++....  ++....++      +||.|.++|.+++.. ..+.||.
T Consensus         6 ~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~g~~--k~~r~~l~------~GDlV~ArV~~~~~~-~~~~Ltc   75 (175)
T 2ja9_A            6 SVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNAS--KKNRPTLQ------VGDLVYARVCTAEKE-LEAEIEC   75 (175)
T ss_dssp             CTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCC--SSSCCCCC------TTCEEEEEEEECCTT-SCCEEES
T ss_pred             CCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCCchh--hhhhccCC------CCCEEEEEEEEecCC-CceEEEe
Confidence            689999999999999999999997  89999999886322  33334444      999999999999753 4677774

>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=97.31  E-value=0.00027  Score=63.53  Aligned_cols=80  Identities=16%  Similarity=0.112  Sum_probs=57.0

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCC-cc--CcCcccchhcccccCCCCEEEEEEEEEecCCcEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPS-HS--CKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVF  172 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~-~~--~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~l  172 (289)
                      .+.|++|.|+|+++..++++|+++ ...+++|.+++++. ..  ..+..+...-...+.+||.|.++|++++. .+.+.|
T Consensus        93 P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~-~~~i~L  171 (308)
T 2nn6_H           93 GEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-DGAVSL  171 (308)
T ss_dssp             CCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-TTEEEE
T ss_pred             CCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCC-CCCEEE
Confidence            479999999999999999999999 68899999998753 11  01110000000124599999999999984 568999


Q ss_pred             Eeecc
Q 022938          173 SEKDA  177 (289)
Q Consensus       173 S~k~~  177 (289)
                      |.+..
T Consensus       172 Str~~  176 (308)
T 2nn6_H          172 HTRSL  176 (308)
T ss_dssp             ECCSS
T ss_pred             EecCc
Confidence            98864

>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=96.95  E-value=0.003  Score=54.79  Aligned_cols=65  Identities=18%  Similarity=0.254  Sum_probs=50.5

Q ss_pred             ccccEEEe--ee-------eeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEE
Q 022938          187 NVEDIFVG--RD-------YGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREK--SRITL  255 (289)
Q Consensus       187 ~~G~iv~G--~~-------~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~--~ri~l  255 (289)
                      ++|++++|  ..       ..+||+++  .+..+.+|++|.+++.      |.+.|++||.|+|.|.+++.+.  ..|.|
T Consensus         6 r~GeIVtG~V~r~~~~v~~~~ViVdlG--~~~~k~EgiLP~~Eqi------p~E~~~~GDrIkayV~~V~~~~~gpqIiL   77 (251)
T 2asb_A            6 REGEIVAGVIQRDSRANARGLVVVRIG--TETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITL   77 (251)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEEC--SSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEE
T ss_pred             cCCCEEEEEEEEccccccCCeEEEEeC--CCCcceEEEEcHHHcC------CCccCCCCCEEEEEEEEEEcCCCCCEEEE
Confidence            57888888  22       36899996  2001289999999986      4688999999999999999764  67889


Q ss_pred             EEec
Q 022938          256 SIKQ  259 (289)
Q Consensus       256 SlK~  259 (289)
                      |...
T Consensus        78 SRt~   81 (251)
T 2asb_A           78 SRTH   81 (251)
T ss_dssp             ESSC
T ss_pred             Eecc
Confidence            8765

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

Probab=95.41  E-value=0.014  Score=51.96  Aligned_cols=66  Identities=8%  Similarity=-0.028  Sum_probs=53.3

Q ss_pred             ccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          185 RVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       185 ~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      -.++||+|.|     ....+.|+|..     ...|++|.+++. +..+..+..|++||.|.|+|++++. .....||+
T Consensus       124 iP~vGDiVIG~Vt~v~~~~~~VdI~s-----~~~a~L~~~~f~-Gatk~~r~~f~~GDlV~ArV~s~~~-~~~~eLsc  194 (289)
T 2nn6_G          124 VPVKGDHVIGIVTAKSGDIFKVDVGG-----SEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVC  194 (289)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECSS-----SSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCT-TSCCEEEC
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEECC-----CceeEEehhhcC-cchhhhhhhcCCCCEEEEEEEEcCC-CCceEEEe
Confidence            3489999999     67788999963     267999998876 3346677889999999999999986 55788888

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

Probab=95.17  E-value=0.045  Score=48.61  Aligned_cols=68  Identities=16%  Similarity=0.097  Sum_probs=54.0

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      ++|++|-|+|+++....+.|+++ -..|+||.+++.-..  ++..+.|      .+||.|.++|.+++. .....||.
T Consensus       126 ~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~Gat--k~~r~~f------~~GDlV~ArV~s~~~-~~~~eLsc  194 (289)
T 2nn6_G          126 VKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGAT--KRNRPNV------QVGDLIYGQFVVANK-DMEPEMVC  194 (289)
T ss_dssp             CSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCS--SCSSSSS------CTTCEEEEEEEECCT-TSCCEEEC
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcCcch--hhhhhhc------CCCCEEEEEEEEcCC-CCceEEEe
Confidence            79999999999999999999999 688999999876221  3333344      499999999999874 34566776

>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=94.70  E-value=0.13  Score=43.54  Aligned_cols=70  Identities=7%  Similarity=-0.032  Sum_probs=49.1

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEE-CCEEEEeecCCCCCCccCcCccc------chhcccccCCCCEEEEEEEEEecCCc
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRF-FSLVGFLPFPQMSPSHSCKEPQK------SIHEIAKGLTGSIISVKVIQANEEMK  168 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l-~gv~g~ip~sels~~~~~~~p~~------~~~~~~~~~vG~~V~vkVl~vd~~~~  168 (289)
                      ..|+++.|+|..+.+.|+.+-+ |=...+||...+...+. -+|.+      .+.......+|+.|+|+|.+++..++
T Consensus       128 f~GevL~G~V~~~s~~~Ig~~~~G~Fn~~Ip~~~ip~~~~-f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~~~~~~~~  204 (214)
T 2rf4_A          128 QVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWT-FVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGR  204 (214)
T ss_dssp             CTTCEEEEEECCCCSSCEEEEETTTEEEEECSTTSCSSCB-CCCCSCC-CCCCCBCSSCCBCCSEEEEEEEEEECCSS
T ss_pred             CCCCEEEEEEEEECCCcEEEEEeCCEEEEEcHHHCCCccc-ccccccccCCCceEcCCCCCCCCEEEEEEEEEEecCC
Confidence            7899999999999998887754 45778999999865443 22211      11111112379999999999986554

>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=93.60  E-value=0.12  Score=49.10  Aligned_cols=59  Identities=14%  Similarity=0.293  Sum_probs=45.6

Q ss_pred             ccccEEEeeeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          187 NVEDIFVGRDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       187 ~~G~iv~G~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      ++|+.+    .|++|++.  +    ..|++|++++..+  -.....|++||.|+|+|.++|+.+++|.+..
T Consensus       402 ~~g~~f----~g~vv~l~--~----~~glV~v~~l~~d--~~~~~~~~lGd~V~V~v~~vd~~~~~i~f~~  460 (469)
T 2r7d_A          402 QPERVW----DAVVVDRR--G----AQATLLIPDLAFD--VQVNTPAAPGTALQVQFADIDLPQMRVRARS  460 (469)
T ss_dssp             CTTCCE----EEEEEEEE--T----TEEEEEEGGGTEE--EEEECCCCTTCEEEEEEEEEETTTTEEEEEE
T ss_pred             CCCCEE----EEEEEEEe--C----cEEEEEECCCCeE--EecCCcCCCCCEEEEEEEEEccCCCEEEEEE
Confidence            456554    45678874  2    5799999999765  2234579999999999999999999998764

>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=90.70  E-value=0.65  Score=43.93  Aligned_cols=61  Identities=7%  Similarity=0.087  Sum_probs=42.4

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      -..|+.++|.|+.+.         +..|+++.+++.....         ....+.+||+|+|+|.++|...+++.+...
T Consensus       401 ~~~g~~f~g~vv~l~---------~~~glV~v~~l~~d~~---------~~~~~~lGd~V~V~v~~vd~~~~~i~f~~~  461 (469)
T 2r7d_A          401 AQPERVWDAVVVDRR---------GAQATLLIPDLAFDVQ---------VNTPAAPGTALQVQFADIDLPQMRVRARSV  461 (469)
T ss_dssp             TCTTCCEEEEEEEEE---------TTEEEEEEGGGTEEEE---------EECCCCTTCEEEEEEEEEETTTTEEEEEEC
T ss_pred             hCCCCEEEEEEEEEe---------CcEEEEEECCCCeEEe---------cCCcCCCCCEEEEEEEEEccCCCEEEEEEE
Confidence            368999999887654         3356666666543211         112345999999999999999998877543

>2eqj_A Metal-response element-binding transcription factor 2; structure genomics,tudor domain, zinc-regulated factor 1, ZIRF1; NMR {Mus musculus}

Probab=90.62  E-value=2.1  Score=28.99  Aligned_cols=35  Identities=20%  Similarity=0.372  Sum_probs=29.7

Q ss_pred             cCCCEEEEEEEEEEc--CcEEEEEC-CEEEEeecCCCC
Q 022938           98 ESGFIYEGKIQGFNG--GGLLVRFF-SLVGFLPFPQMS  132 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~--~G~~V~l~-gv~g~ip~sels  132 (289)
                      ..|..+.|+|++|++  .-|+|+++ |..-.+...++.
T Consensus        25 tDGl~Y~gtI~~V~~~~gtC~V~F~D~s~~w~~~kdi~   62 (66)
T 2eqj_A           25 SDGLFYLGTIKKINILKQSCFIIFEDSSKSWVLWKDIQ   62 (66)
T ss_dssp             TTSCEEEEEEEEEETTTTEEEEEETTTEEEEEETTTEE
T ss_pred             ccCcEEEeEEEEEccCCcEEEEEEccCCEEEEEeeccc
Confidence            478999999999996  46899999 899888877764

>3d0f_A Penicillin-binding 1 transmembrane protein MRCA; BIG_1156.2, STR genomics, PSI-2, protein structure initiative; 1.64A {Nitrosomonas europaea atcc 19718}

Probab=87.99  E-value=1.4  Score=32.59  Aligned_cols=57  Identities=18%  Similarity=0.114  Sum_probs=45.2

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCcc-C---cC-cccchhcccccCCCCEEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHS-C---KE-PQKSIHEIAKGLTGSIISVK  159 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~-~---~~-p~~~~~~~~~~~vG~~V~vk  159 (289)
                      ...|..+.|.|+++.+.++-|.+. |-.+.||.+.|.|... .   +. +.+.++      +|+.|.|+
T Consensus        31 ~~~~~~~~AvV~~v~~~~~~v~~~~g~~~~l~~~~~~WA~~~~~~~~~~~~~~l~------~GdvI~V~   93 (106)
T 3d0f_A           31 GNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAHRFLSNDPKIGEKRIR------PGALIRVK   93 (106)
T ss_dssp             CTTTTCEEEEEEEEETTEEEEEETTSCEEEECGGGGSTTGGGTTTCTTTGGGSCC------TTEEEEEE
T ss_pred             CccCCeEEEEEEEeCCCeEEEEEcCCCeEEEcHHHChhhhhcccccccchhccCC------CCCEEEEE
Confidence            356889999999999999999996 7888899999998742 0   12 333444      99999997

>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=85.21  E-value=1.6  Score=31.49  Aligned_cols=66  Identities=12%  Similarity=0.167  Sum_probs=45.4

Q ss_pred             hhhcccccccccEEEe----eeeeEEEEEecCCCceeEEEEEEcc-CcCcccccCcccccCCCCEEEEEEEEEeC
Q 022938          179 WNKYSSRVNVEDIFVG----RDYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDR  248 (289)
Q Consensus       179 ~~~~~~~~~~G~iv~G----~~~G~fV~i~~~~G~~~i~Glv~~s-els~~~~~~~~~~~~iGd~V~vkV~~id~  248 (289)
                      +.....++-+|++.+|    .++-++|.+-..+   +.+|++--. ++.-++.+++++.+ +|.+|+++|+.+|.
T Consensus        23 ~~~~~~~~~~g~VtkGiVy~kd~~fyV~L~dY~---glEaii~dYvnv~~dr~~klkkkL-VGKtIkVqVIRvD~   93 (102)
T 1jjg_A           23 YRTSAMDLSPGSVHEGIVYFKDGIFKVRLLGYE---GHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADG   93 (102)
T ss_dssp             CSSCCCCCCSSCEEEEEEEEETTEEEEECTTTS---SCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECS
T ss_pred             eeeeccccCCCceEeeEEEEeCCEEEEEecCCC---CceeeeehhhhhhHHHHHHHHHHh-cCceEEEEEEEecc
Confidence            3345667899999999    6666678773222   488887532 23333455565555 79999999999985

>3h8z_A FragIle X mental retardation syndrome-related Pro; tudor domains, FXR2, structura genomics, structural genomics consortium, SGC; 1.92A {Homo sapiens} PDB: 3o8v_A 3kuf_A 2bkd_N*

Probab=81.30  E-value=2.4  Score=32.69  Aligned_cols=57  Identities=14%  Similarity=0.194  Sum_probs=40.6

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECC---EEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFS---LVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI  161 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~g---v~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl  161 (289)
                      +.|..++|+|+.+.+.+++|.+.+   -.--+|++++.....   +.    ....+.+||+|+|.-.
T Consensus        13 ~~G~~y~a~V~~v~~d~~~V~f~n~w~~~~~vp~~~vRlpP~---~~----~~~~f~~gd~VEV~~~   72 (128)
T 3h8z_A           13 SNGAFYKGFVKDVHEDSVTIFFENNWQSERQIPFGDVRLPPP---AD----YNKEITEGDEVEVYSR   72 (128)
T ss_dssp             TTSCEEEEEEEEECSSEEEEEETTCTTCCEEEEGGGEECCCC---C--------CCCTTCEEEEEEC
T ss_pred             CCCCEEEEEEEEEeCCcEEEEEccccCcceEechhhEEcCCC---cc----cccCCCCCCEEEEEec
Confidence            469999999999999999999973   246788888765432   11    1123459999998553

---

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	289
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	3e-14
d1e3pa2	62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	4e-12
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	5e-12
d1kl9a2	86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	6e-12
d2ahob2	84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	2e-11
d1wi5a_	119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	3e-09
d1y14b1	91	b.40.4.5 (B:81-171) C-terminal domain of RNA polym	3e-09
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	4e-09
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	6e-09
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	1e-08
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	4e-08
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	5e-08
d2c35b1	94	b.40.4.5 (B:78-171) C-terminal domain of RNA polym	2e-06
d2ix0a3	87	b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Esche	4e-04
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	6e-04
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	0.001
d2nn6i1	125	b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {H	0.002

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Length = 76

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

 Score = 64.4 bits (157), Expect = 3e-14
 Identities = 27/81 (33%), Positives = 47/81 (58%), Gaps = 11/81 (13%)

Query: 184 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 238
           + + V  ++ G+     D+GAF+ +          GLVH+S+++   ++ + D L  G E
Sbjct: 1   AEIEVGRVYTGKVTRIVDFGAFVAIG-----GGKEGLVHISQIADKRVEKVTDYLQMGQE 55

Query: 239 VRVKVIKIDREKSRITLSIKQ 259
           V VKV+++DR+  RI LSIK+
Sbjct: 56  VPVKVLEVDRQG-RIRLSIKE 75

>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 = 58.2 bits (141), Expect = 4e-12
 Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 9/59 (15%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL----IQDIRDILNEGDEVRVKVIKIDREK 250
            +GAF+ L     L    GL+H+S++        ++++ D+L  G +V+V++ +ID   
Sbjct: 8   TFGAFVSL-----LPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRG 61

>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 = 58.7 bits (142), Expect = 5e-12
 Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 10/84 (11%)

Query: 184 SRVNVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDE 238
             +    +  G      ++GAF+ +       H  GLVH+S +S   ++D  +++  GD 
Sbjct: 14  KDLKPGMVLEGVVTNVTNFGAFVDI-----GVHQDGLVHISALSEKFVKDPYEVVKAGDI 68

Query: 239 VRVKVIKIDREKSRITLSIKQLEE 262
           V+VKV+++D  ++R+ LS++  + 
Sbjct: 69  VKVKVMEVDIPRNRVGLSMRMSDT 92

>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 = 58.5 bits (141), Expect = 6e-12
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 8/78 (10%)

Query: 187 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 241
            VED+ +       + GA++ L   + +    G++ +SE+S   I+ I  ++  G    V
Sbjct: 12  EVEDVVMVNVRSIAEMGAYVSLLEYNNI---EGMILLSELSRRRIRSINKLIRIGRNECV 68

Query: 242 KVIKIDREKSRITLSIKQ 259
            VI++D+EK  I LS ++
Sbjct: 69  VVIRVDKEKGYIDLSKRR 86

>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 = 56.9 bits (137), Expect = 2e-11
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 8/78 (10%)

Query: 187 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 241
           +  +I +       DYG+++ L    GL      +  SEVS   +++IRD+L E  +V V
Sbjct: 10  SEGEILIATVKQVFDYGSYVSLDEYGGL---QAFLPWSEVSSKWVKNIRDVLKENRKVIV 66

Query: 242 KVIKIDREKSRITLSIKQ 259
           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 = 52.1 bits (124), Expect = 3e-09
 Identities = 11/77 (14%), Positives = 29/77 (37%), Gaps = 5/77 (6%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRIT 254
           D+G  + +    G+      + + +    +  ++    L  G  +   V K+      ++
Sbjct: 34  DHGYLVDI----GVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVS 89

Query: 255 LSIKQLEEDPLLETLEK 271
           LS+   E    + T ++
Sbjct: 90  LSVGHSEVSTAIATEQQ 106

>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 = 51.0 bits (122), Expect = 3e-09
 Identities = 15/93 (16%), Positives = 28/93 (30%), Gaps = 22/93 (23%)

Query: 188 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----------DIRDI 232
             ++  G       +G  + +            V    +  DL               D+
Sbjct: 3   KGEVVDGTVVSCSQHGFEVQVGPMKVF------VTKHLMPQDLTFNAGSNPPSYQSSEDV 56

Query: 233 LNEGDEVRVKVIKIDREKSRITLSIKQLEEDPL 265
           +     +RVK+     + S I   I  ++ED L
Sbjct: 57  ITIKSRIRVKIEGCISQVSSIHA-IGSIKEDYL 88

>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 = 51.2 bits (122), Expect = 4e-09
 Identities = 20/99 (20%), Positives = 45/99 (45%), Gaps = 15/99 (15%)

Query: 188 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGL-----VHVSEVSWDLIQDIRDILNEGD 237
           + ++  G      ++G+F+ L   DGL H++ +      +  +    + ++   +L  GD
Sbjct: 3   MYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGD 62

Query: 238 EVRVKVIKIDREK-----SRITLSIKQLEEDPLLETLEK 271
            VR +++ I  +      S+I L+++Q     L    E+
Sbjct: 63  YVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIEEE 101

>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 = 49.9 bits (119), Expect = 6e-09
 Identities = 12/82 (14%), Positives = 30/82 (36%), Gaps = 15/82 (18%)

Query: 188 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----QDIRDILNEGDE 238
             D+ +G          F+ +           ++ V +           D++ +L  GD 
Sbjct: 7   AGDVVIGLIQSVGIMNWFVDIN-----SPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDY 61

Query: 239 VRVKVIKIDREKSRITLSIKQL 260
           ++ 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 = 48.8 bits (116), Expect = 1e-08
 Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 12/85 (14%)

Query: 187 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD-LIQDIRDILNEGDEVR 240
           +V D+ +G        G  +     D        + VSE       +   ++L+ GD + 
Sbjct: 4   SVGDVVIGIIREVAANGWAV-----DIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAII 58

Query: 241 VKVIKIDREKSRITLSIKQLEEDPL 265
            KV+ ID +  ++TL++K     P+
Sbjct: 59  AKVLNIDPKM-KVTLTMKDRICRPI 82

>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 = 48.0 bits (114), Expect = 4e-08
 Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 21/89 (23%)

Query: 188 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWD----------LIQDIRDI 232
           V DI VGR          +          L  ++ +S ++                +R  
Sbjct: 8   VGDIVVGRITEVQQKRWKVET-----NSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGF 62

Query: 233 LNEGDEVRVKVIKIDREKSRITLSIKQLE 261
           L EGD +  +V  +  +   ++L  + L+
Sbjct: 63  LQEGDLISAEVQAVFSDG-AVSLHTRSLK 90

>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 = 47.7 bits (113), Expect = 5e-08
 Identities = 17/82 (20%), Positives = 28/82 (34%), Gaps = 14/82 (17%)

Query: 187 NVEDIFVGR-----DYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDI---RDILNEGDE 238
            + DI +G       YG  + ++           +  S +    I      R  L+ GD 
Sbjct: 6   KINDIVIGLVEDVEIYGWVVDIK-----APYKAYLPASNLLGRSINVGEDLRRYLDVGDY 60

Query: 239 VRVKVIKIDREKSRITLSIKQL 260
           V  ++   DR      LS+K  
Sbjct: 61  VIARIENFDRSI-DPVLSVKGK 81

>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 = 43.0 bits (101), Expect = 2e-06
 Identities = 13/89 (14%), Positives = 28/89 (31%), Gaps = 12/89 (13%)

Query: 188 VEDIFVGR-----DYGAFIHLRFPDGLYHLTGL-----VHVSEVSWDLI-QDIRDILNEG 236
             ++           G F  +           +        +         D   ++ + 
Sbjct: 4   KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQD 63

Query: 237 DEVRVKVIKIDREKSRITLSIKQLEEDPL 265
           DE+R+K++    +K+ I   I  L +D L
Sbjct: 64  DEIRLKIVGTRVDKNDIFA-IGSLMDDYL 91

>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 = 36.3 bits (84), Expect = 4e-04
 Identities = 6/72 (8%), Positives = 15/72 (20%), Gaps = 16/72 (22%)

Query: 196 DYGAFIHLRFPDGLYHLTGLVHVSEVSWD------------LIQDIRDILNEGDEVRVKV 243
             G  + L            +    +               +      +    D + V +
Sbjct: 16  RGGMRVRLVD----NGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTI 71

Query: 244 IKIDREKSRITL 255
            ++  E   I  
Sbjct: 72  AEVRMETRSIIA 83

>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 = 35.9 bits (83), Expect = 6e-04
 Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 11/77 (14%)

Query: 187 NVEDIFVGRDYGAFIHLRFPDGLY-----HLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 241
           +V D  +G      I   F D          + +        +  +  R  L  GD V  
Sbjct: 6   SVNDFVIGV-----IIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYA 60

Query: 242 KVIKIDREKSRITLSIK 258
           +V   ++E     +   
Sbjct: 61  RVCTAEKE-LEAEIECF 76

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]} Length = 88

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

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 6/77 (7%), Positives = 19/77 (24%), Gaps = 12/77 (15%)

Query: 187 NVEDIFVGRDYGAFIHLRFPDGLY-----HLTGLVHVSEVSWDLIQDIRDILNEGDEVRV 241
              D  +G      +  +  D             +          +  R  +  GD +  
Sbjct: 5   VKGDHVIGI-----VTAKSGDIFKVDVGGSEPASLSYLSFEGA-TKRNRPNVQVGDLIYG 58

Query: 242 KVIKIDREKSRITLSIK 258
           + +  +++     +   
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 = 35.2 bits (81), Expect = 0.002
 Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 2/51 (3%)

Query: 211 HLTGLVHVSEVSWDLIQ--DIRDILNEGDEVRVKVIKIDREKSRITLSIKQ 259
              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	289
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.63
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.63
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.63
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.61
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.6
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.58
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.57
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.57
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.51
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.47
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.45
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.44
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.4
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.37
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.33
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.29
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.28
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.28
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.1
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	99.07
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.05
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	99.0
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	98.95
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.95
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	98.9
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.89
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.81
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.76
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.62
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	98.51
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.42
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.36
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.14
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.12
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	97.85
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.73
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.54
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.3
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.02
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	94.38
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	92.25
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	89.97
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	89.34
d1yvca1	69	Hypothetical protein MMP0076 {Methanococcus maripa	88.86
d1yeza1	68	Hypothetical protein MM1357 {Methanosarcina mazei	88.39
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	83.64
d2ix0a2	79	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	81.25

>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=99.63  E-value=5.5e-17  Score=115.66  Aligned_cols=71  Identities=39%  Similarity=0.745  Sum_probs=65.6

Q ss_pred             cccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 022938          184 SRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIK  258 (289)
Q Consensus       184 ~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK  258 (289)
                      +++++|+++.|     .++|+||+|+  +|   +.||+|.++++|.+..++.+.|++||.|+|+|+++|+ ++||.||+|
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--GG---KEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIK   74 (76)
T ss_dssp             CCCCTTSEEEEEEEEEETTEEEEECS--SS---CCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCT-TCCCEEEEC
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEeC--CC---CEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECC-CCCEEEEEE
Confidence            46899999999     8999999995  44   9999999999999999999999999999999999997 578999999


Q ss_pred             cC
Q 022938          259 QL  260 (289)
Q Consensus       259 ~~  260 (289)
                      ++
T Consensus        75 ~a   76 (76)
T d1sroa_          75 EA   76 (76)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=99.63  E-value=1.9e-16  Score=117.42  Aligned_cols=77  Identities=29%  Similarity=0.555  Sum_probs=72.0

Q ss_pred             cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      .++++++|+++.|     .++|+||+|+  +|   +.|+||.++++|.+..++++.|++||.|+|+|+++|+++++|.||
T Consensus        12 ~~~~~k~G~iv~g~V~~v~~~G~~V~l~--~~---i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~~i~LS   86 (94)
T d3bzka4          12 SLKDLKPGMVLEGVVTNVTNFGAFVDIG--VH---QDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLS   86 (94)
T ss_dssp             CGGGCCTTCEEEEEEEEEETTEEEEECS--SS---SCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEE
T ss_pred             HHhcCCCCCEEEEEEEEEECcEEEEEeC--CC---ceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEE
Confidence            4688999999999     9999999995  54   999999999999999999999999999999999999999999999


Q ss_pred             EecCCCCc
Q 022938          257 IKQLEEDP  264 (289)
Q Consensus       257 lK~~~~~p  264 (289)
                      +|+. ++|
T Consensus        87 ~K~~-e~P   93 (94)
T d3bzka4          87 MRMS-DTP   93 (94)
T ss_dssp             SCTT-CCC
T ss_pred             Eecc-CCC
Confidence            9985 677

>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=99.63  E-value=1.4e-16  Score=113.46  Aligned_cols=73  Identities=22%  Similarity=0.354  Sum_probs=67.8

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEee
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEK  175 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k  175 (289)
                      ++.|++++|+|+++.++|+||+++ +++||+|.+++++.+. .+|.+.|+      +||.++|+|+++|+ .+|+.||+|
T Consensus         3 ~kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~~~~-~~~~~~~~------~G~~v~v~Vi~id~-~~ri~LS~k   74 (76)
T d1sroa_           3 IEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRV-EKVTDYLQ------MGQEVPVKVLEVDR-QGRIRLSIK   74 (76)
T ss_dssp             CCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCC-SCHHHHCC------TTCEEEEEEEECCT-TCCCEEEEC
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCcccc-CCHHHccC------CCCEEEEEEEEECC-CCCEEEEEE
Confidence            589999999999999999999998 8999999999999987 88988887      99999999999996 578999999


Q ss_pred             cc
Q 022938          176 DA  177 (289)
Q Consensus       176 ~~  177 (289)
                      ++
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=99.61  E-value=5.9e-16  Score=112.86  Aligned_cols=70  Identities=31%  Similarity=0.517  Sum_probs=52.8

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  259 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~  259 (289)
                      ++|+++.|     +++|+||+|...+|   ++|++|.++++|.+..++.+.|++||.|+|+|+++|+++++|.||+|+
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 EVEDVVMVNVRSIAEMGAYVSLLEYNN---IEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTTTT---EEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCEEEEEEEEEeCCeEEEEEecCCC---EEEEEEeeeccccccccceEEeecccEEEEEEEEEECCCCEEEEEeeC
Confidence            57999999     89999999953234   999999999999999999999999999999999999999999999986

>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=99.60  E-value=1.4e-15  Score=110.77  Aligned_cols=72  Identities=18%  Similarity=0.252  Sum_probs=57.2

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      ++|++++|+|+++.++|+||++.   |++||||.++++|.+. .+|.+.|+      +||.|+|+|+++|++++++.||+
T Consensus        12 ~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~~-~~~~~~~~------~Gd~v~~kV~~vd~~~~ki~LS~   84 (86)
T d1kl9a2          12 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRI-RSINKLIR------IGRNECVVVIRVDKEKGYIDLSK   84 (86)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC-------------C------TTCEEEEEEEEEETTTTEEEEES
T ss_pred             CCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeecccccc-ccceEEee------cccEEEEEEEEEECCCCEEEEEe
Confidence            58999999999999999999994   7999999999999886 88888886      99999999999999999999999


Q ss_pred             ec
Q 022938          175 KD  176 (289)
Q Consensus       175 k~  176 (289)
                      |+
T Consensus        85 Kq   86 (86)
T d1kl9a2          85 RR   86 (86)
T ss_dssp             TT
T ss_pred             eC
Confidence            84

>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=99.58  E-value=9e-16  Score=111.36  Aligned_cols=70  Identities=37%  Similarity=0.634  Sum_probs=59.5

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEec
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQ  259 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~  259 (289)
                      ++|+++.|     +++|+||+|...+|   +.|++|.++++|.+..++.+.|++||.|+|+|+++|+++++|.||+|+
T Consensus        10 ~~G~iv~G~V~~v~~~G~fV~l~~~~g---i~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2          10 SEGEILIATVKQVFDYGSYVSLDEYGG---LQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             CTTCCCEEEEEEEETTEEEEEETTTTT---EEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCcCC---EEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEEcC
Confidence            57999998     89999999952234   999999999999999999999999999999999999999999999986

>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=99.57  E-value=2.2e-15  Score=109.26  Aligned_cols=72  Identities=22%  Similarity=0.282  Sum_probs=63.1

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      ++|++++|+|++++++|+||+++   |++||+|.+++++.+. .+|.+.|+      +||.++|+|+++|++++++.||+
T Consensus        10 ~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~-~~~~~~~~------~G~~v~~kV~~vd~~~~~i~LS~   82 (84)
T d2ahob2          10 SEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWV-KNIRDVLK------ENRKVIVKVIRVDRRKGTVDVSL   82 (84)
T ss_dssp             CTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC------CHHHHTC------SSCEEECEEEEEETTTTEEEEES
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccc-cccceEee------cccEEEEEEEEEECCCCEEEEEE
Confidence            68999999999999999999995   7999999999999886 78888776      99999999999999999999999


Q ss_pred             ec
Q 022938          175 KD  176 (289)
Q Consensus       175 k~  176 (289)
                      |+
T Consensus        83 Kq   84 (84)
T d2ahob2          83 KK   84 (84)
T ss_dssp             SS
T ss_pred             cC
Confidence            85

>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=99.57  E-value=3.3e-15  Score=110.65  Aligned_cols=76  Identities=20%  Similarity=0.344  Sum_probs=70.6

Q ss_pred             HhhcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           95 AYKESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        95 ~~~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      +.+++|++++|+|+++.++|+||+++ |++||||.+++++.+. .+|.+.|+      +||.|+|+|+++|.+++++.||
T Consensus        14 ~~~k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~-~~~~~~~~------vGq~v~~~V~~id~~~~~i~LS   86 (94)
T d3bzka4          14 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFV-KDPYEVVK------AGDIVKVKVMEVDIPRNRVGLS   86 (94)
T ss_dssp             GGCCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCC-SCHHHHCC------TTCEEEEEEEEEETTTTEEEEE
T ss_pred             hcCCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccc-cChhhhhc------cCcEEEEEEEEEECCCCEEEEE
Confidence            34789999999999999999999998 9999999999999886 88888776      9999999999999999999999


Q ss_pred             eecc
Q 022938          174 EKDA  177 (289)
Q Consensus       174 ~k~~  177 (289)
                      +|..
T Consensus        87 ~K~~   90 (94)
T d3bzka4          87 MRMS   90 (94)
T ss_dssp             SCTT
T ss_pred             Eecc
Confidence            9963

>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=99.51  E-value=2e-14  Score=108.68  Aligned_cols=80  Identities=29%  Similarity=0.501  Sum_probs=69.3

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc-----------cCcccccCCCCEEEEEEEEEeCCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI-----------QDIRDILNEGDEVRVKVIKIDREK  250 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~-----------~~~~~~~~iGd~V~vkV~~id~e~  250 (289)
                      ++|+++.|     ++||+||+|+   |   ++||||.++|++++.           .++.+.|++||.|+|+|++||.++
T Consensus         2 ~~gei~~g~V~~v~~~G~FVel~---~---ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~~   75 (106)
T d1go3e1           2 EMYELIEGEVVDVVEFGSFVRLG---P---LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKA   75 (106)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECS---S---SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC
T ss_pred             CCCCEEEEEEEEEeeeEEEEEee---C---eEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchhh
Confidence            57889988     9999999994   4   999999999999876           367789999999999999999988


Q ss_pred             Ce-----EEEEEecCCCCchhHHhhhh
Q 022938          251 SR-----ITLSIKQLEEDPLLETLEKV  272 (289)
Q Consensus       251 ~r-----i~lSlK~~~~~p~~~~~~~~  272 (289)
                      ++     +.||+|+...+||+...++.
T Consensus        76 ~~~~~~~i~ls~K~~~~~~~e~~~~~~  102 (106)
T d1go3e1          76 ERKRGSKIALTMRQPYLGKLEWIEEEK  102 (106)
T ss_dssp             -----CEEEEECCSTTCEEHHHHHHHH
T ss_pred             ccccCceeecccccCCCCcchhhhhHh
Confidence            76     78999999999999877643

>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=99.47  E-value=8.3e-14  Score=100.52  Aligned_cols=73  Identities=23%  Similarity=0.395  Sum_probs=65.6

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD  176 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~  176 (289)
                      +.|+++.|+|+++.++|+||+++ ++.||||.+++++.....+|.+.|+      +||.|.|+|+++|+ .+++.||+|.
T Consensus         4 k~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~------vGd~V~~kV~~vd~-~~~i~LS~k~   76 (83)
T d2ba0a1           4 SVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLD------IGDAIIAKVLNIDP-KMKVTLTMKD   76 (83)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCC------TTCEEEEEEEEECT-TCCEEEECCS
T ss_pred             CCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccccccccChhhhcc------cccEEEEEEEEECC-CCCEEEEecC
Confidence            68999999999999999999999 8999999999998764467777776      99999999999995 5789999997


Q ss_pred             c
Q 022938          177 A  177 (289)
Q Consensus       177 ~  177 (289)
                      .
T Consensus        77 ~   77 (83)
T d2ba0a1          77 R   77 (83)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.45  E-value=2.1e-14  Score=110.80  Aligned_cols=78  Identities=15%  Similarity=0.209  Sum_probs=69.2

Q ss_pred             hhcCCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           96 YKESGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        96 ~~~~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      .+++|++++|+|++++++|+||+|+  +++||||.+++++.+..++|.+.|+      +||.|+|+|+++|++++++.||
T Consensus        18 ~l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~~------vGq~v~~~V~~vd~~~~~i~LS   91 (119)
T d1wi5a_          18 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLK------VGQYLNCIVEKVKGNGGVVSLS   91 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCC------TTCEEEEEEEECCTTSCEEEEE
T ss_pred             hcCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhccccccCCHHHhcc------cceEEEEEEEEEeCCCCEEEEE
Confidence            3789999999999999999999995  7999999999998653367777776      9999999999999999999999


Q ss_pred             eecchh
Q 022938          174 EKDAVW  179 (289)
Q Consensus       174 ~k~~~~  179 (289)
                      +++...
T Consensus        92 ~k~~~~   97 (119)
T d1wi5a_          92 VGHSEV   97 (119)
T ss_dssp             CCCCCS
T ss_pred             ecHHHh
Confidence            997543

>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=99.44  E-value=7.8e-14  Score=100.67  Aligned_cols=73  Identities=26%  Similarity=0.388  Sum_probs=64.4

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccc-ccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  260 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~-~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~  260 (289)
                      ++|++|.|     .++|+||+|+  ++   +.|++|.++++|.. ..++++.|++||.|.|+|+++|+ +++|.||+|+.
T Consensus         4 k~Gd~V~G~V~~v~~~g~~V~i~--~~---~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~LS~k~~   77 (83)
T d2ba0a1           4 SVGDVVIGIIREVAANGWAVDIY--SP---YQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMKDR   77 (83)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECS--SS---SCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECCSS
T ss_pred             CCCCEEEEEEEEEECCEEEEecC--CC---eeEEEecccccccccccChhhhcccccEEEEEEEEECC-CCCEEEEecCC
Confidence            68999999     8999999996  44   99999999999875 67899999999999999999996 57899999998


Q ss_pred             CCCch
Q 022938          261 EEDPL  265 (289)
Q Consensus       261 ~~~p~  265 (289)
                      ...|+
T Consensus        78 ~~~k~   82 (83)
T d2ba0a1          78 ICRPI   82 (83)
T ss_dssp             SCEEE
T ss_pred             CCCCC
Confidence            66553

>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=99.40  E-value=5.7e-13  Score=100.46  Aligned_cols=74  Identities=18%  Similarity=0.292  Sum_probs=62.8

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccC----------cCcccchhcccccCCCCEEEEEEEEEecCC
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSC----------KEPQKSIHEIAKGLTGSIISVKVIQANEEM  167 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~----------~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~  167 (289)
                      +.|++++|+|+++.++|+||++++++||||.+++++.++.          .+|.+.|+      +||.|+|+|+++|.+.
T Consensus         2 ~~gei~~g~V~~v~~~G~FVel~~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~------~Gd~v~vkV~~vd~~~   75 (106)
T d1go3e1           2 EMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLE------IGDYVRARIVAISLKA   75 (106)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC--CEEETTTCCEEC------TTCEEEEEEEEEECCC
T ss_pred             CCCCEEEEEEEEEeeeEEEEEeeCeEEEEEeecccCceeeeccceeEEeeccccccee------ecceEEEEEEEEchhh
Confidence            5799999999999999999999999999999999987652          25556665      9999999999999887


Q ss_pred             cE-----EEEEeecc
Q 022938          168 KK-----LVFSEKDA  177 (289)
Q Consensus       168 ~r-----i~lS~k~~  177 (289)
                      ++     +.+|+|+.
T Consensus        76 ~~~~~~~i~ls~K~~   90 (106)
T d1go3e1          76 ERKRGSKIALTMRQP   90 (106)
T ss_dssp             -----CEEEEECCST
T ss_pred             ccccCceeecccccC
Confidence            76     67788863

>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=99.37  E-value=2.2e-13  Score=104.94  Aligned_cols=78  Identities=15%  Similarity=0.227  Sum_probs=68.9

Q ss_pred             cccccccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccc-ccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 022938          182 YSSRVNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDL-IQDIRDILNEGDEVRVKVIKIDREKSRITL  255 (289)
Q Consensus       182 ~~~~~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~-~~~~~~~~~iGd~V~vkV~~id~e~~ri~l  255 (289)
                      ..+++++|+++.|     .++|+||+|+ .+|   +.||||++++++.+ ..++.+.|++||.|+|+|+++|++++++.|
T Consensus        15 s~~~l~~G~iv~G~V~~i~~~G~~V~lg-~~~---~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~L   90 (119)
T d1wi5a_          15 SAEALKPGMLLTGTVSSLEDHGYLVDIG-VDG---TRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSL   90 (119)
T ss_dssp             CTTTCCTTCEEEEEEEEECSSEEEEECC-CSS---CEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEE
T ss_pred             CHhhcCCCCEEEEEEEEEeccEEEEEEe-ccc---cceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEE
Confidence            3578999999999     8999999995 233   99999999999874 778889999999999999999999999999


Q ss_pred             EEecCCCC
Q 022938          256 SIKQLEED  263 (289)
Q Consensus       256 SlK~~~~~  263 (289)
                      |+|+....
T Consensus        91 S~k~~~~~   98 (119)
T d1wi5a_          91 SVGHSEVS   98 (119)
T ss_dssp             ECCCCCSC
T ss_pred             EecHHHhh
Confidence            99987543

>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=99.33  E-value=1e-12  Score=95.56  Aligned_cols=74  Identities=14%  Similarity=0.159  Sum_probs=64.5

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCcc--CcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHS--CKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~--~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      ++|+++.|+|+++.++|+||+++ +++||||.+++++.+.  ..+|.+.++      +||.|.|+|+++|+ .+++.||+
T Consensus         6 k~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~~~------~Gd~v~~kV~~vd~-~~~i~LS~   78 (87)
T d2je6i1           6 KINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLD------VGDYVIARIENFDR-SIDPVLSV   78 (87)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCC------TTCEEEEEEEEEET-TEEEEEEC
T ss_pred             CCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceeccccccchhhc------ccceEEEEEEEECC-CCCEEEEE
Confidence            67999999999999999999999 8999999999998764  134556665      99999999999995 57999999


Q ss_pred             ecch
Q 022938          175 KDAV  178 (289)
Q Consensus       175 k~~~  178 (289)
                      |...
T Consensus        79 k~~~   82 (87)
T d2je6i1          79 KGKD   82 (87)
T ss_dssp             CSTT
T ss_pred             ecCC
Confidence            9753

>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=99.29  E-value=9.3e-13  Score=95.72  Aligned_cols=69  Identities=26%  Similarity=0.406  Sum_probs=60.5

Q ss_pred             cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc---cCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI---QDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~---~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      -++|+++.|     +++|+||+|+  ++   +.|++|.++++|.+.   .++++.|++||.|.|+|+++|+ .+++.||+
T Consensus         5 Pk~Gdiv~G~V~~i~~~g~fV~i~--~~---~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~-~~~i~LS~   78 (87)
T d2je6i1           5 PKINDIVIGLVEDVEIYGWVVDIK--AP---YKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVLSV   78 (87)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECS--SS---SCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEEEC
T ss_pred             CCCCCEEEEEEEEEECCEEEEEeC--CC---EEEEEehHHhCCceeccccccchhhcccceEEEEEEEECC-CCCEEEEE
Confidence            367999999     8999999996  44   999999999999865   4577889999999999999997 58999999


Q ss_pred             ecC
Q 022938          258 KQL  260 (289)
Q Consensus       258 K~~  260 (289)
                      |+.
T Consensus        79 k~~   81 (87)
T d2je6i1          79 KGK   81 (87)
T ss_dssp             CST
T ss_pred             ecC
Confidence            975

>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=99.28  E-value=1.7e-12  Score=94.50  Aligned_cols=73  Identities=16%  Similarity=0.203  Sum_probs=63.2

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccC---cCcccchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSC---KEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~---~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      +.|+++.|+|+++.++|+||+++ +..||||.+++++.+..   .++.+.++      +||.|.|+|+++|++ +++.||
T Consensus         6 k~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~~~------vGd~V~~kV~~vd~~-~~i~Ls   78 (88)
T d2z0sa1           6 QAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLK------VGDYIKAKVVAFDKT-RSPLLT   78 (88)
T ss_dssp             CTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSC------TTCEEEEEEEEECTT-SCEEEE
T ss_pred             CCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcccccccccchhhhcc------cCcEEEEEEEEECCC-CCEEEE
Confidence            68999999999999999999999 89999999999987652   24445554      999999999999954 689999


Q ss_pred             eecc
Q 022938          174 EKDA  177 (289)
Q Consensus       174 ~k~~  177 (289)
                      +|..
T Consensus        79 ~k~~   82 (88)
T d2z0sa1          79 VQGE   82 (88)
T ss_dssp             CCSS
T ss_pred             EecC
Confidence            9874

>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=99.28  E-value=1.1e-12  Score=95.49  Aligned_cols=69  Identities=17%  Similarity=0.352  Sum_probs=60.4

Q ss_pred             cccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCccccc----CcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          186 VNVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ----DIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       186 ~~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~----~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      -++|+++.|     +++|+||+|+  ++   +.|++|.+++++.+..    ++++.|++||.|.|+|+++|+ .+++.||
T Consensus         5 Pk~GdvV~G~V~~v~~~g~fV~i~--~~---~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~Ls   78 (88)
T d2z0sa1           5 PQAGDVVIGLIQSVGIMNWFVDIN--SP---YVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPLLT   78 (88)
T ss_dssp             CCTTCCEEEEEEEECSSEEEEECS--SS---SCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEEEE
T ss_pred             CCCCCEEEEEEEEEECCeEEEEeC--CC---eEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECC-CCCEEEE
Confidence            368999999     8999999996  43   8999999999988653    677889999999999999996 5789999


Q ss_pred             EecC
Q 022938          257 IKQL  260 (289)
Q Consensus       257 lK~~  260 (289)
                      +|+.
T Consensus        79 ~k~~   82 (88)
T d2z0sa1          79 VQGE   82 (88)
T ss_dssp             CCSS
T ss_pred             EecC
Confidence            9975

>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=99.10  E-value=9.5e-13  Score=89.43  Aligned_cols=57  Identities=14%  Similarity=0.244  Sum_probs=35.5

Q ss_pred             EEEEEEEcCcEEEEEC-CEEEEeecCCCCCCc---cCcCcccchhcccccCCCCEEEEEEEEEecCC
Q 022938          105 GKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSH---SCKEPQKSIHEIAKGLTGSIISVKVIQANEEM  167 (289)
Q Consensus       105 g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~---~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~  167 (289)
                      |+|+++.++|+||+++ |++||||.|+|++.+   ...+|.+.++      +||+|+|+|+++|+++
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~~~~~~v~~~~~~~~------~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLG------VGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC-------------------CC------SSCBCCCCCCCCCSSC
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHcccccccccccCHHHhcC------CCCEEEEEEEEEcCCC
Confidence            7899999999999999 999999999998642   1267888887      9999999999999764

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

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

Probab=99.07  E-value=3.1e-10  Score=81.93  Aligned_cols=75  Identities=15%  Similarity=0.251  Sum_probs=58.1

Q ss_pred             CCCEEEEEEEEEEcCcEEEEEC--CEEEEeecCCCCCCccCcCcc-cch---hc-ccccCCCCEEEEEEEEEecCCcEEE
Q 022938           99 SGFIYEGKIQGFNGGGLLVRFF--SLVGFLPFPQMSPSHSCKEPQ-KSI---HE-IAKGLTGSIISVKVIQANEEMKKLV  171 (289)
Q Consensus        99 ~G~iv~g~V~~v~~~G~~V~l~--gv~g~ip~sels~~~~~~~p~-~~~---~~-~~~~~vG~~V~vkVl~vd~~~~ri~  171 (289)
                      .++.++|+|++++++|+||++.  +++||||.++|++.+..-+.. ..+   .. ...+.+||+|+|+|.++|+++++|.
T Consensus         3 ~~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r~I~   82 (87)
T d2ix0a3           3 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSII   82 (87)
T ss_dssp             SCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTTEEE
T ss_pred             CCCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccCeEE
Confidence            5788999999999999999995  799999999998865421211 100   00 0125599999999999999999997


Q ss_pred             EE
Q 022938          172 FS  173 (289)
Q Consensus       172 lS  173 (289)
                      +.
T Consensus        83 ~~   84 (87)
T d2ix0a3          83 AR   84 (87)
T ss_dssp             EE
T ss_pred             EE
Confidence            64

>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=99.05  E-value=1.7e-12  Score=88.13  Aligned_cols=51  Identities=31%  Similarity=0.643  Sum_probs=30.1

Q ss_pred             eeeeEEEEEecCCCceeEEEEEEccCcCcc----cccCcccccCCCCEEEEEEEEEeCCC
Q 022938          195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD----LIQDIRDILNEGDEVRVKVIKIDREK  250 (289)
Q Consensus       195 ~~~G~fV~i~~~~G~~~i~Glv~~sels~~----~~~~~~~~~~iGd~V~vkV~~id~e~  250 (289)
                      .+||+||+|.  +|   ++||+|+|+|++.    ++.++++.|++||.|+|+|+++|+++
T Consensus         7 ~~fG~FV~l~--~g---~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           7 TTFGAFVSLL--PG---KDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             C-CSCEECCC--------CCCCC-------------------CCSSCBCCCCCCCCCSSC
T ss_pred             EeceEEEEec--CC---ceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCCC
Confidence            8999999996  55   9999999999864    67899999999999999999999854

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

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

Probab=99.00  E-value=9.2e-10  Score=80.11  Aligned_cols=73  Identities=14%  Similarity=0.087  Sum_probs=57.5

Q ss_pred             CCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccc----hhcccccCCCCEEEEEEEEEecCCcEEEE
Q 022938           99 SGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKS----IHEIAKGLTGSIISVKVIQANEEMKKLVF  172 (289)
Q Consensus        99 ~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~----~~~~~~~~vG~~V~vkVl~vd~~~~ri~l  172 (289)
                      .|++++|+|++++++|+||+++.++||+|.++|.+.+. -++...    -+....+.+|+.|+|+|++++.+.+++.+
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg~~eg~i~~~~l~~~~~-~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~i~~   79 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT-FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHA   79 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTCE-ECC-----CEECSSCEECTTCEEEEEEEEEEEETTEEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEEcCeEEEEEhhhcCcceE-EccccceeEecccCeEEeCCCEEEEEEEEEecccCccEE
Confidence            69999999999999999999999999999999987754 222211    00112355999999999999999888754

>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=98.95  E-value=1.6e-10  Score=85.01  Aligned_cols=68  Identities=22%  Similarity=0.312  Sum_probs=56.4

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcc----------cccCcccccCCCCEEEEEEEEEeCCCC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWD----------LIQDIRDILNEGDEVRVKVIKIDREKS  251 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~----------~~~~~~~~~~iGd~V~vkV~~id~e~~  251 (289)
                      ++|++|.|     .++|+||+|+  .+   ..|++|+|+++|.          ...++++.|++||.|.|+|+++|. .+
T Consensus         7 ~vGdiV~G~V~~v~~~g~~V~I~--~~---~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~-dg   80 (95)
T d2nn6h1           7 EVGDIVVGRITEVQQKRWKVETN--SR---LDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-DG   80 (95)
T ss_dssp             CSSBCCCEEEEEEETTEEEEECS--SS---SCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-TT
T ss_pred             CCCCEEEEEEEEEecCcEEEEeC--CC---ceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECC-CC
Confidence            57888888     8999999996  33   7999999999763          234567889999999999999997 68


Q ss_pred             eEEEEEecC
Q 022938          252 RITLSIKQL  260 (289)
Q Consensus       252 ri~lSlK~~  260 (289)
                      ++.||+|..
T Consensus        81 ~i~Ls~r~~   89 (95)
T d2nn6h1          81 AVSLHTRSL   89 (95)
T ss_dssp             EEEEECCSS
T ss_pred             CEEEEeccc
Confidence            999999874

>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=98.95  E-value=2.4e-09  Score=74.21  Aligned_cols=64  Identities=22%  Similarity=0.288  Sum_probs=56.0

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc--EEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK--KLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~--ri~lS~  174 (289)
                      +.|++++|+|..+++.+++|++++++|+||.+|+.       |.+.|+      +|++|+|.|.+|+.+.+  +|.||+
T Consensus         7 ~~geiv~G~V~r~~~~~~~Vdlg~~eaiLp~~eqi-------p~E~~~------~Gdrik~~i~~V~~~~kgpqI~lSR   72 (72)
T d1hh2p1           7 LKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWI-------PGEEIK------AGDLVKVYIIDVVKTTKGPKILVSR   72 (72)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTEEEEEEGGGSC-------TTCCCC------TTCEEEEEEEEEEEETTEEEEEEES
T ss_pred             ccCcEEEEEEEEEcCCCEEEEECCcEEECCHHHcC-------CCCCCC------CCCEEEEEEEEEEEcCCCCeEEEeC
Confidence            68999999999999999999999999999999864       556665      99999999999986654  677775

>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=98.90  E-value=4.6e-10  Score=82.44  Aligned_cols=73  Identities=18%  Similarity=0.124  Sum_probs=58.4

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCc---------CcccchhcccccCCCCEEEEEEEEEecCC
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCK---------EPQKSIHEIAKGLTGSIISVKVIQANEEM  167 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~---------~p~~~~~~~~~~~vG~~V~vkVl~vd~~~  167 (289)
                      +.|+++.|+|+++.++|+||+++ +..|++|.+++++.....         ++.+.|      .+||.|.|+|+++|. .
T Consensus         7 ~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~------~~Gd~V~~kV~~v~~-d   79 (95)
T d2nn6h1           7 EVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFL------QEGDLISAEVQAVFS-D   79 (95)
T ss_dssp             CSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHS------CSSCEECCEEEEEET-T
T ss_pred             CCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchhhhhhhhhc------ccccEEEEEEEEECC-C
Confidence            68999999999999999999999 899999999998643211         122333      499999999999996 5


Q ss_pred             cEEEEEeecc
Q 022938          168 KKLVFSEKDA  177 (289)
Q Consensus       168 ~ri~lS~k~~  177 (289)
                      +++.||++..
T Consensus        80 g~i~Ls~r~~   89 (95)
T d2nn6h1          80 GAVSLHTRSL   89 (95)
T ss_dssp             TEEEEECCSS
T ss_pred             CCEEEEeccc
Confidence            8999998864

>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=98.89  E-value=4.5e-09  Score=76.84  Aligned_cols=73  Identities=11%  Similarity=0.141  Sum_probs=56.8

Q ss_pred             CCCEEEEEEEEEEcCcEEEEECCEEEEeecCCCCCCcc-CcCccc-ch---hcccccCCCCEEEEEEEEEecCCcEEE
Q 022938           99 SGFIYEGKIQGFNGGGLLVRFFSLVGFLPFPQMSPSHS-CKEPQK-SI---HEIAKGLTGSIISVKVIQANEEMKKLV  171 (289)
Q Consensus        99 ~G~iv~g~V~~v~~~G~~V~l~gv~g~ip~sels~~~~-~~~p~~-~~---~~~~~~~vG~~V~vkVl~vd~~~~ri~  171 (289)
                      .|++++|+|++++++|+||+++.++||+|.++|.+.+. ..+... .+   .....+.+|+.|++||.+++.+.+++.
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~I~   81 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIF   81 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEecCceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCcce
Confidence            69999999999999999999998999999999997752 112111 00   011234599999999999999888775

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

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

Probab=98.81  E-value=5e-09  Score=75.42  Aligned_cols=57  Identities=12%  Similarity=0.111  Sum_probs=47.7

Q ss_pred             eeeeEEEEEecCCCceeEEEEEEccCcCccccc------------CcccccCCCCEEEEEEEEEeCCCCeEEE
Q 022938          195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQ------------DIRDILNEGDEVRVKVIKIDREKSRITL  255 (289)
Q Consensus       195 ~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~------------~~~~~~~iGd~V~vkV~~id~e~~ri~l  255 (289)
                      +++|+||+|. ..|   ++||+|.++|.+++..            +....|++||+|+|+|.++|+++++|.+
T Consensus        15 ~~~GifV~L~-e~~---~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r~I~~   83 (87)
T d2ix0a3          15 SRGGMRVRLV-DNG---AIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIA   83 (87)
T ss_dssp             ETTEEEEEET-TTC---CEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTTEEEE
T ss_pred             EcCeEEEEEe-cCC---cEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccCeEEE
Confidence            9999999995 133   9999999999987531            2345699999999999999999999864

>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=98.76  E-value=1.4e-08  Score=73.63  Aligned_cols=71  Identities=20%  Similarity=0.255  Sum_probs=56.7

Q ss_pred             cccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc----------cCcccccCCCCEEEEEEEEEeCCCCe
Q 022938          188 VEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI----------QDIRDILNEGDEVRVKVIKIDREKSR  252 (289)
Q Consensus       188 ~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~----------~~~~~~~~iGd~V~vkV~~id~e~~r  252 (289)
                      +|++++|     +++|+||+++  +    ++|++|.++|.+++.          .+....|++||.|++||+++|.++++
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg--~----~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~   76 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVG--P----MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSS   76 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET--T----EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTE
T ss_pred             CCCEEEEEEEEEEeeEEEEEEc--C----eEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccCc
Confidence            5788888     9999999995  2    899999999987743          34456799999999999999999999


Q ss_pred             EEEEEecCCCCchh
Q 022938          253 ITLSIKQLEEDPLL  266 (289)
Q Consensus       253 i~lSlK~~~~~p~~  266 (289)
                      |.. +..+ .+||.
T Consensus        77 i~~-ig~~-~~d~L   88 (91)
T d1y14b1          77 IHA-IGSI-KEDYL   88 (91)
T ss_dssp             EEE-EEEC-CSTTC
T ss_pred             cEE-EEEc-cCCCC
Confidence            965 4443 33454

>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=98.62  E-value=3.7e-08  Score=71.77  Aligned_cols=72  Identities=15%  Similarity=0.258  Sum_probs=56.9

Q ss_pred             cccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccc------------cCcccccCCCCEEEEEEEEEeCCC
Q 022938          188 VEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI------------QDIRDILNEGDEVRVKVIKIDREK  250 (289)
Q Consensus       188 ~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~------------~~~~~~~~iGd~V~vkV~~id~e~  250 (289)
                      .|++++|     +++|+||+++  +    ++|++|.++|.+++.            ++....|++||.|++||++++.+.
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg--~----~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~   77 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIG--P----MSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDK   77 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET--T----EEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEET
T ss_pred             CCCEEEEEEEEEEeeEEEEEec--C----ceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCc
Confidence            4778877     9999999995  2    899999999998752            234456999999999999999999


Q ss_pred             CeEEEEEecCCCCchhH
Q 022938          251 SRITLSIKQLEEDPLLE  267 (289)
Q Consensus       251 ~ri~lSlK~~~~~p~~~  267 (289)
                      ++|..-  ..-.+||++
T Consensus        78 ~~I~~i--gt~~~d~LG   92 (94)
T d2c35b1          78 NDIFAI--GSLMDDYLG   92 (94)
T ss_dssp             TEEEEE--EECCSTTCE
T ss_pred             CcceEE--EEccCCCcc
Confidence            999642  234556654

>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=98.51  E-value=1.4e-07  Score=65.74  Aligned_cols=64  Identities=22%  Similarity=0.317  Sum_probs=53.2

Q ss_pred             cCCCEEEEEEEEEEcCc----EEEEEC----CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCc-
Q 022938           98 ESGFIYEGKIQGFNGGG----LLVRFF----SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMK-  168 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G----~~V~l~----gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~-  168 (289)
                      +.|++++|+|..+....    ++|++|    +++|+||.+|+.       |.+.|+      .|++++|.|.+|+...+ 
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqi-------p~E~y~------~Gdrik~~i~~V~~~~kG   69 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV-------PGESYE------HGNRLRCYVVGVTRGARE   69 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC-------TTCCCC------TTCEEEEEEEEEECCSSS
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcC-------CCcccC------CCCEEEEEEEEEEecCCC
Confidence            58999999999998543    799996    499999999854       666665      99999999999987654 


Q ss_pred             -EEEEEe
Q 022938          169 -KLVFSE  174 (289)
Q Consensus       169 -ri~lS~  174 (289)
                       +|.||+
T Consensus        70 p~IilSR   76 (76)
T d2asba1          70 PLITLSR   76 (76)
T ss_dssp             CEEEEES
T ss_pred             CEEEEeC
Confidence             788885

>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=98.42  E-value=3.1e-07  Score=65.85  Aligned_cols=71  Identities=17%  Similarity=0.123  Sum_probs=59.9

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD  176 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~  176 (289)
                      +.|+++-|+|+++..++++|+++ ...|++|.++++..-  ++..+.++      +||.|.|+|.+++. .+++.||...
T Consensus         5 ~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~g~~--k~~r~~l~------~GD~V~arV~~v~~-~~~~~Lscvd   75 (88)
T d2nn6g1           5 VKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGAT--KRNRPNVQ------VGDLIYGQFVVANK-DMEPEMVCID   75 (88)
T ss_dssp             CSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCS--SCSSSSSC------TTCEEEEEEEECCT-TSCCEEECSB
T ss_pred             CCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcCccc--cccCcccC------CCCEEEEEEEEeCC-CCCEEEEEEc
Confidence            68999999999999999999999 899999999996532  45555555      99999999999984 5688888765


Q ss_pred             c
Q 022938          177 A  177 (289)
Q Consensus       177 ~  177 (289)
                      +
T Consensus        76 ~   76 (88)
T d2nn6g1          76 S   76 (88)
T ss_dssp             T
T ss_pred             c
Confidence            3

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

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

Probab=98.36  E-value=1.7e-07  Score=67.31  Aligned_cols=67  Identities=7%  Similarity=0.004  Sum_probs=58.2

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  260 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~  260 (289)
                      ++||+|.|     +.+++||+|+  .+   ..|++|.++++ ...++.+..+++||.|.|+|.++|+ .+++.||+...
T Consensus         5 ~~GD~ViG~V~~~~~~~~~VdI~--s~---~~a~L~~~~f~-g~~k~~r~~l~~GD~V~arV~~v~~-~~~~~Lscvd~   76 (88)
T d2nn6g1           5 VKGDHVIGIVTAKSGDIFKVDVG--GS---EPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVCIDS   76 (88)
T ss_dssp             CSSEEEEEEEEEEETTEEEEECS--SS---SCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCT-TSCCEEECSBT
T ss_pred             CCCCEEEEEEEEEeCCeEEEEcC--CC---eeEEEeHHHcC-ccccccCcccCCCCEEEEEEEEeCC-CCCEEEEEEcc
Confidence            67899988     8999999997  33   78999999985 4677888899999999999999997 68999998764

>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=98.14  E-value=3.4e-06  Score=60.53  Aligned_cols=72  Identities=15%  Similarity=0.081  Sum_probs=59.7

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEeec
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSEKD  176 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~k~  176 (289)
                      +.|+++-|+|+++...+.+|+++ ...|++|.++..+... ++....+.      +||.|.|+|.++|+ .+.+.||.+.
T Consensus         6 ~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g~~-k~~r~~l~------~GDlV~arV~~v~~-~~~~~Lsc~~   77 (90)
T d2ja9a1           6 SVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNAS-KKNRPTLQ------VGDLVYARVCTAEK-ELEAEIECFD   77 (90)
T ss_dssp             CTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCC-SSSCCCCC------TTCEEEEEEEECCT-TSCCEEESSC
T ss_pred             CCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCccc-cccCCccC------CCCEEEEEEEEECC-CCCEEEEEec
Confidence            68999999999999999999999 6899999877665554 55555555      99999999999985 5678888865


Q ss_pred             c
Q 022938          177 A  177 (289)
Q Consensus       177 ~  177 (289)
                      +
T Consensus        78 ~   78 (90)
T d2ja9a1          78 S   78 (90)
T ss_dssp             T
T ss_pred             c
Confidence            4

>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=98.12  E-value=1.3e-06  Score=62.76  Aligned_cols=68  Identities=15%  Similarity=0.085  Sum_probs=58.3

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  260 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~  260 (289)
                      ++||+|.|     ...+.||+|+.  .   ..|++|.++..+...++.+..|++||.|.|+|.++|+ ...+.||++..
T Consensus         6 ~~gD~ViG~V~~~~~~~~~vdI~~--~---~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~-~~~~~Lsc~~~   78 (90)
T d2ja9a1           6 SVNDFVIGVIIGTFSDSYKVSLQN--F---SSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEK-ELEAEIECFDS   78 (90)
T ss_dssp             CTTCEEEEEEEEECSSEEEEESST--T---SCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEESSCT
T ss_pred             CCCCEEEEEEEEEeCCcEEEEcCC--c---chhhhhhhhccCccccccCCccCCCCEEEEEEEEECC-CCCEEEEEecc
Confidence            67888888     88999999962  2   6788898888888888888999999999999999997 67899998653

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

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

Probab=97.85  E-value=4.1e-05  Score=52.26  Aligned_cols=58  Identities=19%  Similarity=0.128  Sum_probs=46.6

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCCe--EEEE
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKSR--ITLS  256 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~r--i~lS  256 (289)
                      ++|+++.|     .+..++|+++   +   .+|++|.++..      |.+.|++||.|+|.|.+++.+.+.  |.||
T Consensus         7 ~~geiv~G~V~r~~~~~~~Vdlg---~---~eaiLp~~eqi------p~E~~~~Gdrik~~i~~V~~~~kgpqI~lS   71 (72)
T d1hh2p1           7 LKGTVTTAEVIRVMGEWADIRIG---K---LETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVS   71 (72)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEET---T---EEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEE
T ss_pred             ccCcEEEEEEEEEcCCCEEEEEC---C---cEEECCHHHcC------CCCCCCCCCEEEEEEEEEEEcCCCCeEEEe
Confidence            67888888     6667899994   3   99999998865      568999999999999999865543  4444

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

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

Probab=97.73  E-value=2.9e-05  Score=58.94  Aligned_cols=73  Identities=21%  Similarity=0.231  Sum_probs=50.3

Q ss_pred             ccccEEEe-----eeeeEEEEEecCCC---ceeEEEEEEccCcCcc--cccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 022938          187 NVEDIFVG-----RDYGAFIHLRFPDG---LYHLTGLVHVSEVSWD--LIQDIRDILNEGDEVRVKVIKIDREKSRITLS  256 (289)
Q Consensus       187 ~~G~iv~G-----~~~G~fV~i~~~~G---~~~i~Glv~~sels~~--~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lS  256 (289)
                      ++|++|.|     ....++|+|...+|   .....|++|.+++...  ...++.+.|++||.|+|+|+++...+..+.||
T Consensus         6 ~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~~~~Ls   85 (125)
T d2nn6i1           6 DVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLT   85 (125)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEEE
T ss_pred             CCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCccEEEE
Confidence            45555555     55556666532111   0026688998888433  34568899999999999999998756679999


Q ss_pred             Eec
Q 022938          257 IKQ  259 (289)
Q Consensus       257 lK~  259 (289)
                      .++
T Consensus        86 t~~   88 (125)
T d2nn6i1          86 TAE   88 (125)
T ss_dssp             CCS
T ss_pred             ecC
Confidence            876

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

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

Probab=97.54  E-value=0.00016  Score=54.69  Aligned_cols=74  Identities=20%  Similarity=0.270  Sum_probs=57.6

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC---------CEEEEeecCCCCCCcc-CcCcccchhcccccCCCCEEEEEEEEEecCC
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF---------SLVGFLPFPQMSPSHS-CKEPQKSIHEIAKGLTGSIISVKVIQANEEM  167 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~---------gv~g~ip~sels~~~~-~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~  167 (289)
                      ++|+++.|+|+++....++|++.         ...|+++.++...... ..+..+.|+      +||.|+++|+++...+
T Consensus         6 ~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr------~GDiV~A~Vis~~~~~   79 (125)
T d2nn6i1           6 DVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFR------PGDIVLAKVISLGDAQ   79 (125)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCC------SSSEEEEEEEEEETTT
T ss_pred             CCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcC------CCCEEEEEEEEccCCC
Confidence            68999999999999999999983         3668899888743221 123444454      9999999999998666


Q ss_pred             cEEEEEeecc
Q 022938          168 KKLVFSEKDA  177 (289)
Q Consensus       168 ~ri~lS~k~~  177 (289)
                      ..+.||.+.+
T Consensus        80 ~~~~Lst~~~   89 (125)
T d2nn6i1          80 SNYLLTTAEN   89 (125)
T ss_dssp             TEEEEECCSS
T ss_pred             ccEEEEecCC
Confidence            6788998775

>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=97.30  E-value=0.00042  Score=47.52  Aligned_cols=57  Identities=14%  Similarity=0.240  Sum_probs=43.3

Q ss_pred             ccccEEEe----eee-----eEEEEEecCCCceeEEEEEEccCcCcccccCcccccCCCCEEEEEEEEEeCCCC
Q 022938          187 NVEDIFVG----RDY-----GAFIHLRFPDGLYHLTGLVHVSEVSWDLIQDIRDILNEGDEVRVKVIKIDREKS  251 (289)
Q Consensus       187 ~~G~iv~G----~~~-----G~fV~i~~~~G~~~i~Glv~~sels~~~~~~~~~~~~iGd~V~vkV~~id~e~~  251 (289)
                      ++|+++.|    .+.     -++|+|+...+  +++|++|.++.-      |.+.|++||.|+|.|.+++...+
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~--~~EaiLp~~eqi------p~E~y~~Gdrik~~i~~V~~~~k   68 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETK--ASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAR   68 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSS--CEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSS
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCC--CEEEECCHHHcC------CCcccCCCCEEEEEEEEEEecCC
Confidence            57899999    121     27999962112  399999998764      56899999999999999986543

>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=97.02  E-value=0.00078  Score=47.38  Aligned_cols=71  Identities=20%  Similarity=0.252  Sum_probs=47.9

Q ss_pred             CEEEEEEEEEEc--CcEEEEEC-CEEEEeecCCCCCCccCcCcc----cchhcccccCCCCEEEEEEEEEecCCcEEEEE
Q 022938          101 FIYEGKIQGFNG--GGLLVRFF-SLVGFLPFPQMSPSHSCKEPQ----KSIHEIAKGLTGSIISVKVIQANEEMKKLVFS  173 (289)
Q Consensus       101 ~iv~g~V~~v~~--~G~~V~l~-gv~g~ip~sels~~~~~~~p~----~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS  173 (289)
                      .|+.|+|.+|.+  .++||++| +-.||+|.+++...+...+..    ....  .....||.+-|.|.+=...++-..||
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~~~~~~~~~~~~~i~--~~l~~G~~ilVQV~Ke~~~~KGprlT   79 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIK--DVLREGQEVIVQIDKEERGNKGAALT   79 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGGCSSCCCSSSCCCGG--GTCCTTCEEEEEEEECCBTTBCCEEE
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccceeeeccccccccccchh--hhccCCCeEEEEEeecccCCCCceEE
Confidence            478999999998  58999999 999999999987654311110    0111  12349999999998544333333333

>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=94.38  E-value=0.061  Score=36.25  Aligned_cols=71  Identities=32%  Similarity=0.497  Sum_probs=52.1

Q ss_pred             cccccEEEe----eeeeEEEEEecCCCceeEEEEEEcc-CcCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEecC
Q 022938          186 VNVEDIFVG----RDYGAFIHLRFPDGLYHLTGLVHVS-EVSWDLIQDIRDILNEGDEVRVKVIKIDREKSRITLSIKQL  260 (289)
Q Consensus       186 ~~~G~iv~G----~~~G~fV~i~~~~G~~~i~Glv~~s-els~~~~~~~~~~~~iGd~V~vkV~~id~e~~ri~lSlK~~  260 (289)
                      -.+|++.+|    .++-++|.+-..+   +.++++--. ++.-++..++++.+ +|.+|+++|+.+|.-++-|.+..|..
T Consensus         6 PnigdVtkGiVy~kd~~fyV~L~dY~---g~ea~l~dy~~~~~d~~~klk~kL-VGKtIkvqVIR~d~lKGYIDVr~~~~   81 (85)
T d1luza_           6 PNAGDVIKGRVYEKDYALYIYLFDYP---HFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKRM   81 (85)
T ss_dssp             CCTTCEEEEEEEEETTEEEEEETTCT---TSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEEE
T ss_pred             CCCCceeeeEEEEeCCEEEEEecCCC---CceEEeeehhhhhhHHHHHHHHHh-cCceEEEEEEEEcceeeEEEehhhhh
Confidence            368999999    6666788884222   488887532 33333555666655 79999999999999999999998864

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=92.25  E-value=0.12  Score=35.57  Aligned_cols=58  Identities=26%  Similarity=0.434  Sum_probs=42.1

Q ss_pred             eeeeEEEEEecCCCceeEEEEEEccCcCcccc---------cCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 022938          195 RDYGAFIHLRFPDGLYHLTGLVHVSEVSWDLI---------QDIRDILNEGDEVRVKVIKIDREKSRITLSI  257 (289)
Q Consensus       195 ~~~G~fV~i~~~~G~~~i~Glv~~sels~~~~---------~~~~~~~~iGd~V~vkV~~id~e~~ri~lSl  257 (289)
                      .=.++||+++  .+   -.||+|.+++...+.         ....+.+++||.|-|.|.+=...++--.||.
T Consensus        14 gl~AAFVDiG--~~---k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~KGprlT~   80 (87)
T d1smxa_          14 SLEAAFVDYG--AE---RHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTT   80 (87)
T ss_dssp             GGTEEEEESS--SS---SCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTTBCCEEES
T ss_pred             CceEEEEEeC--CC---ccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecccCCCCceEEE
Confidence            4568999997  43   789999999876532         2456779999999999887554444445543

>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=89.97  E-value=0.19  Score=34.61  Aligned_cols=66  Identities=12%  Similarity=0.166  Sum_probs=46.1

Q ss_pred             hhhcccccccccEEEe----eeeeEEEEEecCCCceeEEEEEEc-cCcCcccccCcccccCCCCEEEEEEEEEeC
Q 022938          179 WNKYSSRVNVEDIFVG----RDYGAFIHLRFPDGLYHLTGLVHV-SEVSWDLIQDIRDILNEGDEVRVKVIKIDR  248 (289)
Q Consensus       179 ~~~~~~~~~~G~iv~G----~~~G~fV~i~~~~G~~~i~Glv~~-sels~~~~~~~~~~~~iGd~V~vkV~~id~  248 (289)
                      +.....++-+|++.+|    .++-++|.+-..+   +..+++-- -++.-++..++++.+ +|.+|+++|+.+|.
T Consensus        23 ~~~~~~~~~~G~V~kGiVy~rd~~fyV~L~dY~---g~eail~dY~n~~~dr~~klkkkL-VGKTIkVqVIRvDk   93 (102)
T d1jjga_          23 YRTSAMDLSPGSVHEGIVYFKDGIFKVRLLGYE---GHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADG   93 (102)
T ss_dssp             CSSCCCCCCSSCEEEEEEEEETTEEEEECTTTS---SCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECS
T ss_pred             eeeeecccCCCcEeeeEEEEeCCEEEEEecCCC---CceeeeeehhhhhHHHHHHHHHHh-cCceEEEEEEEecc
Confidence            3445667899999999    6666788874222   48888542 233444556666655 79999999999983

>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=89.34  E-value=0.66  Score=30.12  Aligned_cols=47  Identities=17%  Similarity=0.098  Sum_probs=38.1

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQA  163 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~v  163 (289)
                      ...|++=+|.+.+..+.|++|++| +--++|-- .                   +.+|+++.|+|.++
T Consensus         8 p~vGEiReG~~~rr~~~g~~vDiGlD~la~~k~-~-------------------~~~~~r~tfrIvs~   55 (71)
T d1k3ra1           8 PVTGEYRQGLTVKRVKKGTLVDIGADKLALCRE-K-------------------LTVNRIMSFRVVRL   55 (71)
T ss_dssp             CCTTCEEEEEEEEECSSSEEEESSSSCEEECSS-C-------------------CCSSCEEEEEEEEC
T ss_pred             CcccceeeEEEEEecCCcEEEEecCCceeeeec-c-------------------cccCcEEEEEEEEc
Confidence            368999999999999999999997 65555541 1                   12899999999987

>d1yvca1 b.40.4.12 (A:1-69) Hypothetical protein MMP0076 {Methanococcus maripaludis [TaxId: 39152]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: TRAM domain
domain: Hypothetical protein MMP0076
species: Methanococcus maripaludis [TaxId: 39152]

Probab=88.86  E-value=1  Score=29.14  Aligned_cols=48  Identities=38%  Similarity=0.526  Sum_probs=39.5

Q ss_pred             hcCCCEEEEEEEEEEcCcE-EEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEec
Q 022938           97 KESGFIYEGKIQGFNGGGL-LVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANE  165 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~-~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~  165 (289)
                      ++.|++++.+|.++...|- +.+++|..-|+|..                     .+|++|.++|.++.+
T Consensus        13 vk~g~~~~v~I~~l~~~G~Giar~~g~vvfV~~a---------------------lPGe~V~v~I~k~kk   61 (69)
T d1yvca1          13 VEAGKEYEVTIEDMGKGGDGIARIDGFVVFVPNA---------------------EKGSVINVKVTAVKE   61 (69)
T ss_dssp             SCTTCEEEEECCEECTTSCEEEEETTEEEEETTC---------------------CTTCEEEEEEEEECS
T ss_pred             CCCCCEEEEEEEECCCCCcEEEEECCEEEEeCCC---------------------CCCCEEEEEEEEecC
Confidence            4789999999999997764 67778888888832                     289999999998853

>d1yeza1 b.40.4.12 (A:1-68) Hypothetical protein MM1357 {Methanosarcina mazei [TaxId: 2209]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: TRAM domain
domain: Hypothetical protein MM1357
species: Methanosarcina mazei [TaxId: 2209]

Probab=88.39  E-value=1.7  Score=27.96  Aligned_cols=48  Identities=27%  Similarity=0.355  Sum_probs=39.7

Q ss_pred             hcCCCEEEEEEEEEEcCcE-EEEECCEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEec
Q 022938           97 KESGFIYEGKIQGFNGGGL-LVRFFSLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANE  165 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~-~V~l~gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~  165 (289)
                      .+.|+.++.+|.++...|- +..++|..-|+|..                     .+|++|.++|.++..
T Consensus        11 v~~g~~~~l~I~~l~~~G~Gi~~~~g~vvfV~ga---------------------lpGe~v~v~i~k~kk   59 (68)
T d1yeza1          11 VEEGEVYDVTIQDIARQGDGIARIEGFVIFVPGT---------------------KVGDEVRIKVERVLP   59 (68)
T ss_dssp             CCTTEEEEEECCEEETTTEEEEEETTEEEEEESC---------------------CTTCEEEEEEEEECS
T ss_pred             cCCCCEEEEEEEECCCCCcEEEEECCEEEEeCCC---------------------CCCCEEEEEEEEEeC
Confidence            4789999999999998775 66778999999833                     289999999998853

>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=83.64  E-value=2.5  Score=28.06  Aligned_cols=71  Identities=17%  Similarity=0.211  Sum_probs=48.1

Q ss_pred             cCCCEEEEEEEEEEcCcEEEEEC---CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEEEEecCCcEEEEEe
Q 022938           98 ESGFIYEGKIQGFNGGGLLVRFF---SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVIQANEEMKKLVFSE  174 (289)
Q Consensus        98 ~~G~iv~g~V~~v~~~G~~V~l~---gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl~vd~~~~ri~lS~  174 (289)
                      ..|++.+|.|. +.++-+.|.+.   |.++++--.- +..   .+.-+.+   .+-.+|.+|+++|..+|.-++-+-++-
T Consensus         7 nigdVtkGiVy-~kd~~fyV~L~dY~g~ea~l~dy~-~~~---~d~~~kl---k~kLVGKtIkvqVIR~d~lKGYIDVr~   78 (85)
T d1luza_           7 NAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESV-KMH---MDRYVEY---RDKLVGKTVKVKVIRVDYTKGYIDVNY   78 (85)
T ss_dssp             CTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGS-SCC---HHHHHHH---HHHHTTCEEEEEEEEEETTTTEEEEEE
T ss_pred             CCCceeeeEEE-EeCCEEEEEecCCCCceEEeeehh-hhh---hHHHHHH---HHHhcCceEEEEEEEEcceeeEEEehh
Confidence            58999999764 55666778875   6888875321 110   1111222   234499999999999999999888876


Q ss_pred             ec
Q 022938          175 KD  176 (289)
Q Consensus       175 k~  176 (289)
                      |.
T Consensus        79 ~~   80 (85)
T d1luza_          79 KR   80 (85)
T ss_dssp             EE
T ss_pred             hh
Confidence            64

>d2ix0a2 b.40.4.5 (A:4-82) 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=81.25  E-value=1  Score=30.07  Aligned_cols=49  Identities=20%  Similarity=0.164  Sum_probs=37.1

Q ss_pred             hcCCCEEEEEEEEEEcCcEEEEEC-CEEEEeecCCCCCCccCcCcccchhcccccCCCCEEEEEEE
Q 022938           97 KESGFIYEGKIQGFNGGGLLVRFF-SLVGFLPFPQMSPSHSCKEPQKSIHEIAKGLTGSIISVKVI  161 (289)
Q Consensus        97 ~~~G~iv~g~V~~v~~~G~~V~l~-gv~g~ip~sels~~~~~~~p~~~~~~~~~~~vG~~V~vkVl  161 (289)
                      ......++|++....++-.||... +-+-|||..+|....                -||+|.|+|.
T Consensus        13 ~~~~~~~~G~i~~~~~G~GFv~~d~~~DifI~~~~~~~A~----------------~GD~V~v~i~   62 (79)
T d2ix0a2          13 HSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVM----------------HGDRIIAVIH   62 (79)
T ss_dssp             HHTSCEEEEEEECCC--CEEEEEETTEEEEECHHHHTTCC----------------TTCEEEEEEE
T ss_pred             hhcCCEEEEEEEEeCCCcEEEEECCCCcEEECHHHHcCCC----------------CCCEEEEEEE
Confidence            467889999998887654577776 788999988875432                6999999985