Citrus Sinensis ID: 011538

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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-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480---
Protein Sequence
MQTPVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKEVHIIFLFILLFNKQYSVWFLVHLR
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccEEccccccccccccccccccccccccccccEEEEEcccccccccccccccccccccccccccccEEcccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEccEEEEEccccccccEEccccccccHHHHHHHHHHccccccccEEEEEEEEEcccccEEccccccccccccccccEEEEEEEEEcccccEEEEHHHHHHHHHHHHHHHHHHccccEEEEEEEEEEcEEEEEEccEEEEEcccccccccccccccccccccEEEEEEEEEEcccccEEEEHHHHHHHHccccccEEEEEEEEEcccEEEEEcccccccccEEEEccccccccccccccccccEEEEEEEEcccccEEEEEcccccccccccccccEEEEEEccEEEEEEccccEEEEEEc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEEEcccccccccEEEcccccccccccccccccccccEEEEccEEEEEcccccccccccccEccccccccccEcccEEEEcccccccccccccEEEEcccccHHHHHHHHHHHHHHcccccEEEEEEEEEEEEEEcccEEEEEcccccccEcHHHcccccccccEEEEEEccccEEEEEEEEcccccEEEEEEHHHHHHHHHHHHHHHHHcccccEEEEEEEEEEccEEEEEcccccccEEEEEcccEEEEEEEEEcccccEEEEcHHHHcccHHHHHHHHcccccEEEEEEEEEEccEEEEEcccccEEEEccccccccccccccEEEcccEEEEEEEEEccccccEEEEHHHHHHHHHcccccEEEEEEEEEccccEEEEEcccccEEEEEEEHccHHcccccccEEEcccEEEEEEEccccccEEEEEHHcccccHHHHHHHcccccEEcEEEEEEEEcEEEEEEEEc
Coil and Loop (DISEMBL)
MQTPVQACKSFTFtllnsapplstcsfvqngnakyplqqsrkfhSFAASFRFLRSThivfcsqkdvfddlssaqfpenveneglegneelellnkpnlvpisngvasevdkksekpdeeealapflkffkprdsaeeveeegsevgvsresidvddkvgedkvsveyyepkpgdFVIGVVVSgnenkldvNVGADLLGTmltkevlplYDKEMDFLLCDLKKDAEEFMVRgkmgivkdddaiamsggsgpgrpvveTGTVLFAEVLGrtlsgrpllsTRRLFRKMAWHRVRQIKQLnepievkftewntggllTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLRegtllegtvkkiypygaqirigdsnrsgllhisnmsrtRVTSVSDLLNEGERVKVLVVKSmfpdkislsiadlesepglfvsdkeVHIIFLFILLFNKQYSVWFLVHLR
Flexible Loop (DISEMBL)
MQTPVQACKSFTFtllnsapplSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVasevdkksekpdeeealapflkffkprDSAEeveeegsevgvsresidvddkvgeDKVSveyyepkpgdFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVlgrtlsgrpllstrRLFRKMAWHRVRQikqlnepievkftewntgGLLTRIEGLRAFlpkaellsrvnnftelkekvgrrMYVQItrinedtndliLSEREAWATLNlregtllegtvkkIYPYGAQIRIGDSNRSGLLHISNMSRTRVtsvsdllnegERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKEVHIIFLFILLFNKQYSVWFLVHLR
Low Complexity Region (SEG)
MQTPVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPenveneglegneelellnkpnlvpISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAeeveeegsevgvsresIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKEVHIIFLFILLFNKQYSVWFLVHLR
Disordered region (IsUnstruct)
******ACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDL********************************************************************************************VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA********RPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKEVHIIFLFILLFNKQYSVWFLVH**
Disordered Region (DISOPRED)
*******CKSFTFTLLNSAPPLSTCSFVQNG****************ASFRFLRSTHIVFCSQ****************************LL*************************************************************************YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKEVHIIFLFILLFNKQYSVWFLVHLR
Disordered Region (DISEMBL)
MQTPVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVA************EEALAPFLKFFKPR*****************ESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKEVHIIFLFILLFNKQYSVWFLVHLR
Disordered Region (DISPRO)
****VQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKEVHIIFLFILLFNKQYSVWFLVHLR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQTPVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKEVHIIFLFILLFNKQYSVWFLVHLR
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	483	2.2.26 [Sep-21-2011]
P73530	328	30S ribosomal protein S1	N/A	no	0.376	0.554	0.355	5e-21
P74142	305	30S ribosomal protein S1	N/A	no	0.457	0.724	0.303	8e-21
P29344	411	30S ribosomal protein S1,	N/A	no	0.356	0.418	0.320	2e-20
P46228	307	30S ribosomal protein S1	yes	no	0.378	0.596	0.367	4e-19
P51345	263	30S ribosomal protein S1,	N/A	no	0.322	0.593	0.315	1e-17
O33698	295	30S ribosomal protein S1	no	no	0.362	0.593	0.329	1e-17
Q1XDE2	263	30S ribosomal protein S1,	N/A	no	0.322	0.593	0.309	2e-16
O06147	481	30S ribosomal protein S1	yes	no	0.397	0.399	0.289	1e-13
O06000	382	30S ribosomal protein S1	yes	no	0.354	0.447	0.291	4e-13
P14129	568	30S ribosomal protein S1	yes	no	0.478	0.406	0.281	6e-13

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

 Score =  102 bits (255), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 69/194 (35%), Positives = 105/194 (54%), Gaps = 12/194 (6%)

Query: 272 GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR 331
           G+  LS RR+    AW RVRQ++  +  +       N GG L RIEGLR F+P + + +R
Sbjct: 93  GQLTLSIRRIEYMRAWERVRQLQAEDATVRSNVFATNRGGALVRIEGLRGFIPGSHISAR 152

Query: 332 VNNFTELKEK-VGRRMYVQITRINEDTNDLILSEREAWA--TLN-LREGTLLEGTVKKIY 387
                E KE  VG  + ++   ++E+ N L+LS R A     +N L    ++ G+V+ I 
Sbjct: 153 -----EAKEDLVGEDLPLKFLEVDEERNRLVLSHRRALVERKMNGLEVAQVVVGSVRGIK 207

Query: 388 PYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDKISLSIAD 446
           PYGA I IG    SGLLHIS +S   + +   + N  + +KV+++       +ISLS   
Sbjct: 208 PYGAFIDIG--GVSGLLHISEISHDHIDTPHSVFNVNDEIKVMIIDLDAERGRISLSTKQ 265

Query: 447 LESEPGLFVSDKEV 460
           LE EPG  + D+++
Sbjct: 266 LEPEPGAMLKDRDL 279

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

>sp|P74142|RS1B_SYNY3 30S ribosomal protein S1 homolog B OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=rps1b PE=3 SV=1

 Score =  102 bits (253), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 124/247 (50%), Gaps = 26/247 (10%)

Query: 229 VRGKMGIVKDDDAIAMSGGSGPG-RPVVETGTVLFAEVLG---------------RTLSG 272
           V GK+    ++      GG  PG  PV E G    AE+                 +   G
Sbjct: 32  VHGKICQHANEGVYVDFGGKSPGFVPVQELGLRPHAEIEDSFPLDSAWDFLVTSEQNDEG 91

Query: 273 RPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRV 332
           +  LS R+L  + +W  + ++++  + +E+  T  N GG++  +EGLR F+P++ L+ + 
Sbjct: 92  QVRLSRRQLQIQQSWENLAELEESGKTLEMVVTGTNKGGVVGDVEGLRGFIPRSHLMHKD 151

Query: 333 NNFTELKEKVGRRMYVQITRINEDTNDLILSER---EAWATLNLREGTLLEGTVKKIYPY 389
           N    +   VG+ +   I   N+D N L+L++R   +A +   +  G + EG V KI PY
Sbjct: 152 N----MDALVGQVLKAHILEANQDNNKLVLTQRRIQQAESMGKIAAGNIYEGKVAKIQPY 207

Query: 390 GAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDKISLSIADLE 448
           G  + I     +GLLH+S +S TRV S++ L   G+ + V V +   + ++ISLS   LE
Sbjct: 208 GVFVEI--EGVTGLLHVSQVSGTRVDSLNTLFAFGQAISVYVQEIDEYKNRISLSTRILE 265

Query: 449 SEPGLFV 455
           + PG  V
Sbjct: 266 TYPGELV 272

Binds mRNA.

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

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

 Score =  100 bits (250), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 58/181 (32%), Positives = 108/181 (59%), Gaps = 9/181 (4%)

Query: 275 LLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNN 334
           +LS R++  ++AW R RQ++  +  ++ K    N GG++  +EGLR F+P     S++++
Sbjct: 162 ILSLRQIQYELAWERCRQLQAEDVVVKGKIVGANKGGVVALVEGLRGFVP----FSQISS 217

Query: 335 FTELKEKVGRRMYVQITRINEDTNDLILSEREAWA--TLNLREGTLLEGTVKKIYPYGAQ 392
            +  +E + + + ++   ++E+ + L++S R+A A     L  G+++ GTV+ + PYGA 
Sbjct: 218 KSSAEELLEKEIPLKFVEVDEEQSRLVMSNRKAMADSQAQLGIGSVVTGTVQSLKPYGAF 277

Query: 393 IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDKISLSIADLESEP 451
           I IG  N  GLLH+S +S  RV+ ++ +L  G+ +KV+++       ++SLS   LE  P
Sbjct: 278 IDIGGIN--GLLHVSQISHDRVSDIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP 335

Query: 452 G 452
           G
Sbjct: 336 G 336

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|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 = 96.7 bits (239), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 71/193 (36%), Positives = 104/193 (53%), Gaps = 10/193 (5%)

Query: 272 GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR 331
           G+  LS RR+    AW RVRQ++  +  +  +    N GG L RIEGLR F+P + + +R
Sbjct: 94  GQLTLSIRRIEYMRAWERVRQLQTEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTR 153

Query: 332 VNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA--TLN-LREGTLLEGTVKKIYP 388
                  ++ VG  + ++   ++ED N L+LS R A     +N L  G ++ G V+ I P
Sbjct: 154 KAK----EDLVGEELPLKFLEVDEDRNRLVLSHRRALVERKMNRLEVGEVVVGAVRGIKP 209

Query: 389 YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDKISLSIADL 447
           YGA I IG    SGLLHIS +S   + +   + N  + VKV+++       +ISLS   L
Sbjct: 210 YGAFIDIGGV--SGLLHISEISHDHIETPHSVFNVNDEVKVMIIDLDAERGRISLSTKQL 267

Query: 448 ESEPGLFVSDKEV 460
           E EPG  V + EV
Sbjct: 268 EPEPGDMVRNPEV 280

Binds mRNA.

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

>sp|P51345|RR1_PORPU 30S ribosomal protein S1, chloroplastic OS=Porphyra purpurea GN=rps1 PE=3 SV=1

 Score = 91.7 bits (226), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 52/165 (31%), Positives = 93/165 (56%), Gaps = 9/165 (5%)

Query: 271 SGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS 330
           S + +LS RRL    AW R+RQ+   +  ++V+   +N GG++  +EG+  F+P + L  
Sbjct: 88  SRQLILSIRRLEYIRAWKRIRQLLAEDSLLDVRIKGFNKGGMIVNLEGISGFVPNSHL-- 145

Query: 331 RVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAW---ATLNLREGTLLEGTVKKIY 387
             NNF++      + + +++  + E +N+LILS R A    A+ NL  G ++EG + +I 
Sbjct: 146 --NNFSKNTSSTNKFIKLKLLNVEEKSNNLILSHRRALIAQASSNLIVGNIIEGVINQIT 203

Query: 388 PYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432
           PYG  I+ G  N  GL+HIS ++  +V  +      G+ +K +++
Sbjct: 204 PYGLFIKAG--NLKGLVHISEINVKQVERIPSQFKIGDTIKAVII 246

Porphyra purpurea (taxid: 2787)

>sp|O33698|RS1_SYNE7 30S ribosomal protein S1 OS=Synechococcus elongatus (strain PCC 7942) GN=rpsA PE=3 SV=1

 Score = 91.7 bits (226), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 61/185 (32%), Positives = 99/185 (53%), Gaps = 10/185 (5%)

Query: 272 GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR 331
           G+  +S R L  + AW RV ++++  + ++VK T  N GG+   +EGLRAF+P+    S 
Sbjct: 90  GQVTVSLRALALEQAWTRVAELQEGGQTVQVKVTGSNKGGVTADLEGLRAFIPR----SH 145

Query: 332 VNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLRE---GTLLEGTVKKIYP 388
           +N   +L    G+ + V    +N     L+LSER+A  T  +RE   G L+ G V  + P
Sbjct: 146 LNEKEDLDSLKGKTLTVAFLEVNRADKKLVLSERQAARTALVREIEVGQLINGKVTGLKP 205

Query: 389 YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDKISLSIADL 447
           +G  + +G +  + LL I+ +S+  V  V  +   G+ ++ LVV       +ISLS   L
Sbjct: 206 FGVFVDLGGA--TALLPINQISQKFVADVGAIFKIGDPIQALVVAIDNTKGRISLSTKVL 263

Query: 448 ESEPG 452
           E+ PG
Sbjct: 264 ENHPG 268

Binds mRNA.

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

>sp|Q1XDE2|RR1_PORYE 30S ribosomal protein S1, chloroplastic OS=Porphyra yezoensis GN=rps1 PE=3 SV=2

 Score = 87.8 bits (216), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/165 (30%), Positives = 92/165 (55%), Gaps = 9/165 (5%)

Query: 271 SGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS 330
           S + +LS RRL    AW R+RQ+   +  + V    +N GG++  +EG+  F+P + L  
Sbjct: 88  SKQLILSIRRLEYIRAWKRIRQLLAEDSLLNVMIKGFNKGGMIINLEGISGFVPNSHL-- 145

Query: 331 RVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAW---ATLNLREGTLLEGTVKKIY 387
              NF + ++   + + +++  + E +N+LILS R A    A+ NL  G ++EG + +I 
Sbjct: 146 --GNFQKSEQFNNKFIKLKLLNVEEKSNNLILSHRRALISQASSNLIVGNIIEGIINQIT 203

Query: 388 PYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432
           PYG  I++G  N  GL+HIS ++   +  +S     G+ +K +++
Sbjct: 204 PYGLFIKVG--NLKGLVHISEINIKNLEQISSQFKIGDTIKAVII 246

Porphyra yezoensis (taxid: 2788)

>sp|O06147|RS1_MYCTU 30S ribosomal protein S1 OS=Mycobacterium tuberculosis GN=rpsA PE=3 SV=1

 Score = 78.2 bits (191), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/211 (28%), Positives = 111/211 (52%), Gaps = 19/211 (9%)

Query: 254 VVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL 312
           VV  G  + A VL +    GR +LS +R   + AW  +  +K+ +E ++    E   GGL
Sbjct: 79  VVSVGDEVEALVLTKEDKEGRLILSKKRAQYERAWGTIEALKEKDEAVKGTVIEVVKGGL 138

Query: 313 LTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATL- 371
           +  I GLR FLP +  L  +    +L+  +G+ +  +I  ++++ N+++LS R AW    
Sbjct: 139 ILDI-GLRGFLPAS--LVEMRRVRDLQPYIGKEIEAKIIELDKNRNNVVLS-RRAWLEQT 194

Query: 372 ----------NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLL 421
                     NL++GT+ +G V  I  +GA + +G  +  GL+H+S +S   +   S+++
Sbjct: 195 QSEVRSEFLNNLQKGTIRKGVVSSIVNFGAFVDLGGVD--GLVHVSELSWKHIDHPSEVV 252

Query: 422 NEGERVKVLVVK-SMFPDKISLSIADLESEP 451
             G+ V V V+   M  +++SLS+   + +P
Sbjct: 253 QVGDEVTVEVLDVDMDRERVSLSLKATQEDP 283

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

Mycobacterium tuberculosis (taxid: 1773)

>sp|O06000|RS1H_BACC1 30S ribosomal protein S1 homolog OS=Bacillus cereus (strain ATCC 10987) GN=BCE_1625 PE=3 SV=1

 Score = 76.6 bits (187), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 55/189 (29%), Positives = 106/189 (56%), Gaps = 18/189 (9%)

Query: 275 LLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVN 333
           +LS R +  + AW  +++        +V   +   GGL+  + G+R F+P + + +  V 
Sbjct: 81  VLSKRAVDAEKAWIELQEKFTSGHVFDVTVKDIVNGGLVVDL-GVRGFIPASLVEVHYVE 139

Query: 334 NFTELKEKVGRRMYVQITRINEDTNDLILSER----------EAWATLNLREGTLLEGTV 383
           +FT+ K   G+ + V+I  ++ + N +ILS +          +  A  +L+EG ++EGTV
Sbjct: 140 DFTDYK---GKTLAVKIVELDREKNRVILSHKAVVELELDSKKKEAISSLKEGDVVEGTV 196

Query: 384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLS 443
           +++  +GA + +G  +  GL+HIS +S  RV   S++L +G++VKV V+ S+  D   +S
Sbjct: 197 QRLTDFGAFVNVGGVD--GLVHISQISHERVEQPSEVLEQGQKVKVKVL-SVDADTQRIS 253

Query: 444 IADLESEPG 452
           ++   ++PG
Sbjct: 254 LSIKAAQPG 262

Bacillus cereus (strain ATCC 10987) (taxid: 222523)

>sp|P14129|RS1_RHIME 30S ribosomal protein S1 OS=Rhizobium meliloti (strain 1021) GN=rpsA PE=3 SV=2

 Score = 75.9 bits (185), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 75/266 (28%), Positives = 130/266 (48%), Gaps = 35/266 (13%)

Query: 212 EMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR-PVVETGTV---------- 260
           E  F   DL   AE ++ +G +  ++ D AI   G    GR P+ E G            
Sbjct: 16  EESFAKTDL---AEGYVAKGIVTAIEKDVAIVDVGLKVEGRVPLKEFGAKAKDGTLKVGD 72

Query: 261 ---LFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE 317
              ++ E +   L G  +LS  +  R+ +W R+    +  E +E        GG    ++
Sbjct: 73  EVEVYVERIENAL-GEAVLSREKARREESWQRLEVKFEAGERVEGIIFNQVKGGFTVDLD 131

Query: 318 GLRAFLPKAELLSR-VNNFTELKEKVGRRMYVQITRINEDTNDLILSER----EAWA--- 369
           G  AFLP++++  R + + T L          +I ++++   ++++S R    E+ A   
Sbjct: 132 GAVAFLPRSQVDIRPIRDVTPLMHN---PQPFEILKMDKRRGNIVVSRRTVLEESRAEQR 188

Query: 370 ---TLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGER 426
                NL EG ++EG VK I  YGA + +G  +  GLLH+++M+  RV   S++LN G++
Sbjct: 189 SEIVQNLEEGQVVEGVVKNITDYGAFVDLGGID--GLLHVTDMAWRRVNHPSEILNIGQQ 246

Query: 427 VKVLVVK-SMFPDKISLSIADLESEP 451
           VKV +++ +    +ISL +  LES+P
Sbjct: 247 VKVQIIRINQETHRISLGMKQLESDP 272

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

Rhizobium meliloti (strain 1021) (taxid: 266834)

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	483
255572295	476	conserved hypothetical protein [Ricinus	0.834	0.846	0.761	1e-175
359495207	513	PREDICTED: uncharacterized protein LOC10	0.898	0.846	0.692	1e-169
449446381	530	PREDICTED: 30S ribosomal protein S1 homo	0.840	0.766	0.735	1e-168
449527959	529	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.838	0.765	0.699	1e-157
297739376	435	unnamed protein product [Vitis vinifera]	0.741	0.822	0.754	1e-156
356534027	513	PREDICTED: uncharacterized protein LOC10	0.853	0.803	0.670	1e-148
297839005	501	predicted protein [Arabidopsis lyrata su	0.801	0.772	0.658	1e-146
334183835	500	small subunit ribosomal protein S1 [Arab	0.801	0.774	0.659	1e-145
224066601	486	predicted protein [Populus trichocarpa]	0.836	0.831	0.591	1e-141
422778917	487	plastid S1 binding domain protein precur	0.774	0.767	0.642	1e-137

>gi|255572295|ref|XP_002527086.1| conserved hypothetical protein [Ricinus communis] gi|223533509|gb|EEF35249.1| conserved hypothetical protein [Ricinus communis]

 Score =  620 bits (1600), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 309/406 (76%), Positives = 358/406 (88%), Gaps = 3/406 (0%)

Query: 55  STHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVASEVDKKSE 114
           ST I FCSQ D FD+LSS Q PE  E + +  NEELELLNKP+ V I+NG++ EVDK+SE
Sbjct: 19  STQISFCSQNDTFDNLSSTQVPEEQEEDRIRENEELELLNKPSPVVINNGLSIEVDKESE 78

Query: 115 KPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGE-DKVSVEYYEPKPG 173
             D++EALAPFLKFF+PRDS EE++EEG E+GV   + + +++  E  KV+V+YYEPKPG
Sbjct: 79  TIDKDEALAPFLKFFEPRDSLEEIKEEGKELGVIEGNSNGNNEDKEAKKVNVDYYEPKPG 138

Query: 174 DFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKM 233
           DFV+GVVVSGNE+KLDVNVGADLLGTMLTKEVLPLYDKEM++LLCD++KDAE FMVRGK+
Sbjct: 139 DFVVGVVVSGNESKLDVNVGADLLGTMLTKEVLPLYDKEMEYLLCDMEKDAERFMVRGKI 198

Query: 234 GIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQI 293
           GI+KD+   AMSGG G GRPVVETGT+LFAEVLGRTLSGRPLLSTRRLFR++AWHRVRQI
Sbjct: 199 GIIKDE--AAMSGGPGLGRPVVETGTILFAEVLGRTLSGRPLLSTRRLFRRIAWHRVRQI 256

Query: 294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRI 353
           K+LNEPIEV+ TEWNTGGLLTRIEGLRAFLPKAEL++RV NF ELKE V RR+ V ITRI
Sbjct: 257 KELNEPIEVRITEWNTGGLLTRIEGLRAFLPKAELMNRVKNFKELKENVSRRINVLITRI 316

Query: 354 NEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR 413
           NED N+LILSEREAW  LNLREGTLLEG V+KI+PYGAQ+RIG++NRSGLLHISN++R+R
Sbjct: 317 NEDNNELILSEREAWEMLNLREGTLLEGNVRKIFPYGAQVRIGETNRSGLLHISNITRSR 376

Query: 414 VTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKE 459
           VT+VSDLL   ERVKVLVVKSMFPDKISLSIADLESEPGLFVS+KE
Sbjct: 377 VTAVSDLLKVDERVKVLVVKSMFPDKISLSIADLESEPGLFVSNKE 422

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359495207|ref|XP_002263508.2| PREDICTED: uncharacterized protein LOC100240915 [Vitis vinifera]

 Score =  599 bits (1545), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 318/459 (69%), Positives = 370/459 (80%), Gaps = 25/459 (5%)

Query: 10  SFTFTLLNSAPPL-STCSFVQNGNA-KYPLQ--QSRKFHSFAASFRFLRSTHIVFCSQKD 65
           SF F+   S PPL S  SF    N  K PL+  QS+   S   S    R+T I FCS  D
Sbjct: 13  SFRFS---SHPPLNSNISFTSFHNTPKLPLRKPQSKTLVSPKNS-PVWRTTQISFCSPND 68

Query: 66  VFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVASEVDKKSEKPDEEEALAPF 125
           +F D+SS Q PE  E +G++  EELELL KP+ VP++NG AS++D + +KPD++EALAPF
Sbjct: 69  IFYDISSTQLPETPEIDGVQDIEELELLGKPSPVPLNNGSASDIDSELKKPDKDEALAPF 128

Query: 126 LKFFKPRDSAEEVE----EEGSEVGVSRESIDVDDKVGEDK-VSVEYYEPKPGDFVIGVV 180
           LKFFKPR+S+EE      E+GSE+  S          G  K VSVEYYEPKPGDFV+GVV
Sbjct: 129 LKFFKPRESSEEANGASGEDGSEISES----------GSTKLVSVEYYEPKPGDFVVGVV 178

Query: 181 VSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDD 240
           VSGNENKLDVNVGADLLGTMLTKEVLPLYDKEM++LLCD++KDAEEFMV GKM IV++DD
Sbjct: 179 VSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMEYLLCDVEKDAEEFMVHGKMSIVRNDD 238

Query: 241 AIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPI 300
           A++     G   PVVETGTVLFAEVLGRTLSGRPLLSTRR FR++AWHRVRQIKQLNEPI
Sbjct: 239 ALSRVPMQG--SPVVETGTVLFAEVLGRTLSGRPLLSTRRFFRRIAWHRVRQIKQLNEPI 296

Query: 301 EVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDL 360
           EV+ TEWNTGGLLTRIEGLRAFLPKAELL+RV +FTELKE VGRR+YVQITRI+E  NDL
Sbjct: 297 EVRITEWNTGGLLTRIEGLRAFLPKAELLNRVKSFTELKENVGRRLYVQITRIDEAKNDL 356

Query: 361 ILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDL 420
           ILSE++AW   +L+EGTLLEGTVKKI+PYGAQI IG+SNRSGLLHISN++R RVTSVSDL
Sbjct: 357 ILSEKDAWEKSHLQEGTLLEGTVKKIFPYGAQIMIGESNRSGLLHISNITRARVTSVSDL 416

Query: 421 LNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKE 459
           L   E+VKV+VVKSMFP+KI+LSIADLESEPGLF+S+KE
Sbjct: 417 LTVDEKVKVMVVKSMFPNKIALSIADLESEPGLFLSNKE 455

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446381|ref|XP_004140950.1| PREDICTED: 30S ribosomal protein S1 homolog A-like [Cucumis sativus]

 Score =  598 bits (1542), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 301/409 (73%), Positives = 354/409 (86%), Gaps = 3/409 (0%)

Query: 52  FLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVASEVDK 111
           F R + ++FCS+ D+FD+LSS Q P+    +G++  +E+ LLNKP+  PISNGV+SE+D+
Sbjct: 71  FRRRSSVLFCSRNDIFDNLSSTQLPDKPRVDGIQEIDEIGLLNKPSPAPISNGVSSEIDQ 130

Query: 112 KSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVG-EDKVSVEYYEP 170
           + E PDE EALAPF+KFFK +DSA+E EEE   +    E+ID DD+    +K++VEYYEP
Sbjct: 131 EVENPDENEALAPFMKFFKNKDSADEKEEEERALRAFEETIDGDDETEIANKLNVEYYEP 190

Query: 171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVR 230
           KPGD V+GVVVSGNENKLD+NVGADLLGTMLTKEVLPLYDKEM+ L CDL KDAE FM+ 
Sbjct: 191 KPGDVVVGVVVSGNENKLDINVGADLLGTMLTKEVLPLYDKEMESLTCDLDKDAESFMMN 250

Query: 231 GKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRV 290
           GKMG+VK +DA   S G GPGRPVVE GTVLFAEVLGRTLSGRPLLSTRRLFR++AWHRV
Sbjct: 251 GKMGLVKYEDA--FSRGQGPGRPVVENGTVLFAEVLGRTLSGRPLLSTRRLFRRLAWHRV 308

Query: 291 RQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQI 350
           RQIK L+EPIEVK +EWNTGGLLTRIEGLRAFLPKAELL+RVNNFTELKE VGRR++VQI
Sbjct: 309 RQIKGLDEPIEVKISEWNTGGLLTRIEGLRAFLPKAELLNRVNNFTELKENVGRRIFVQI 368

Query: 351 TRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS 410
           TR++E  NDLILSE++AW TL LREGTLLEGTVKKI+PYGAQIRIGD+NRSGLLH+SN++
Sbjct: 369 TRMDEAKNDLILSEKQAWETLYLREGTLLEGTVKKIFPYGAQIRIGDTNRSGLLHVSNIT 428

Query: 411 RTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKE 459
           R RVTSVSDLL+ GE+V VLVVKSMFPDKISLSIADLESEPGLF+++KE
Sbjct: 429 RARVTSVSDLLSVGEKVNVLVVKSMFPDKISLSIADLESEPGLFITNKE 477

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449527959|ref|XP_004170975.1| PREDICTED: LOW QUALITY PROTEIN: uncharacterized protein LOC101224960 [Cucumis sativus]

 Score =  561 bits (1445), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 286/409 (69%), Positives = 342/409 (83%), Gaps = 4/409 (0%)

Query: 52  FLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVASEVDK 111
           F R + ++FCS+ D+FD+LSS Q P+    +G++  +E+ LLNKP+  PISNGV+SE+D+
Sbjct: 71  FRRRSSVLFCSRNDIFDNLSSTQLPDKPRVDGIQEIDEIGLLNKPSPAPISNGVSSEIDQ 130

Query: 112 KSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVG-EDKVSVEYYEP 170
           + E PDE EALAPF+KFFK +DSA+E EEE   +    E+ID DD+    +K++VEYYEP
Sbjct: 131 EVENPDENEALAPFMKFFKNKDSADEKEEEERALRAFEETIDGDDETEIANKLNVEYYEP 190

Query: 171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVR 230
           KPGD V+GVVVSGNEN   ++     +   + KEVLPLYDKEM+ L CDL KDAE FM+ 
Sbjct: 191 KPGDVVVGVVVSGNENSW-ISTWGGFVRNNVDKEVLPLYDKEMESLTCDLDKDAESFMMN 249

Query: 231 GKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRV 290
           GKMG+VK +DA   S G GPGRPVVE GTVLFAEVLGRTLSGRPLLSTRRLFR++AWHRV
Sbjct: 250 GKMGLVKYEDA--FSRGQGPGRPVVENGTVLFAEVLGRTLSGRPLLSTRRLFRRLAWHRV 307

Query: 291 RQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQI 350
           RQIK L+EPIEVK +EWNTGGLLTRIEGLRAFLPKAELL+RVNNFTELKE VGRR++VQI
Sbjct: 308 RQIKGLDEPIEVKISEWNTGGLLTRIEGLRAFLPKAELLNRVNNFTELKENVGRRIFVQI 367

Query: 351 TRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS 410
           TR++E  NDLILSE++AW TL LREGTLLEGTVKKI+PYGAQIRIGD+NRSGLLH+SN++
Sbjct: 368 TRMDEAKNDLILSEKQAWETLYLREGTLLEGTVKKIFPYGAQIRIGDTNRSGLLHVSNIT 427

Query: 411 RTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKE 459
           R RVTSVSDLL+ GE+V VLVVKSMFPDKISLSIADLESEPGLF+++KE
Sbjct: 428 RARVTSVSDLLSVGEKVNVLVVKSMFPDKISLSIADLESEPGLFITNKE 476

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297739376|emb|CBI29366.3| unnamed protein product [Vitis vinifera]

 Score =  556 bits (1434), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 283/375 (75%), Positives = 325/375 (86%), Gaps = 17/375 (4%)

Query: 90  LELLNKPNLVPISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVE----EEGSEV 145
           LELL KP+ VP++NG AS++D + +KPD++EALAPFLKFFKPR+S+EE      E+GSE+
Sbjct: 15  LELLGKPSPVPLNNGSASDIDSELKKPDKDEALAPFLKFFKPRESSEEANGASGEDGSEI 74

Query: 146 GVSRESIDVDDKVGEDK-VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKE 204
             S          G  K VSVEYYEPKPGDFV+GVVVSGNENKLDVNVGADLLGTMLTKE
Sbjct: 75  SES----------GSTKLVSVEYYEPKPGDFVVGVVVSGNENKLDVNVGADLLGTMLTKE 124

Query: 205 VLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAE 264
           VLPLYDKEM++LLCD++KDAEEFMV GKM IV++DDA  +S     G PVVETGTVLFAE
Sbjct: 125 VLPLYDKEMEYLLCDVEKDAEEFMVHGKMSIVRNDDA--LSRVPMQGSPVVETGTVLFAE 182

Query: 265 VLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLP 324
           VLGRTLSGRPLLSTRR FR++AWHRVRQIKQLNEPIEV+ TEWNTGGLLTRIEGLRAFLP
Sbjct: 183 VLGRTLSGRPLLSTRRFFRRIAWHRVRQIKQLNEPIEVRITEWNTGGLLTRIEGLRAFLP 242

Query: 325 KAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVK 384
           KAELL+RV +FTELKE VGRR+YVQITRI+E  NDLILSE++AW   +L+EGTLLEGTVK
Sbjct: 243 KAELLNRVKSFTELKENVGRRLYVQITRIDEAKNDLILSEKDAWEKSHLQEGTLLEGTVK 302

Query: 385 KIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI 444
           KI+PYGAQI IG+SNRSGLLHISN++R RVTSVSDLL   E+VKV+VVKSMFP+KI+LSI
Sbjct: 303 KIFPYGAQIMIGESNRSGLLHISNITRARVTSVSDLLTVDEKVKVMVVKSMFPNKIALSI 362

Query: 445 ADLESEPGLFVSDKE 459
           ADLESEPGLF+S+KE
Sbjct: 363 ADLESEPGLFLSNKE 377

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356534027|ref|XP_003535559.1| PREDICTED: uncharacterized protein LOC100820145 [Glycine max]

 Score =  532 bits (1371), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 293/437 (67%), Positives = 341/437 (78%), Gaps = 25/437 (5%)

Query: 36  PLQQSRKFHSFAASFRF-------------LRSTHIVFCSQKDVFDDLSSAQFPENVENE 82
           P +   KF SFA    +             L  TH    S+ D FD  S+    ++  ++
Sbjct: 37  PRKNPTKFRSFAKVVLYTPRASIVSKKDPILGYTHFTLRSRSDGFDGFSTDVSQDDGTSQ 96

Query: 83  GLEGNEELELLNKPNLVPISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEG 142
            LE   +LELLNKP+ V ++   +SEV+ + EKP +EEALAPFLKFFK +DS +EVEE+G
Sbjct: 97  ELE---QLELLNKPSPVLVTEESSSEVEVEEEKPSKEEALAPFLKFFKGKDSGQEVEEDG 153

Query: 143 SEVGVSRESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLT 202
             +    E  D        KVSVEYYEPKPGDFV+GVVVSGNENKLDVNVGADLLGTMLT
Sbjct: 154 EGLEGENEEGD-------KKVSVEYYEPKPGDFVVGVVVSGNENKLDVNVGADLLGTMLT 206

Query: 203 KEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLF 262
           KEVLPLY KEM+ LLCD+ KDAE+FMV GKMGIVK+++AI  SG   PGRPV+E GT+LF
Sbjct: 207 KEVLPLYGKEMENLLCDVDKDAEDFMVNGKMGIVKNEEAI--SGVPVPGRPVLEIGTILF 264

Query: 263 AEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAF 322
           AEVLGRTLSGRPLLSTRRLFR++AWHRVRQIKQLNEPIEV+ TEWNTGGLLTRIEGLRAF
Sbjct: 265 AEVLGRTLSGRPLLSTRRLFRRIAWHRVRQIKQLNEPIEVRITEWNTGGLLTRIEGLRAF 324

Query: 323 LPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGT 382
           LPKAEL+ R N+FTELKE VG RMYVQIT+I+E  N+LILSEREAW  L LREGTLL+GT
Sbjct: 325 LPKAELVKRANSFTELKENVGCRMYVQITQIDETKNNLILSEREAWQKLYLREGTLLDGT 384

Query: 383 VKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL 442
           VKKI PYGAQI++G +NRSGLLH+SN+SR  VTSVS++L+  E VK LVVKSMFPDKISL
Sbjct: 385 VKKILPYGAQIKLGKTNRSGLLHVSNISRAEVTSVSNILSVDENVKALVVKSMFPDKISL 444

Query: 443 SIADLESEPGLFVSDKE 459
           SIADLESEPGLF+S+KE
Sbjct: 445 SIADLESEPGLFLSNKE 461

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297839005|ref|XP_002887384.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297333225|gb|EFH63643.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  525 bits (1352), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 278/422 (65%), Positives = 327/422 (77%), Gaps = 35/422 (8%)

Query: 42  KFHSFAASFRF-LRSTH-IVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLV 99
           +F SFA    F  R  + I FCS++DV            VEN G+   EELELLNKP+ V
Sbjct: 56  RFRSFAICRDFATRGAYGIRFCSREDV----------SGVENGGIVAEEELELLNKPSPV 105

Query: 100 PISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVG 159
           P      SE +K++ K D++E L PFLKFFKP    E +E E                  
Sbjct: 106 P-----KSENEKENGKADDDEILEPFLKFFKPEGEGEGIEAEEET--------------- 145

Query: 160 EDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCD 219
            D+VSVEYY+PKPGDFV+GVVVSGNENKLDV++GAD+LGTMLTKE+LPLYDKE+D+LLCD
Sbjct: 146 -DRVSVEYYDPKPGDFVVGVVVSGNENKLDVSIGADMLGTMLTKEILPLYDKELDYLLCD 204

Query: 220 LKKDAEEFMVRGKMGIVKDDD--AIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLS 277
           LK DAEEF+V GKMGI KDDD   + ++  +  GRPVVE GTV+FAEVLGRTLSGRPLLS
Sbjct: 205 LKYDAEEFLVNGKMGIFKDDDDEGVEIAEFARQGRPVVEIGTVVFAEVLGRTLSGRPLLS 264

Query: 278 TRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTE 337
           +RR FR+++WHRVRQIKQ+NEPIEVK TEWNTGGLLTRIEGLRAF+PK EL+ +VNNFTE
Sbjct: 265 SRRYFRRISWHRVRQIKQVNEPIEVKITEWNTGGLLTRIEGLRAFIPKQELVKKVNNFTE 324

Query: 338 LKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGD 397
           LKE VGRR+ VQITR+NED NDLILSE+ AW  L LREGTLLEGTV KI PYGAQ+++GD
Sbjct: 325 LKENVGRRLLVQITRLNEDKNDLILSEKVAWEKLYLREGTLLEGTVAKILPYGAQVKLGD 384

Query: 398 SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSD 457
           S+RSGLLHISN++R R+ SVSD+L   E VKVLVVKS+FPDKISLSIADLESEPGLF+SD
Sbjct: 385 SSRSGLLHISNITRRRIGSVSDVLQVDESVKVLVVKSLFPDKISLSIADLESEPGLFISD 444

Query: 458 KE 459
           +E
Sbjct: 445 RE 446

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334183835|ref|NP_177317.2| small subunit ribosomal protein S1 [Arabidopsis thaliana] gi|7239499|gb|AAF43225.1|AC012654_9 Contains S1 RNA binding domain PF|00575. EST gb|AI997850 comes from this gene [Arabidopsis thaliana] gi|332197102|gb|AEE35223.1| small subunit ribosomal protein S1 [Arabidopsis thaliana]

 Score =  521 bits (1342), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 277/420 (65%), Positives = 325/420 (77%), Gaps = 33/420 (7%)

Query: 43  FHSFAASFRF-LRSTH-IVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVP 100
           F  F+    F +R  + I FCS++DV            V N G+   EE+ELLNKPN +P
Sbjct: 56  FRGFSICREFAVRGAYGIRFCSREDV----------SGVGNGGIVAEEEIELLNKPNPLP 105

Query: 101 ISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGE 160
            S       +++S K D++  L PFLKFFKP +  E       E  VS E+         
Sbjct: 106 KSE------NEESGKADDDAILEPFLKFFKPEEEGEG-----IESEVSDET--------- 145

Query: 161 DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDL 220
           D+VSVEYY+PKPGDFV+GVVVSGNENKLDVN+GAD+LGTMLTKE+LPLYDKE+D+LLCDL
Sbjct: 146 DRVSVEYYDPKPGDFVVGVVVSGNENKLDVNIGADMLGTMLTKEILPLYDKELDYLLCDL 205

Query: 221 KKDAEEFMVRGKMGIVKDDD-AIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTR 279
           K DAEEF+V GKMGIVKDDD  + ++  +  GRPVVE GTV+FAEVLGRTLSGRPLLS+R
Sbjct: 206 KYDAEEFLVNGKMGIVKDDDEGVEIAEFARQGRPVVEIGTVVFAEVLGRTLSGRPLLSSR 265

Query: 280 RLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELK 339
           R FR++AWHRVRQIKQLNEPIEVK TEWNTGGLLTRIEGLRAF+PK EL+ +VN FTELK
Sbjct: 266 RYFRRIAWHRVRQIKQLNEPIEVKITEWNTGGLLTRIEGLRAFIPKQELVKKVNTFTELK 325

Query: 340 EKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSN 399
           E VGRR  VQITR+NED NDLILSE+ AW  L LREGTLLEGTV KI PYGAQ+++GDS+
Sbjct: 326 ENVGRRFLVQITRLNEDKNDLILSEKVAWEKLYLREGTLLEGTVVKILPYGAQVKLGDSS 385

Query: 400 RSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKE 459
           RSGLLHISN++R R+ SVSD+L   E VKVLVVKS+FPDKISLSIADLESEPGLF+SD+E
Sbjct: 386 RSGLLHISNITRRRIGSVSDVLQVDESVKVLVVKSLFPDKISLSIADLESEPGLFISDRE 445

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224066601|ref|XP_002302157.1| predicted protein [Populus trichocarpa] gi|222843883|gb|EEE81430.1| predicted protein [Populus trichocarpa]

 Score =  509 bits (1312), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 282/477 (59%), Positives = 336/477 (70%), Gaps = 73/477 (15%)

Query: 5   VQACKSFTFTLLNSAPPLSTCSFV---------QNGNAKYPLQQSRKFHSFAA------- 48
           +Q CKS T  L + + P +T S V          N  AK P      FHSF +       
Sbjct: 6   LQPCKSLT--LFSYSLPSNTDSLVITHKRSIVHHNKCAKPPC-----FHSFCSLGTLKAI 58

Query: 49  ----SFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNG 104
               + +  +S+ +  CSQ DVFDD SS Q PE   ++ ++ NEELELLNKP+ V  +NG
Sbjct: 59  FLSKNSQLWKSSLVTLCSQNDVFDDFSSTQLPEKERDDRIQVNEELELLNKPSPVIFNNG 118

Query: 105 VASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGED-KV 163
           +  E DK+SEKP ++EALAPFLKFFK  DS +EV E+  ++GV  E   VD++  E  K+
Sbjct: 119 LDVEADKESEKPGKDEALAPFLKFFKSNDSLDEVSEDERDLGVVEERSGVDNEDKEPRKI 178

Query: 164 SVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKD 223
           +V+YYEPKPGDFV+GVVVSGNENKLDVN+GADLLGTMLTKEVLPLYDKEM+FLLCD KKD
Sbjct: 179 NVDYYEPKPGDFVVGVVVSGNENKLDVNIGADLLGTMLTKEVLPLYDKEMEFLLCDTKKD 238

Query: 224 AEEFMVRGKMGIVKDDDAIAMS-GGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLF 282
            +EFMV+GKMGIVKD+  +AMS G  G G+PVVETGTVLF+EVLGRTLSGRPLLSTRRLF
Sbjct: 239 VKEFMVKGKMGIVKDE--VAMSPGPPGLGKPVVETGTVLFSEVLGRTLSGRPLLSTRRLF 296

Query: 283 RKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKV 342
           R++AW RVRQ                         GLRAFLPKAEL++RVNNF ELKE V
Sbjct: 297 RRLAWQRVRQ-------------------------GLRAFLPKAELMNRVNNFKELKENV 331

Query: 343 GRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSG 402
           GR++YV I RINE  N+LILSEREAW  +NLREGTLLEGTVKK++PYGAQ+RIG++NRS 
Sbjct: 332 GRQIYVLIKRINESNNELILSEREAWEMINLREGTLLEGTVKKLFPYGAQVRIGETNRSD 391

Query: 403 LLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKE 459
           LL +                  E+VKVLV KSMFPDKISLSIADLESEPGLFVS+KE
Sbjct: 392 LLKVD-----------------EKVKVLVAKSMFPDKISLSIADLESEPGLFVSNKE 431

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|422778917|gb|AFX82591.1| plastid S1 binding domain protein precursor [Arabidopsis thaliana]

 Score =  496 bits (1277), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 270/420 (64%), Positives = 317/420 (75%), Gaps = 46/420 (10%)

Query: 43  FHSFAASFRF-LRSTH-IVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVP 100
           F  F+    F +R  + I FCS++DV            V N G+   EE+ELLNKPN +P
Sbjct: 56  FRGFSICREFAVRGAYGIRFCSREDV----------SGVGNGGIVAEEEIELLNKPNPLP 105

Query: 101 ISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGE 160
            S       +++S K D++  L PFLKFFKP +  E +E E     VS E+         
Sbjct: 106 KSE------NEESGKADDDAILEPFLKFFKPEEEGEGIESE-----VSDET--------- 145

Query: 161 DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDL 220
           D+VSVEYY+PKPGDFV+GVVVSGNENKLDVN+GAD+LGTMLTKE+LPLYDKE+D+LLCDL
Sbjct: 146 DRVSVEYYDPKPGDFVVGVVVSGNENKLDVNIGADMLGTMLTKEILPLYDKELDYLLCDL 205

Query: 221 KKDAEEFMVRGKMGIVKDDD-AIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTR 279
           K DAEEF+V GKMGIVKDDD  + ++  +  GRPVVE GTV+FAEVLGRTLSGRPLLS+R
Sbjct: 206 KYDAEEFLVNGKMGIVKDDDEGVEIAEFARQGRPVVEIGTVVFAEVLGRTLSGRPLLSSR 265

Query: 280 RLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELK 339
           R FR++AWHRVRQIKQLNEPIEVK TEWNTGGLLTRIEGLRAF+PK EL           
Sbjct: 266 RYFRRIAWHRVRQIKQLNEPIEVKITEWNTGGLLTRIEGLRAFIPKQEL----------- 314

Query: 340 EKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSN 399
             VGRR  VQITR+NED NDLILSE+ AW  L LREGTLLEGTV KI PYGAQ+++GDS+
Sbjct: 315 --VGRRFLVQITRLNEDKNDLILSEKVAWEKLYLREGTLLEGTVVKILPYGAQVKLGDSS 372

Query: 400 RSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKE 459
           RSGLLHISN++R R+ SVSD+L   E VKVLVVKS+FPDKISLSIADLESEPGLF+SD+E
Sbjct: 373 RSGLLHISNITRRRIGSVSDVLQVDESVKVLVVKSLFPDKISLSIADLESEPGLFISDRE 432

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	483
TAIR|locus:2145860	416	RPS1 "ribosomal protein S1" [A	0.356	0.413	0.348	7.5e-19
UNIPROTKB|O06147	481	rpsA "30S ribosomal protein S1	0.397	0.399	0.289	4.3e-14
TIGR_CMR|BA_1519	382	BA_1519 "ribosomal protein S1"	0.395	0.5	0.285	1e-13
TAIR|locus:2095203	392	AT3G23700 [Arabidopsis thalian	0.360	0.443	0.317	2.7e-12
TIGR_CMR|GSU_2603	586	GSU_2603 "ribosomal protein S1	0.376	0.310	0.323	1.3e-11
TIGR_CMR|ECH_0402	567	ECH_0402 "putative ribosomal p	0.436	0.372	0.288	5.5e-11
TIGR_CMR|GSU_1200	402	GSU_1200 "ribosomal protein S1	0.306	0.368	0.331	5.9e-11
TIGR_CMR|NSE_0408	553	NSE_0408 "ribosomal protein S1	0.416	0.363	0.273	7.9e-11
TIGR_CMR|SPO_0802	558	SPO_0802 "ribosomal protein S1	0.451	0.390	0.263	3.3e-10
UNIPROTKB|P0AG67	557	rpsA "30S ribosomal subunit pr	0.378	0.328	0.267	3.7e-10

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

 Score = 249 (92.7 bits), Expect = 7.5e-19, P = 7.5e-19
 Identities = 63/181 (34%), Positives = 104/181 (57%)

Query:   275 LLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNN 334
             LLS R +  ++AW R RQ++  +  ++ K    N GGL+  +EGLR F+P +++ S+   
Sbjct:   165 LLSLRNIQYELAWERCRQLQAEDVIVKAKVIGANKGGLVALVEGLRGFVPFSQISSKAAA 224

Query:   335 FTELKEKVGRRMYVQITRINEDTNDLILSEREAWAT--LNLREGTLLEGTVKKIYPYGAQ 392
               EL EK    + ++   ++E+   L+LS R+A A     L  G+++ G V+ + PYGA 
Sbjct:   225 -EELLEK---EIPLKFVEVDEEQTKLVLSNRKAVADSQAQLGIGSVVLGVVQSLKPYGAF 280

Query:   393 IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDKISLSIADLESEP 451
             I IG  N  GLLH+S +S  RV+ ++ +L  G+ +KV+++       ++SLS   LE  P
Sbjct:   281 IDIGGIN--GLLHVSQISHDRVSDIATVLQPGDTLKVMILSHDRDRGRVSLSTKKLEPTP 338

Query:   452 G 452
             G
Sbjct:   339 G 339

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

GO:0005739 "mitochondrion" evidence=ISM

GO:0009507 "chloroplast" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

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

GO:0006364 "rRNA processing" evidence=RCA

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

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

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

GO:0034660 "ncRNA metabolic process" evidence=RCA

UNIPROTKB|O06147 rpsA "30S ribosomal protein S1" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 206 (77.6 bits), Expect = 4.3e-14, Sum P(2) = 4.3e-14
 Identities = 61/211 (28%), Positives = 111/211 (52%)

Query:   254 VVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL 312
             VV  G  + A VL +    GR +LS +R   + AW  +  +K+ +E ++    E   GGL
Sbjct:    79 VVSVGDEVEALVLTKEDKEGRLILSKKRAQYERAWGTIEALKEKDEAVKGTVIEVVKGGL 138

Query:   313 LTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATL- 371
             +  I GLR FLP +  L  +    +L+  +G+ +  +I  ++++ N+++LS R AW    
Sbjct:   139 ILDI-GLRGFLPAS--LVEMRRVRDLQPYIGKEIEAKIIELDKNRNNVVLSRR-AWLEQT 194

Query:   372 ----------NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLL 421
                       NL++GT+ +G V  I  +GA + +G  +  GL+H+S +S   +   S+++
Sbjct:   195 QSEVRSEFLNNLQKGTIRKGVVSSIVNFGAFVDLGGVD--GLVHVSELSWKHIDHPSEVV 252

Query:   422 NEGERVKVLVVK-SMFPDKISLSIADLESEP 451
               G+ V V V+   M  +++SLS+   + +P
Sbjct:   253 QVGDEVTVEVLDVDMDRERVSLSLKATQEDP 283

GO:0005618 "cell wall" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0040007 "growth" evidence=IMP

TIGR_CMR|BA_1519 BA_1519 "ribosomal protein S1" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 194 (73.4 bits), Expect = 1.0e-13, Sum P(2) = 1.0e-13
 Identities = 60/210 (28%), Positives = 114/210 (54%)

Query:   254 VVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLL 313
             VVE    L  +V+ +      +LS R +  + AW  +++        +V   +   GGL+
Sbjct:    61 VVELDQTLELKVI-KLEENDLVLSKRAVDAEKAWVELQEKFNSGHVFDVTVKDIVNGGLV 119

Query:   314 TRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER------- 365
               + G+R F+P + + +  V +FT+ K   G+ + V+I  ++ + N +ILS +       
Sbjct:   120 VDL-GVRGFIPASLVEVHYVEDFTDYK---GKTLAVKIVELDREKNRVILSHKAVVELEL 175

Query:   366 ---EAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLN 422
                +  A  +L+EG ++EGTV+++  +GA + +G  +  GL+HIS +S  RV   S++L 
Sbjct:   176 DSKKKEAISSLKEGDVVEGTVQRLTDFGAFVNVGGVD--GLVHISQISHERVEQPSEVLE 233

Query:   423 EGERVKVLVVKSMFPDKISLSIADLESEPG 452
             +G++VKV V+ S+  D   +S++   ++PG
Sbjct:   234 QGQKVKVKVL-SVDADTQRISLSIKAAQPG 262

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

GO:0006412 "translation" evidence=ISS

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

 Score = 193 (73.0 bits), Expect = 2.7e-12, Sum P(2) = 2.7e-12
 Identities = 60/189 (31%), Positives = 95/189 (50%)

Query:   287 WHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL-SRV-----NNFTEL-K 339
             W   +   +  +  E +   +N GGLL R   L  FLP  +L  SR       +  E+ K
Sbjct:    97 WKTAKAYCKSGDTFEGEVQGFNGGGLLIRFHSLVGFLPYPQLSPSRSCKEPQKSIHEIAK 156

Query:   340 EKVGRRMYVQITRINEDTNDLILSEREA-WA--TLNLREGTLLEGTVKKIYPYGA--QIR 394
               VG ++ V++ + +E+   LILSE+ A W   + N+  G +  G V  +  YGA   +R
Sbjct:   157 TLVGSKLPVKVVQADEENRKLILSEKLALWPKYSQNVNVGDVFNGRVGSVEDYGAFIHLR 216

Query:   395 IGDS--NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDKISLSIADLESEP 451
               D   + +GL+H+S +S   V  V D+L +G+ V+V+V        +I+LSI  LE +P
Sbjct:   217 FDDGLYHLTGLVHVSEVSWDYVQDVRDVLRDGDEVRVIVTNIDKEKSRITLSIKQLEDDP 276

Query:   452 GLFVSDKEV 460
              L   DK +
Sbjct:   277 LLETLDKVI 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

TIGR_CMR|GSU_2603 GSU_2603 "ribosomal protein S1" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 189 (71.6 bits), Expect = 1.3e-11, P = 1.3e-11
 Identities = 64/198 (32%), Positives = 99/198 (50%)

Query:   272 GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR 331
             G  +LS R+  R  AW  +         +E K T    GGL   I G++AFLP +++  R
Sbjct:   106 GYAVLSKRKADRLSAWDSIDAAGGEGGIVEGKITGKVKGGLTVDI-GVQAFLPASQVDLR 164

Query:   332 VNNFTELKEKVGRRMYVQITRINEDTNDLILSER----EAWA-----TL-NLREGTLLEG 381
                   L + +G     ++ ++N+   +++LS R    E  A     TL NL EG   EG
Sbjct:   165 PGG--NLDKYIGVTDRFKVLKLNKKRGNIVLSRRVLLEEERAGVRTETLANLAEGQTREG 222

Query:   382 TVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDKI 440
              VK I  YGA + IG  +  GLLH+++MS  R+   S++L  G+++ V ++K      KI
Sbjct:   223 VVKNITDYGAFVDIGGVD--GLLHVTDMSWGRLGHPSEMLKPGDKLSVKILKYDQEKGKI 280

Query:   441 SLSIADLESEPGLFVSDK 458
             SL +  +  +P L V  K
Sbjct:   281 SLGLKQITPDPWLAVEQK 298

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

GO:0006412 "translation" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

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

 Score = 183 (69.5 bits), Expect = 5.5e-11, P = 5.5e-11
 Identities = 68/236 (28%), Positives = 119/236 (50%)

Query:   261 LFAEVL-GRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIE-VKFTEWNTGGLLTRIEG 318
             L+ E + GR  +G  +LS  +  R   W ++ +  +  E +E V F+    G  +  I+G
Sbjct:   109 LYLEKIEGR--NGSVVLSREKAIRDELWQKLEEAAEKKEDVEGVIFSSIKCGYTVD-IKG 165

Query:   319 LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER----EAWATLN- 372
             + AFLP + + L +V + T L   +G++   +I ++++   ++++S +    E+ A    
Sbjct:   166 VVAFLPASHVALRQVKDITPL---LGKKQKFRILKMDKKQGNIVVSRKAILEESLADAKS 222

Query:   373 -----LREGTLLEGTVKKIYPYGAQIRIGDSNR----SGLLHISNMSRTRVTSVSDLLNE 423
                  L EG ++EG VK I  YG  I I +S       GLLHI+++S +RV+  S + + 
Sbjct:   223 LYLSQLNEGDIIEGKVKSITKYGVFIEIHESPSVGVVDGLLHITDISWSRVSHPSAVFSC 282

Query:   424 GERVKVLVVK-SMFPDKISLSIADLESEPGLFVSDK-EVHIIFLFILLFNKQYSVW 477
             G+ VK  ++K      KISL +  LE  P   +  K  V  I   I+   ++Y V+
Sbjct:   283 GQTVKTKIIKIDRENKKISLGVKQLEESPWSNIEKKYPVDSIHKGIVTSIEEYGVF 338

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

TIGR_CMR|GSU_1200 GSU_1200 "ribosomal protein S1" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 180 (68.4 bits), Expect = 5.9e-11, P = 5.9e-11
 Identities = 55/166 (33%), Positives = 90/166 (54%)

Query:   299 PIEVKFTEWNTGGLLTRIEG-LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINED 356
             P+E    +   GG   ++ G +RAF P +++ L R  N  E    VGR++  ++    E 
Sbjct:   118 PVEGNVEKEIKGGFEIKVGGTVRAFCPYSQISLRRAANPAEF---VGRQLLFKVVEFAER 174

Query:   357 TNDLILS--------EREAWATLN--LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHI 406
               +++LS        ER+    L   L+EGT L GTV ++ P+GA + IG     GL+ I
Sbjct:   175 GRNIVLSHRAILEEEERQKREALKDTLKEGTTLTGTVTRLMPFGAFVDIGGVE--GLIPI 232

Query:   407 SNMSRTRVTSVSDLLNEGERVKVLVVKSMFPD-KISLSIADLESEP 451
             S    +RV  + D+L+ GE+V  LV +  + + KISLS+ D++++P
Sbjct:   233 SEAGWSRVKEIGDVLSVGEQVTALVKRIDWENNKISLSLRDVQADP 278

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

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

 Score = 187 (70.9 bits), Expect = 7.9e-11, Sum P(2) = 7.9e-11
 Identities = 61/223 (27%), Positives = 113/223 (50%)

Query:   255 VETGTVLFAEV-LGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNT--GG 311
             +E G+ +   V    T SG  +LS  +  ++  W+R+ ++       +V      T   G
Sbjct:    84 LEVGSKIIVYVEKTETGSGNLVLSYTKALKQKVWNRLYEMYLNGSDEDVMGVILYTIKSG 143

Query:   312 LLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATL 371
              +  +EGL AFLP + L   V   ++    VG ++  +I +++  T  + +S R+A   +
Sbjct:   144 CIVEVEGLNAFLPNSHL--DVRPVSDPATLVGVKLKFRILKMDPKTGKIFVSRRKALGAV 201

Query:   372 N----------LREGTLLEGTVKKIYPYGAQIRIGDSNR----SGLLHISNMSRTRVTSV 417
             +          ++EG +++G VK I  YG  ++I +S++     GLL+++++S  RVT  
Sbjct:   202 HEAARSEYISTIKEGDIIDGRVKSIASYGVFVQIHESDKVGVVDGLLYVNDISWARVTHP 261

Query:   418 SDLLNEGERVKVLVVKSMFPDK--ISLSIADLESEPGLFVSDK 458
             S + + G+ V+V V+ ++ P+K  ISL +  L   P   VS K
Sbjct:   262 SSIYSVGQEVRVKVI-AVDPEKGRISLGVKQLTENPWKDVSKK 303

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

TIGR_CMR|SPO_0802 SPO_0802 "ribosomal protein S1" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 177 (67.4 bits), Expect = 3.3e-10, Sum P(2) = 3.3e-10
 Identities = 62/235 (26%), Positives = 110/235 (46%)

Query:   237 KDDDAIAMSGGSGPGR-PVVETGTVLFAEV-LGRTLSGRPLLSTRRLFRKMAWHRVRQIK 294
             K +  + +   + PG  P +  G  +   +       G  ++S     R+ AW R+ +  
Sbjct:    47 KMEGRVELKEFANPGEAPEISIGDEVEVYLRAAENARGEAVISREMARREEAWDRLEKAY 106

Query:   295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRIN 354
               ++ +E        GG    + G  AFLP +++   V    +    +G +   QI +++
Sbjct:   107 ADDQRVEGAIFGRVKGGFTVDLGGAVAFLPGSQV--DVRPVRDAGPLMGLKQPFQILKMD 164

Query:   355 EDTNDLILSER--------EAWATL--NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLL 404
                 ++++S R        E  A +  NL EG  ++G VK I  YGA + +G  +  GLL
Sbjct:   165 RRRGNIVVSRRAILEESRAEQRAEVIGNLTEGQTVDGVVKNITEYGAFVDLGGVD--GLL 222

Query:   405 HISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDKISLSIADLESEPGLFVSDK 458
             H+++M+  RV   +++LN GE VKV V+K +    +ISL +  L+ +P   V  K
Sbjct:   223 HVTDMAWRRVNHPNEILNIGETVKVQVIKINKDTHRISLGMKQLQEDPWDLVGAK 277

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 = 172 (65.6 bits), Expect = 3.7e-10, Sum P(2) = 3.7e-10
 Identities = 53/198 (26%), Positives = 98/198 (49%)

Query:   272 GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR 331
             G  LLS  +  R  AW  + +  +  E +         GG    + G+RAFLP +  L  
Sbjct:    80 GETLLSREKAKRHEAWITLEKAYEDAETVTGVINGKVKGGFTVELNGIRAFLPGS--LVD 137

Query:   332 VNNFTELKEKVGRRMYVQITRINEDTNDLILSER---------EAWATL-NLREGTLLEG 381
             V    +     G+ +  ++ ++++  N++++S R         E    L NL+EG  ++G
Sbjct:   138 VRPVRDTLHLEGKELEFKVIKLDQKRNNVVVSRRAVIESENSAERDQLLENLQEGMEVKG 197

Query:   382 TVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDKI 440
              VK +  YGA + +G  +  GLLHI++M+  RV   S+++N G+ + V V+K      ++
Sbjct:   198 IVKNLTDYGAFVDLGGVD--GLLHITDMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRV 255

Query:   441 SLSIADLESEPGLFVSDK 458
             SL +  L  +P + ++ +
Sbjct:   256 SLGLKQLGEDPWVAIAKR 273

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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	483
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	3e-28
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	1e-26
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	1e-25
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	2e-25
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	9e-24
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	2e-17
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	3e-15
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	3e-13
cd04465	67	cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec	4e-13
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	5e-13
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	8e-13
cd05708	77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	2e-12
cd05684	79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	8e-12
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	1e-11
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	1e-11
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	2e-11
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	3e-11
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	6e-11
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	2e-10
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	7e-10
COG1098	129	COG1098, VacB, Predicted RNA binding protein (cont	1e-09
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	2e-09
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	2e-09
pfam00575	74	pfam00575, S1, S1 RNA binding domain	1e-08
PRK05807	136	PRK05807, PRK05807, hypothetical protein; Provisio	3e-08
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	4e-08
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-07
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	1e-07
PRK07252	120	PRK07252, PRK07252, hypothetical protein; Provisio	1e-07
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	2e-07
cd05686	73	cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-b	2e-07
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	3e-07
PRK08059	123	PRK08059, PRK08059, general stress protein 13; Val	1e-06
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	2e-06
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	1e-05
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	3e-05
PRK08582	139	PRK08582, PRK08582, hypothetical protein; Provisio	5e-05
PRK03987	262	PRK03987, PRK03987, translation initiation factor	6e-05
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	4e-04
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	6e-04
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	0.001
COG2183	780	COG2183, Tex, Transcriptional accessory protein [T	0.002
pfam00575	74	pfam00575, S1, S1 RNA binding domain	0.003

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

 Score =  115 bits (290), Expect = 3e-28
 Identities = 75/215 (34%), Positives = 118/215 (54%), Gaps = 26/215 (12%)

Query: 254 VVETGTVLFAEVLGRTLS-GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL 312
           VV+ G  L   VL      G  LLS RRL  + AW ++ +  +  E +EVK TE   GGL
Sbjct: 62  VVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGL 121

Query: 313 LTRIEGLRAFLPKAELLS--RVNNFTELKEKVGRRMYVQITRINEDTNDLILSER----- 365
           +  +EG+R F+P A L+S   V +F++ K   G+ + V+I  ++ + N +ILS R     
Sbjct: 122 VVDVEGVRGFIP-ASLISTRFVEDFSDFK---GKTLEVKIIELDPEKNRVILSRRAVVEE 177

Query: 366 -------EAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVS 418
                  E  ++L   EG ++EGTV ++  +GA + IG  +  GL+HIS +S  RV   S
Sbjct: 178 ERAAKKEELLSSLK--EGDVVEGTVARLTDFGAFVDIGGVD--GLVHISELSHERVEKPS 233

Query: 419 DLLNEGERVKVLVVKSMFPD--KISLSIADLESEP 451
           ++++ G+ V+V  V S+  +  +ISLS+ D    P
Sbjct: 234 EVVSVGQEVEV-KVLSIDWETERISLSLKDTLPGP 267

Length = 390

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

 Score =  113 bits (284), Expect = 1e-26
 Identities = 86/314 (27%), Positives = 141/314 (44%), Gaps = 73/314 (23%)

Query: 160 EDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCD 219
            + ++    + + GD V G VVS NEN++ V+VG    G      V+PL  +E+     +
Sbjct: 290 LEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEG------VIPL--RELTL--DE 339

Query: 220 LKKDAEEFMVRGKMGI----VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPL 275
           +    E   V  ++ +    ++D+D                               G  +
Sbjct: 340 ISSLKESVKVGDEIEVKVLKLEDED-------------------------------GYVV 368

Query: 276 LSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNN 334
           LS +   R+ AW  + +  +  EP++ K  E   GGLL    G+RAFLP + + L  V +
Sbjct: 369 LSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVELGYVED 428

Query: 335 FTELKEKVGRRMYVQITRINEDTN-DLILSER------------EAWATLNLREGTLLEG 381
              L E  G+ + V+I   N      ++LS +            E W +L   EG ++EG
Sbjct: 429 ---LSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLE--EGDVVEG 483

Query: 382 TVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPD--- 438
            VK++  +GA + IG  +  GLLH+S +S  RV   SD+L  G+ +KV ++     D   
Sbjct: 484 EVKRLTDFGAFVDIGGVD--GLLHVSEISWGRVEKPSDVLKVGDEIKVYILDI---DKEN 538

Query: 439 -KISLSIADLESEP 451
            K+SLS+  L  +P
Sbjct: 539 KKLSLSLKKLLPDP 552

Length = 647

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

 Score =  106 bits (267), Expect = 1e-25
 Identities = 70/194 (36%), Positives = 107/194 (55%), Gaps = 12/194 (6%)

Query: 272 GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR 331
           G+  LS RR+    AW RVRQ+++ +  +  +    N GG L RIEGLR F+P + + +R
Sbjct: 94  GQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTR 153

Query: 332 VNNFTELKEK-VGRRMYVQITRINEDTNDLILSEREAWA--TLN-LREGTLLEGTVKKIY 387
                + KE+ VG  + ++   ++E+ N L+LS R A     +N L  G ++ GTV+ I 
Sbjct: 154 -----KPKEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIK 208

Query: 388 PYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDKISLSIAD 446
           PYGA I IG    SGLLHIS +S   + +   + N  + +KV+++       +ISLS   
Sbjct: 209 PYGAFIDIG--GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQ 266

Query: 447 LESEPGLFVSDKEV 460
           LE EPG  + D + 
Sbjct: 267 LEPEPGDMLKDPQK 280

Length = 318

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

 Score =  108 bits (273), Expect = 2e-25
 Identities = 87/304 (28%), Positives = 139/304 (45%), Gaps = 59/304 (19%)

Query: 168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEF 227
            E +PGD V G VVS  ++ + V++G        ++ V+P+                 EF
Sbjct: 17  EEFEPGDVVKGTVVSIEKDGVLVDIGGK------SEGVIPI----------------SEF 54

Query: 228 MVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAW 287
                  +V+  D + +               VL  E       G  +LS R+  R+ AW
Sbjct: 55  SNEPVEDVVQVGDEVEV--------------LVLRVEDGE----GELVLSRRKAERERAW 96

Query: 288 HRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRM 346
            ++ +  +  E +E K T    GGL   IEG+RAFLP + + +  V +   L   +G+ +
Sbjct: 97  EKLEEAFENGEIVEGKITGKVKGGLTVDIEGVRAFLPGSLVDVRPVRDLDPL---IGKEL 153

Query: 347 YVQITRINEDTNDLILSEREA---------WATLN-LREGTLLEGTVKKIYPYGAQIRIG 396
             +I  +++  N+++LS R              LN L  G ++EG VK I  YGA + IG
Sbjct: 154 EFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIG 213

Query: 397 DSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDK--ISLSIADLESEPGLF 454
                GLLHIS +S  RV   S+++  G+ VKV  V S+  ++  +SLS+  LE +P   
Sbjct: 214 --GVDGLLHISEISWKRVDHPSEVVKVGDEVKV-KVISLDEERGRVSLSLKQLEEDPWEG 270

Query: 455 VSDK 458
           +  K
Sbjct: 271 IEKK 274

Length = 541

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

 Score =  104 bits (261), Expect = 9e-24
 Identities = 58/196 (29%), Positives = 100/196 (51%), Gaps = 25/196 (12%)

Query: 272 GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LS 330
           G  +LS  +  R  AW ++ +  +  E +E        GG    + G+ AFLP +++ + 
Sbjct: 90  GETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAFLPGSQVDVR 149

Query: 331 RVNNFTELKEKVGRRMYVQITRINEDTNDLILSER--------EAWATL--NLREGTLLE 380
            V +   L    G+ +  ++ ++++  N++++S R        E    L  NL EG ++E
Sbjct: 150 PVRDTDPL---EGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVE 206

Query: 381 GTVKKIYPYGAQIRIG--DSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPD 438
           G VK I  YGA + +G  D    GLLHI+++S  RV   S+++N G+ VKV V+K  F  
Sbjct: 207 GVVKNITDYGAFVDLGGVD----GLLHITDISWKRVNHPSEVVNVGDEVKVKVLK--FDK 260

Query: 439 ---KISLSIADLESEP 451
              ++SL +  L  +P
Sbjct: 261 EKKRVSLGLKQLGEDP 276

Length = 565

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

 Score = 84.8 bits (210), Expect = 2e-17
 Identities = 59/201 (29%), Positives = 101/201 (50%), Gaps = 21/201 (10%)

Query: 272 GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR 331
           G  +LS  +  R   W ++ +  +    +E K      GG +  + G+ AFLP +     
Sbjct: 76  GETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGS--QVD 133

Query: 332 VNNFTELKEKVGRRMYVQITRINEDTNDLILSER--------EAWATL--NLREGTLLEG 381
           V    +L   +G+ +  +I ++++  N++++S R        +A   L  NL+EG +++G
Sbjct: 134 VKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKG 193

Query: 382 TVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDK-- 439
            VK I  +GA + +G  +  GLLHI++MS  RV   S+ +  G+ VKV V+K    DK  
Sbjct: 194 VVKNITDFGAFVDLGGVD--GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKF---DKEK 248

Query: 440 --ISLSIADLESEPGLFVSDK 458
             ISLS+  L  +P   +  K
Sbjct: 249 GRISLSLKQLGEDPWEAIEKK 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|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

 Score = 70.0 bits (172), Expect = 3e-15
 Identities = 31/69 (44%), Positives = 47/69 (68%), Gaps = 1/69 (1%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435
           G+++EGTV ++ P+GA + +G    SGL+HIS ++  RV  V D+L EG++VKV V+   
Sbjct: 1   GSVVEGTVTRLKPFGAFVELGGG-ISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59

Query: 436 FPDKISLSI 444
              +ISLSI
Sbjct: 60  ARGRISLSI 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 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|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional

 Score = 71.3 bits (175), Expect = 3e-13
 Identities = 53/176 (30%), Positives = 88/176 (50%), Gaps = 20/176 (11%)

Query: 299 PIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEK-VGRRMYVQITRINEDT 357
           P+E K T    GG    + G RAF P +++  R   + E  E  VG+     ITR+ E+ 
Sbjct: 118 PVEGKVTGTCKGGFNVEVLGRRAFCPVSQIDLR---YVEDPESYVGQTFQFLITRVEENG 174

Query: 358 NDLILSER--------EAWATL--NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHIS 407
            ++++S R        EA       ++EG ++EGTV ++ P+GA + +      G++HIS
Sbjct: 175 RNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVEL-APGVEGMVHIS 233

Query: 408 NMSRTRVTSVSDLLNEGERVKVLVV-----KSMFPDKISLSIADLESEPGLFVSDK 458
            +S +RV    + ++ G+ V+V V+     K     +ISLSI     +P   V D+
Sbjct: 234 ELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDR 289

Length = 491

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

 Score = 64.0 bits (157), Expect = 4e-13
 Identities = 28/70 (40%), Positives = 43/70 (61%), Gaps = 4/70 (5%)

Query: 297 NEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINE 355
            E +E K TE   GGL+  IEG+RAFLP +++ L  V +   L E VG+ +  +I  I+ 
Sbjct: 1   GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVED---LDEYVGKELKFKIIEIDR 57

Query: 356 DTNDLILSER 365
           + N+++LS R
Sbjct: 58  ERNNIVLSRR 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|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 70.8 bits (174), Expect = 5e-13
 Identities = 40/162 (24%), Positives = 74/162 (45%), Gaps = 10/162 (6%)

Query: 298 EPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDT 357
           E +E         G    I G+   L  +E+  +  +      KVG  + V++  ++E+ 
Sbjct: 194 EVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEER 253

Query: 358 NDLILSEREA----WATL--NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR 411
             + LS ++     W  +      G  +EG V  +  YGA + I +    GL+H+S +S 
Sbjct: 254 GRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEG-VEGLVHVSEISW 312

Query: 412 TRVTSVSDLLNEGERVKVLVVKSMFPD--KISLSIADLESEP 451
           T+    S+++  G+ V+V  V  + P+  +ISL +  L+  P
Sbjct: 313 TKKNVPSEVVKVGQEVEV-KVLDIDPERRRISLGLKQLKENP 353

Length = 541

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

 Score = 70.4 bits (173), Expect = 8e-13
 Identities = 47/151 (31%), Positives = 79/151 (52%), Gaps = 12/151 (7%)

Query: 311 GLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE--- 366
           G    I G+   L  +E+   RV   +++  KVG  + V I  I+++   L LS ++   
Sbjct: 492 GAFVDIGGVDGLLHVSEISWGRVEKPSDVL-KVGDEIKVYILDIDKENKKLSLSLKKLLP 550

Query: 367 -AWATL--NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNE 423
             W  +      G+++ G V +I P+GA + +      GL+HIS +S  R+    D+L+E
Sbjct: 551 DPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPG-VDGLVHISQISWKRIDKPEDVLSE 609

Query: 424 GERVKVLVVKSMFPD--KISLSIADLESEPG 452
           GE VK  ++  + P+  +I LSI ++E EPG
Sbjct: 610 GEEVKAKIL-EVDPEEKRIRLSIKEVEEEPG 639

Length = 647

>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 = 62.0 bits (151), Expect = 2e-12
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434
            G  ++GTV+++  YG  I I  +N SGL H S +S  RV   S L   G++V+  V+K 
Sbjct: 2   VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKI 61

Query: 435 -MFPDKISLSI 444
                +ISL +
Sbjct: 62  DAEKKRISLGL 72

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|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 = 60.3 bits (147), Expect = 8e-12
 Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 4/74 (5%)

Query: 376 GTLLEGTVKKIYPYGAQIRI--GDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVV 432
           G + +G V  I  +G  +++      + GL+HIS +S   RV + SD++  G++VKV V+
Sbjct: 1   GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVI 60

Query: 433 KSMFPDKISLSIAD 446
            S+   KISLS+ D
Sbjct: 61  -SIQNGKISLSMKD 73

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

 Score = 66.8 bits (164), Expect = 1e-11
 Identities = 28/73 (38%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435
           G + EGTV +I  +GA + +    + GL+HIS +++ RV  V D+L EG+ VKV V++  
Sbjct: 620 GEVYEGTVVRIVDFGAFVELLP-GKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEID 678

Query: 436 FPDKISLSIADLE 448
              +I LSI  + 
Sbjct: 679 KQGRIRLSIKAVL 691

Length = 692

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

 Score = 66.6 bits (164), Expect = 1e-11
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434
            G + EG V +I  +GA + I    + GL+HIS ++  RV  V D+L EG+ VKV V++ 
Sbjct: 621 VGEIYEGKVVRIVDFGAFVEILP-GKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEI 679

Query: 435 MFPDKISLSIADLE 448
               +I LS   + 
Sbjct: 680 DKRGRIRLSRKAVL 693

Length = 693

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

 Score = 58.7 bits (143), Expect = 2e-11
 Identities = 29/69 (42%), Positives = 40/69 (57%), Gaps = 1/69 (1%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435
           G + EG V KI  +GA + I    + GL+HIS +S  RV  V D+L  G+ VKV V++  
Sbjct: 1   GKIYEGKVVKIKDFGAFVEIL-PGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD 59

Query: 436 FPDKISLSI 444
              +ISLS 
Sbjct: 60  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|240193 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

 Score = 58.4 bits (142), Expect = 3e-11
 Identities = 28/59 (47%), Positives = 41/59 (69%), Gaps = 2/59 (3%)

Query: 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433
           EG ++EGTVK I  +GA + +G  +  GLLHIS+MS  RV   S+++N G+ V+V V+K
Sbjct: 1   EGDVVEGTVKSITDFGAFVDLGGVD--GLLHISDMSWGRVKHPSEVVNVGDEVEVKVLK 57

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

 Score = 63.9 bits (156), Expect = 6e-11
 Identities = 62/212 (29%), Positives = 111/212 (52%), Gaps = 21/212 (9%)

Query: 254 VVETGTVLFAEVLGRTLS-GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL 312
           VVE G  + A VL +    GR +LS +R   + AW  + +IK+ +  +     E   GGL
Sbjct: 79  VVEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGL 138

Query: 313 LTRIEGLRAFLPKAEL--LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER----- 365
           +  I GLR FLP A L  + RV    +L+  +G+ +  +I  ++++ N+++LS R     
Sbjct: 139 ILDI-GLRGFLP-ASLVEMRRVR---DLQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQ 193

Query: 366 ---EAWATL--NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDL 420
              E  +     L++G + +G V  I  +GA + +G  +  GL+H+S +S   +   S++
Sbjct: 194 TQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVD--GLVHVSELSWKHIDHPSEV 251

Query: 421 LNEGERVKVLVVK-SMFPDKISLSIADLESEP 451
           +  G+ V V V+   M  +++SLS+   + +P
Sbjct: 252 VEVGQEVTVEVLDVDMDRERVSLSLKATQEDP 283

Length = 486

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

 Score = 61.8 bits (151), Expect = 2e-10
 Identities = 43/130 (33%), Positives = 72/130 (55%), Gaps = 11/130 (8%)

Query: 330 SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----W--ATLNLREGTLLEGTV 383
            RV   +E+   VG+ + V++  I+ +T  + LS ++     W      L EG ++EGTV
Sbjct: 227 ERVEKPSEVV-SVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTV 285

Query: 384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPD--KIS 441
           K++  +GA + +      GL+HIS +S   + + S++L EG+ VKV V+  +  +  +IS
Sbjct: 286 KRLTDFGAFVEVLPG-VEGLVHISQISHKHIATPSEVLEEGQEVKVKVL-EVNEEEKRIS 343

Query: 442 LSIADLESEP 451
           LSI  LE  P
Sbjct: 344 LSIKALEEAP 353

Length = 390

>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 = 54.5 bits (132), Expect = 7e-10
 Identities = 26/69 (37%), Positives = 41/69 (59%), Gaps = 2/69 (2%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435
           G +LEG V  +  +GA + IG   + GL+HIS M+   V+  SD+++ G+ V+V V+   
Sbjct: 1   GMVLEGVVTNVTDFGAFVDIG-VKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISID 59

Query: 436 FP-DKISLS 443
               +ISLS
Sbjct: 60  EERGRISLS 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|224023 COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]

 Score = 56.1 bits (136), Expect = 1e-09
 Identities = 31/76 (40%), Positives = 45/76 (59%), Gaps = 1/76 (1%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435
           G+ L+G +  I PYGA + + +  ++GL+HIS ++   V  + D L  G+ VKV V+   
Sbjct: 6   GSKLKGKITGITPYGAFVEL-EGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDID 64

Query: 436 FPDKISLSIADLESEP 451
              KISLSI  LE EP
Sbjct: 65  ENGKISLSIRKLEEEP 80

Length = 129

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

 Score = 59.4 bits (145), Expect = 2e-09
 Identities = 24/57 (42%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432
           G + EG V +I  +GA + I    + GL+HIS ++  RV  V D+L EG+ VKV V+
Sbjct: 619 GKIYEGKVVRIMDFGAFVEIL-PGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVL 674

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433
             G ++EGTV +I P GA + +G+    GL+ IS +S  RV    ++L  G+ VKV V+ 
Sbjct: 1   EVGDVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLS 59

Query: 434 SMFPDK-ISLSI 444
                  I LS+
Sbjct: 60  VDEEKGRIILSL 71

Length = 72

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLV 431
              EG +++GTV ++   GA + +G+    G + IS +S  RV    ++L  G+ V+V V
Sbjct: 1   KPEEGDVVKGTVTRVTKGGAFVDLGN-GVEGFIPISEISDDRVEDPDEVLKVGDEVEVKV 59

Query: 432 VK 433
           +K
Sbjct: 60  LK 61

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|235614 PRK05807, PRK05807, hypothetical protein; Provisional

 Score = 52.1 bits (125), Expect = 3e-08
 Identities = 30/73 (41%), Positives = 48/73 (65%), Gaps = 4/73 (5%)

Query: 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432
           L+ G++LEGTV  I  +GA + +    ++GL+HIS ++ T V  + + L E ++VKV V+
Sbjct: 3   LKAGSILEGTVVNITNFGAFVEV--EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVI 60

Query: 433 KSMFPD-KISLSI 444
            S+  + KISLSI
Sbjct: 61  -SIDDNGKISLSI 72

Length = 136

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

 Score = 55.6 bits (135), Expect = 4e-08
 Identities = 32/124 (25%), Positives = 63/124 (50%), Gaps = 12/124 (9%)

Query: 330 SRVNNFTELKEKVGRRMYVQITRINEDTNDLILS----EREAWATL--NLREGTLLEGTV 383
            RVN+ +E+   VG  + V++ + +++   + L       + W  +      G+ ++G V
Sbjct: 236 KRVNHPSEVV-NVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKV 294

Query: 384 KKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVVKSMFPDK--I 440
             I  YGA + + +    GL+H+S MS T +    S +++ G+ V+V +V  +  +K  I
Sbjct: 295 TNITDYGAFVELEE-GIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEV-MVLEIDEEKRRI 352

Query: 441 SLSI 444
           SL +
Sbjct: 353 SLGL 356

Length = 565

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

 Score = 54.0 bits (130), Expect = 1e-07
 Identities = 34/151 (22%), Positives = 74/151 (49%), Gaps = 13/151 (8%)

Query: 311 GLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE--- 366
           G    + G+   L   ++   RV + +E   KVG+ + V++ + +++   + LS ++   
Sbjct: 202 GAFVDLGGVDGLLHITDMSWKRVKHPSEYV-KVGQEVKVKVIKFDKEKGRISLSLKQLGE 260

Query: 367 -AWATL--NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTS-VSDLLN 422
             W  +      G  + G V  +  YG  + I +    GL+H+S MS  +  S  S ++ 
Sbjct: 261 DPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEE-GIEGLVHVSEMSWVKKNSHPSKVVK 319

Query: 423 EGERVKVLVVKSMFPD--KISLSIADLESEP 451
           +G+ V+V+++  + P+  ++SL +   ++ P
Sbjct: 320 KGDEVEVMILD-IDPERRRLSLGLKQCKANP 349

This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by PFAM model pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 516

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

 Score = 53.6 bits (129), Expect = 1e-07
 Identities = 37/106 (34%), Positives = 58/106 (54%), Gaps = 11/106 (10%)

Query: 362 LSEREA----WATL--NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RV 414
           LS ++A    W T+   L+ G  + G V ++ P+GA + I      GL+H+S MS T RV
Sbjct: 273 LSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEIL-PGIEGLVHVSEMSWTRRV 331

Query: 415 TSVSDLLNEGERVKVLVVKSMFPDK--ISLSIADLESEPGLFVSDK 458
               D++  G+ V V  +K + P K  ISLS+ D E +P   V+++
Sbjct: 332 NKPEDVVAPGDAVAV-KIKDIDPAKRRISLSLRDAEGDPWADVAER 376

Length = 491

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

 Score = 50.1 bits (120), Expect = 1e-07
 Identities = 29/76 (38%), Positives = 43/76 (56%), Gaps = 2/76 (2%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-S 434
           G  L+GT+  I PYGA + + ++  +GL+HIS +    + ++  LL  GE V V VV   
Sbjct: 4   GDKLKGTITGIKPYGAFVAL-ENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFD 62

Query: 435 MFPDKISLSIADLESE 450
            +  K SLS+  LE E
Sbjct: 63  EYTGKASLSLRTLEEE 78

Length = 120

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

 Score = 53.5 bits (129), Expect = 2e-07
 Identities = 35/142 (24%), Positives = 64/142 (45%), Gaps = 8/142 (5%)

Query: 317 EGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWATL- 371
           EG+   +  +E+     N      KVG+ + V++  I+ +   + L  ++     W    
Sbjct: 299 EGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFA 358

Query: 372 -NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVL 430
                G ++EG VK I  +GA + +      GL+H+S++S  R    ++   +G+ V+  
Sbjct: 359 DKHPVGDVVEGKVKSITDFGAFVELEG-GIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAK 417

Query: 431 VVKSMFPD-KISLSIADLESEP 451
           V+       +ISL I  LE  P
Sbjct: 418 VLAVDKEKERISLGIKQLEESP 439

Length = 541

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

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 24/68 (35%), Positives = 40/68 (58%)

Query: 377 TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMF 436
            + +G V  +  YGA ++I    + GL+H S+MS  RV   S++++ GE+V V V+    
Sbjct: 5   QIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREM 64

Query: 437 PDKISLSI 444
            DK+ LS+
Sbjct: 65  KDKMKLSL 72

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

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 379 LEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433
           + G V  I  +G  + + D    GL+HIS +S   V   S++   G+ V+V V++
Sbjct: 1   VTGKVVSITKFGVFVELED-GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLE 54

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|181215 PRK08059, PRK08059, general stress protein 13; Validated

 Score = 47.0 bits (112), Expect = 1e-06
 Identities = 31/84 (36%), Positives = 43/84 (51%), Gaps = 8/84 (9%)

Query: 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLV 431
               G+++ G V  I PYGA + + D    GL+HIS ++   V  + D L+ G+ VK   
Sbjct: 4   QYEVGSVVTGKVTGIQPYGAFVAL-DEETQGLVHISEITHGFVKDIHDFLSVGDEVK--- 59

Query: 432 VKSMFPD----KISLSIADLESEP 451
           VK +  D    KISLSI   E  P
Sbjct: 60  VKVLSVDEEKGKISLSIRATEEAP 83

Length = 123

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 4/73 (5%)

Query: 374 REGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432
            EG L+  TVK I   GA + + +  N  G++ +S +SR R+ S+  L+  G +  V+ V
Sbjct: 2   EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKE-VVKV 60

Query: 433 KSMFPDK--ISLS 443
             +  +K  I LS
Sbjct: 61  IRVDKEKGYIDLS 73

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

 Score = 47.5 bits (114), Expect = 1e-05
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-S 434
           G+++ GTV ++   GA + + D    GL+  S +SR RV   +++L  G+ V+  V+   
Sbjct: 461 GSIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINID 519

Query: 435 MFPDKISLSIADLESE 450
               +ISLSI  L+  
Sbjct: 520 RKNRRISLSIKALDEA 535

Length = 565

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

 Score = 45.4 bits (108), Expect = 3e-05
 Identities = 22/62 (35%), Positives = 38/62 (61%), Gaps = 3/62 (4%)

Query: 374 REGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERV--KVL 430
            EG ++ GTVK++  YGA + + +   + G +HIS ++   V ++ D + EG++V  KVL
Sbjct: 10  EEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVL 69

Query: 431 VV 432
            V
Sbjct: 70  RV 71

Length = 269

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

 Score = 42.7 bits (101), Expect = 5e-05
 Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 1/69 (1%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435
           G+ L+G V  I  +GA + + +  ++GL+HIS ++   V  ++D L  G+ V+V V+   
Sbjct: 6   GSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE 64

Query: 436 FPDKISLSI 444
              KI LSI
Sbjct: 65  DDGKIGLSI 73

Length = 139

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

 Score = 44.4 bits (106), Expect = 6e-05
 Identities = 21/61 (34%), Positives = 38/61 (62%), Gaps = 3/61 (4%)

Query: 375 EGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERV--KVLV 431
           EG L+ GTVK++  +GA + + +   + G +HIS ++   V ++ D + EG++V  KV+ 
Sbjct: 8   EGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIR 67

Query: 432 V 432
           V
Sbjct: 68  V 68

Length = 262

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

 Score = 42.5 bits (101), Expect = 4e-04
 Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 9/82 (10%)

Query: 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTS-VSDLLNEGERVKVLVVK 433
            G ++EG VK I  +GA + +      GL+H+S++S  +      +L  +G+ V+ +V+K
Sbjct: 373 VGDVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLK 431

Query: 434 SMFPD----KISLSIADLESEP 451
               D    +ISL I  LE +P
Sbjct: 432 V---DVEKERISLGIKQLEEDP 450

Length = 565

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

 Score = 42.0 bits (99), Expect = 6e-04
 Identities = 34/145 (23%), Positives = 63/145 (43%), Gaps = 12/145 (8%)

Query: 317 EGLRAFLPKAELLSRVNNFTELKE--KVGRRMYVQITRINEDTNDLILSEREA----WAT 370
           EG+   +  +E+ S V   +   +  K G  + V I  I+ +   L L  ++     W  
Sbjct: 294 EGIEGLVHVSEM-SWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQ 352

Query: 371 LNLRE--GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGER-V 427
              +   G  + G +KKI  +GA + +      GL+H+S++S  +    +D L +    +
Sbjct: 353 FEEKHPVGDRVTGKIKKITDFGAFVELEG-GIDGLIHLSDISWDKDGREADHLYKKGDEI 411

Query: 428 KVLVVKSMFPDK-ISLSIADLESEP 451
           + +V+      K ISL +  L   P
Sbjct: 412 EAVVLAVDKEKKRISLGVKQLTENP 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|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein S1; Provisional

 Score = 41.6 bits (97), Expect = 0.001
 Identities = 57/241 (23%), Positives = 100/241 (41%), Gaps = 35/241 (14%)

Query: 246 GGSGPGRPVVET---------GTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQL 296
           GG   GR  VE          G  ++ E   R     P LS  +  R     ++R  ++ 
Sbjct: 342 GGKSEGRVPVEEFEAPPKAGDGVRVYVE---RVTPYGPELSKTKADRLGLKVKLRDAERD 398

Query: 297 NEPIE---VKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRI 353
             P+E   V+ TE  +G  +    G+ AFLP ++  S        +  +G      I RI
Sbjct: 399 GTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQ--SDCQKVDAPESLIGLTSKFYIERI 456

Query: 354 NEDT----NDLILSEREAWATLNLREG-----------TLLEGTVKKIYPYGAQIRIGDS 398
           ++      ND I+  R  +     R+              + G VK    +GA I +G  
Sbjct: 457 SQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLGGF 516

Query: 399 NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDKISLSIADLESEPGLFVSD 457
           +  GLLH+++MS   V    + + +G+ +++ V++      +I+LS+   + +P L   +
Sbjct: 517 D--GLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFEN 574

Query: 458 K 458
           K
Sbjct: 575 K 575

Length = 863

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

 Score = 40.7 bits (96), Expect = 0.002
 Identities = 29/88 (32%), Positives = 47/88 (53%), Gaps = 4/88 (4%)

Query: 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLV 431
           +L+ G +LEGTV+ +  +GA + IG     GL+HIS +S   V   ++++  G+ VKV  
Sbjct: 655 DLKPGMILEGTVRNVVDFGAFVDIGVHQ-DGLVHISQLSDKFVKDPNEVVKVGDIVKV-K 712

Query: 432 VKSMFPD--KISLSIADLESEPGLFVSD 457
           V  +     +I+LS+   E E  L    
Sbjct: 713 VIEVDTARKRIALSMRLDEEEGKLNSGR 740

Length = 780

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 310 GGLLTRI-EGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER 365
           GG    +  G+  F+P +E+        +   KVG  + V++ +++++   +ILS R
Sbjct: 18  GGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLKVDKERGRIILSIR 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	483
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
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	100.0
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	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
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	99.88
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.76
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.72
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.71
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.7
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.66
PRK08582	139	hypothetical protein; Provisional	99.57
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.53
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.52
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.48
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.48
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.46
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.45
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	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
PRK07252	120	hypothetical protein; Provisional	99.42
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.42
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.41
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.4
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.39
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.39
PRK05807	136	hypothetical protein; Provisional	99.38
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.38
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.37
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.36
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.35
PRK08059	123	general stress protein 13; Validated	99.34
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.33
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.31
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.28
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.25
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.25
PHA02945	88	interferon resistance protein; Provisional	99.23
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.21
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.21
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.2
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.2
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.2
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.2
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.17
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.15
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.15
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.14
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.14
PRK03987	262	translation initiation factor IF-2 subunit alpha;	99.14
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	99.13
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.13
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.12
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.11
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.11
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.1
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	99.09
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.07
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.05
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.04
PRK09202	470	nusA transcription elongation factor NusA; Validat	99.04
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.03
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.03
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.0
COG2183	780	Tex Transcriptional accessory protein [Transcripti	98.99
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.98
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.97
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	98.97
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	98.96
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.96
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.95
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.95
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.95
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.94
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	98.93
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.9
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	98.89
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	98.89
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.89
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	98.89
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	98.85
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.83
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.83
PRK07252	120	hypothetical protein; Provisional	98.83
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.83
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	98.81
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.81
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.79
PRK08582	139	hypothetical protein; Provisional	98.79
PRK05807	136	hypothetical protein; Provisional	98.76
TIGR01953	341	NusA transcription termination factor NusA. This m	98.76
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.76
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.73
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	98.72
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.71
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	98.69
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.66
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.65
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.65
PRK08059	123	general stress protein 13; Validated	98.64
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.63
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.62
PHA02945	88	interferon resistance protein; Provisional	98.62
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.61
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.56
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.55
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	98.54
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.53
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.5
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.49
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.48
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.48
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.46
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.39
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.35
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.35
PRK11642	813	exoribonuclease R; Provisional	98.34
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.32
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.32
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.28
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.26
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	98.23
COG2183	780	Tex Transcriptional accessory protein [Transcripti	98.21
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.2
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.19
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.11
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.11
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.04
TIGR01953	341	NusA transcription termination factor NusA. This m	98.01
PRK12327	362	nusA transcription elongation factor NusA; Provisi	97.99
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.91
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.91
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	97.89
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	97.86
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	97.82
KOG2916	304	consensus Translation initiation factor 2, alpha s	97.82
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.64
PRK05054	644	exoribonuclease II; Provisional	97.6
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	97.57
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.55
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.53
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.52
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.49
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	97.48
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.45
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.44
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.44
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.43
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	97.4
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	97.4
PRK12329	449	nusA transcription elongation factor NusA; Provisi	97.37
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.34
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.23
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	97.14
PRK11642	813	exoribonuclease R; Provisional	97.13
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	97.09
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	97.07
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	97.06
COG0557	706	VacB Exoribonuclease R [Transcription]	97.03
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.01
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	96.84
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	96.68
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.65
PRK10811	1068	rne ribonuclease E; Reviewed	96.63
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	96.61
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	96.04
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	95.82
PRK11712	489	ribonuclease G; Provisional	95.67
PRK05054	644	exoribonuclease II; Provisional	95.56
KOG2916	304	consensus Translation initiation factor 2, alpha s	95.54
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	95.37
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	94.96
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	94.95
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	94.78
KOG3013	301	consensus Exosomal 3'-5' exoribonuclease complex,	94.58
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	93.51
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	93.32
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	93.14
COG0557	706	VacB Exoribonuclease R [Transcription]	91.95
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	91.65
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	91.02
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	90.81
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	90.6
PRK11712	489	ribonuclease G; Provisional	89.99
PRK10811	1068	rne ribonuclease E; Reviewed	89.93
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	89.05
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	88.06
PRK12442	87	translation initiation factor IF-1; Reviewed	87.02
KOG1004	230	consensus Exosomal 3'-5' exoribonuclease complex s	85.42
TIGR00008	68	infA translation initiation factor IF-1. This fami	84.68
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	80.42

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

Probab=100.00  E-value=2.2e-45  Score=391.59  Aligned_cols=267  Identities=30%  Similarity=0.378  Sum_probs=240.8

Q ss_pred             hhhcccc---ccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccce
Q 011538          158 VGEDKVS---VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMG  234 (483)
Q Consensus       158 ~~~~~~~---~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~  234 (483)
                      +|++.+.   ...+.+++|++|.|+|+++++++++||+|++++|++|++|+...+                         
T Consensus         4 ~f~~~~~~~~~~~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~~~-------------------------   58 (541)
T COG0539           4 EFAELFEESDKSDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEP-------------------------   58 (541)
T ss_pred             hHHHHHHhhhcchhccCCCCEEEEEEEEEeCCeEEEEecCccccEeEHHHhcccc-------------------------
Confidence            3444444   467889999999999999999999999999999999999986431                         


Q ss_pred             eeeccccccccCCCCCCCCcccCCCEEEEEEEE-EcCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEE
Q 011538          235 IVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLG-RTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLL  313 (483)
Q Consensus       235 vv~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~-~d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~f  313 (483)
                                      ....+++||.+.+.|.. .+.+|.++||++++...++|..|.++++.|++|+|+|+...++|++
T Consensus        59 ----------------~~~~~~~gd~v~v~v~~~e~~~g~~~lS~~k~~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~  122 (541)
T COG0539          59 ----------------VEDVVQVGDEVEVLVLRVEDGEGELVLSRRKAERERAWEKLEEAFENGEIVEGKITGKVKGGLT  122 (541)
T ss_pred             ----------------ccceecCCCEEEEEEEEEecCCceEEeeHHHHHHHHhHHHHHHHHhcCCeEEEEEEEEecCcEE
Confidence                            11258899999999998 4667899999999999999999999999999999999999999999


Q ss_pred             EEECCeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh----------hcCCCCCcEEEEE
Q 011538          314 TRIEGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGT  382 (483)
Q Consensus       314 V~I~Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e----------~~~l~vG~iv~G~  382 (483)
                      |+++|++||+|.|++. +++++...   .+|+.+.++|+++|++++++++|||..++          ..++++|++++|+
T Consensus       123 Vdi~gvr~FlP~S~v~~r~v~d~~~---~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~  199 (541)
T COG0539         123 VDIEGVRAFLPGSLVDVRPVRDLDP---LIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGV  199 (541)
T ss_pred             EEECCEEEeccHHHhcccccccccc---cCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEE
Confidence            9999999999999994 55655444   58999999999999999999999998764          2589999999999


Q ss_pred             EEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCccccccccc
Q 011538          383 VKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVH  461 (483)
Q Consensus       383 V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V  461 (483)
                      |++|++|||||+|+  |++||||+++|||.|+.+|++.|++||+|+|+|+++| +++||+||||++.+|||+.+.++|++
T Consensus       200 V~~It~~GafVdig--GvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~  277 (541)
T COG0539         200 VKNITDYGAFVDIG--GVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPV  277 (541)
T ss_pred             EEEeecCcEEEEec--CeeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCC
Confidence            99999999999999  5999999999999999999999999999999999999 89999999999999999999999999


Q ss_pred             ceeeEEEEe
Q 011538          462 IIFLFILLF  470 (483)
Q Consensus       462 ~~~~~~~~~  470 (483)
                      ++.+.=.+-
T Consensus       278 g~~v~G~Vt  286 (541)
T COG0539         278 GDKVEGKVT  286 (541)
T ss_pred             CCEEEEEEE
Confidence            999854443

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=3.9e-44  Score=365.47  Aligned_cols=266  Identities=31%  Similarity=0.426  Sum_probs=236.4

Q ss_pred             chhhhccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhccccee
Q 011538          156 DKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI  235 (483)
Q Consensus       156 ~~~~~~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~v  235 (483)
                      ..+|+++|+.+.+.+++|++|.|+|++++++|++||+|++..||||++|++..+.           .+            
T Consensus        15 ~~~f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~-----------~~------------   71 (318)
T PRK07400         15 HEDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRV-----------EG------------   71 (318)
T ss_pred             HHHHHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccc-----------cC------------
Confidence            3679999986666799999999999999999999999999999999999864311           11            


Q ss_pred             eeccccccccCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEE
Q 011538          236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT  314 (483)
Q Consensus       236 v~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV  314 (483)
                                     ....+++|+.+.|.|++. +.+|++.||+|++.....|+++.++++.|++|+|+|++++++|++|
T Consensus        72 ---------------~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V  136 (318)
T PRK07400         72 ---------------PEEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALV  136 (318)
T ss_pred             ---------------HHHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEE
Confidence                           123478999999999985 4678999999999877899999999999999999999999999999


Q ss_pred             EECCeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh---hcCCCCCcEEEEEEEEEeCceE
Q 011538          315 RIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA---TLNLREGTLLEGTVKKIYPYGA  391 (483)
Q Consensus       315 ~I~Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e---~~~l~vG~iv~G~V~~I~~~Ga  391 (483)
                      +++|++||||.|++..+.  ..+.  .+|+.+.|+|+++|++++++.||+|.++.   ..++++|+++.|+|++|++||+
T Consensus       137 ~l~Gv~gfip~s~ls~~~--~~~~--~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~  212 (318)
T PRK07400        137 RIEGLRGFIPGSHISTRK--PKEE--LVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGA  212 (318)
T ss_pred             EECCEEEEEEHHHcCccC--Cccc--cCCCEEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeE
Confidence            999999999999994321  2222  59999999999999999999999998753   3479999999999999999999


Q ss_pred             EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccceee
Q 011538          392 QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHIIFL  465 (483)
Q Consensus       392 FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~~  465 (483)
                      ||+++  |+.||+|+++++|.++.++.+.|++||.|+|+|+++| ++++|.||+|++++|||+.+.+++.+|+-+
T Consensus       213 fV~i~--gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~~~~~~~~~~~~  285 (318)
T PRK07400        213 FIDIG--GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDPQKVFDKA  285 (318)
T ss_pred             EEEEC--CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhhhhhhHHHHHHHH
Confidence            99996  6899999999999999999999999999999999998 789999999999999999999999988643

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=2.6e-42  Score=368.44  Aligned_cols=266  Identities=26%  Similarity=0.392  Sum_probs=238.2

Q ss_pred             hhhhccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceee
Q 011538          157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV  236 (483)
Q Consensus       157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv  236 (483)
                      .+|.+.++..+..+++|++|.|+|+++++++++||+|++.+|+||.+|++...+           .+             
T Consensus        20 e~f~~~~e~~~~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~-----------~~-------------   75 (486)
T PRK07899         20 EDFLAAIDKTIKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHD-----------VD-------------   75 (486)
T ss_pred             HHHHHHHHHHHhcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhccccc-----------CC-------------
Confidence            678888888888899999999999999999999999999999999999864310           11             


Q ss_pred             eccccccccCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEE
Q 011538          237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR  315 (483)
Q Consensus       237 ~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~  315 (483)
                                    ....+++||+|+|.|++. +.+|+++||+|++.....|..+.++++.|++++|+|+++.++|++|+
T Consensus        76 --------------~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vd  141 (486)
T PRK07899         76 --------------PNEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILD  141 (486)
T ss_pred             --------------hhhcCCCCCEEEEEEEEEECCCCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEE
Confidence                          123488999999999985 46789999999998889999999999999999999999999999999


Q ss_pred             ECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh----------hcCCCCCcEEEEEEE
Q 011538          316 IEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGTVK  384 (483)
Q Consensus       316 I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e----------~~~l~vG~iv~G~V~  384 (483)
                      + |++||||.|++ +.+..++..   .+|+.|+|+|+++|+++++++||+|..++          ...+++|+++.|+|+
T Consensus       142 l-Gi~gflP~Sel~~~~~~~~~~---~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~  217 (486)
T PRK07899        142 I-GLRGFLPASLVEMRRVRDLQP---YIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVS  217 (486)
T ss_pred             E-CCEEEEEhhHhcccccCChhh---cCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEE
Confidence            9 89999999999 555555544   59999999999999999999999996432          147999999999999


Q ss_pred             EEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccce
Q 011538          385 KIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHII  463 (483)
Q Consensus       385 ~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~  463 (483)
                      +++++|+||+|+  |++||||+++++|.++.++.+.|++||.|+|+|+++| +++||.||+|++.++||+.+.+++++++
T Consensus       218 ~i~~~G~FVdlg--gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~  295 (486)
T PRK07899        218 SIVNFGAFVDLG--GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQ  295 (486)
T ss_pred             EEECCeEEEEEC--CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCC
Confidence            999999999996  6999999999999999999999999999999999998 7899999999999999999999998888


Q ss_pred             eeE
Q 011538          464 FLF  466 (483)
Q Consensus       464 ~~~  466 (483)
                      .+.
T Consensus       296 vv~  298 (486)
T PRK07899        296 IVP  298 (486)
T ss_pred             EEE
Confidence            773

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=6.3e-40  Score=357.42  Aligned_cols=271  Identities=26%  Similarity=0.354  Sum_probs=242.0

Q ss_pred             cchhhhccccccc--cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhccc
Q 011538          155 DDKVGEDKVSVEY--YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGK  232 (483)
Q Consensus       155 ~~~~~~~~~~~~~--~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~  232 (483)
                      +..+|+++++.+.  +++++|++|+|+|+++++++++||+|++.+||||.+|+.+..                       
T Consensus        11 ~~~~f~~~l~~~~~~~~~~~G~~v~G~V~~v~~~~~~Vdig~k~~g~lp~~e~~~~~-----------------------   67 (565)
T PRK06299         11 MEESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQ-----------------------   67 (565)
T ss_pred             chHHHHHHHHhhcccccCCCCCEEEEEEEEEECCEEEEEeCCCeEEEEEHHHhcCcc-----------------------
Confidence            3467999998776  779999999999999999999999999999999999985310                       


Q ss_pred             ceeeeccccccccCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCe
Q 011538          233 MGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGG  311 (483)
Q Consensus       233 v~vv~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G  311 (483)
                                        ....+++||+++|.|++. +.+|+++||++++.....|+++.++++.|++++|+|+++.++|
T Consensus        68 ------------------~~~~~~vG~~i~~~V~~~~~~~~~i~lS~k~~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G  129 (565)
T PRK06299         68 ------------------GELEVKVGDEVEVYVERIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGG  129 (565)
T ss_pred             ------------------ccccCCCCCEEEEEEEEEECCCCcEEEechHHHHHHHHHHHHHHhhCCCEEEEEEEEEECCE
Confidence                              012478999999999995 5678999999999999999999999999999999999999999


Q ss_pred             EEEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh----------hcCCCCCcEEE
Q 011538          312 LLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLE  380 (483)
Q Consensus       312 ~fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e----------~~~l~vG~iv~  380 (483)
                      ++|+++|++||||.+++ +.+.+++.   ..+|+++.|+|+++|++++++.+|+|++++          ...+++|+++.
T Consensus       130 ~~V~~~g~~gfip~s~~~~~~~~~~~---~~vG~~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~  206 (565)
T PRK06299        130 FTVDLNGVEAFLPGSQVDVRPVRDTD---PLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVE  206 (565)
T ss_pred             EEEEECCEEEEEEHHHccCcCCCChH---HhCCCEEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEE
Confidence            99999999999999999 55555543   369999999999999999999999997643          14799999999


Q ss_pred             EEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCccccccc
Q 011538          381 GTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKE  459 (483)
Q Consensus       381 G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~  459 (483)
                      |+|++++++|+||+++  |++||+|.++++|.++.++.+.|++||+|+|+|+++| ++++|.||+|++.+|||+.+.+++
T Consensus       207 g~V~~v~~~G~~V~i~--g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~~  284 (565)
T PRK06299        207 GVVKNITDYGAFVDLG--GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKY  284 (565)
T ss_pred             EEEEEEeCCeEEEEEC--CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhhC
Confidence            9999999999999997  6999999999999999999999999999999999998 789999999999999999999999


Q ss_pred             ccceeeEEEEee
Q 011538          460 VHIIFLFILLFN  471 (483)
Q Consensus       460 ~V~~~~~~~~~~  471 (483)
                      ++++.+.-.+.+
T Consensus       285 ~~G~~v~g~V~~  296 (565)
T PRK06299        285 PVGSKVKGKVTN  296 (565)
T ss_pred             CCCCEEEEEEEE
Confidence            999988444443

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

Probab=100.00  E-value=1.9e-40  Score=353.74  Aligned_cols=276  Identities=21%  Similarity=0.232  Sum_probs=242.7

Q ss_pred             hhhhccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceee
Q 011538          157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV  236 (483)
Q Consensus       157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv  236 (483)
                      -+.++.|.........|.+|.|+|+...+.|+.|+++. ..||||.|++..+.                          +
T Consensus        90 ~~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~g-vr~FlP~S~v~~r~--------------------------v  142 (541)
T COG0539          90 AERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEG-VRAFLPGSLVDVRP--------------------------V  142 (541)
T ss_pred             HHHHHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEECC-EEEeccHHHhcccc--------------------------c
Confidence            35567777777778899999999999999999999964 99999999985331                          0


Q ss_pred             eccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHH---hhhHHHHHHhhCCCeEEEEEEEEECCeE
Q 011538          237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRK---MAWHRVRQIKQLNEPIEVKFTEWNTGGL  312 (483)
Q Consensus       237 ~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~~---~~w~~L~~~~k~GeiV~GkV~~v~k~G~  312 (483)
                        .            .....+|..+.+.|++.| .++++++|+|.....   +....+.+.++.|++++|+|++++++|+
T Consensus       143 --~------------d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~Ga  208 (541)
T COG0539         143 --R------------DLDPLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGA  208 (541)
T ss_pred             --c------------cccccCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcE
Confidence              0            011348999999999976 578999999998653   2233445567999999999999999999


Q ss_pred             EEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh----Hhhh--cCCCCCcEEEEEEEE
Q 011538          313 LTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLEGTVKK  385 (483)
Q Consensus       313 fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~----~~e~--~~l~vG~iv~G~V~~  385 (483)
                      ||+++|++|++|.++| |.|+.+|+++. ++||+|+|+|+++|++++|+.||+|+    ||+.  ..+.+|+.+.|+|++
T Consensus       209 fVdigGvdGLlHiseiS~~rv~~P~~vv-kvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~  287 (541)
T COG0539         209 FVDIGGVDGLLHISEISWKRVDHPSEVV-KVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTN  287 (541)
T ss_pred             EEEecCeeeEEehhhccccccCCHHHhc-ccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEE
Confidence            9999999999999999 89999999986 99999999999999999999999997    5654  589999999999999


Q ss_pred             EeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCccccccccccee
Q 011538          386 IYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHIIF  464 (483)
Q Consensus       386 I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~  464 (483)
                      +++|||||++.+ |++||+|+|||||.+...|++++++||+|.|+|+++| +++||+||||++.+|||+.+.++|++++.
T Consensus       288 i~~~GafVei~~-GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~  366 (541)
T COG0539         288 LTDYGAFVEIEE-GVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPVGDV  366 (541)
T ss_pred             eecCcEEEEecC-CccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcCCCCe
Confidence            999999999999 8999999999999999999999999999999999998 88999999999999999999999999999


Q ss_pred             eEEEEeecccc
Q 011538          465 LFILLFNKQYS  475 (483)
Q Consensus       465 ~~~~~~~~~~~  475 (483)
                      +.=.+.++..-
T Consensus       367 v~g~v~~~t~~  377 (541)
T COG0539         367 VEGKVKSITDF  377 (541)
T ss_pred             EEEEEeeeccc
Confidence            96666665543

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=3.4e-38  Score=329.42  Aligned_cols=268  Identities=31%  Similarity=0.413  Sum_probs=237.5

Q ss_pred             hhhhccccccccCCCCCcEEEEEEEEEeCCeEEEEe-CCceeeEeecccccccccchhhhhhhhhhhhhhHHhhccccee
Q 011538          157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNV-GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI  235 (483)
Q Consensus       157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~Vdi-G~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~v  235 (483)
                      .+|++.+. ...++++|++|.|+|++++++|++|++ |.+.+|+||.+|+...+.                         
T Consensus         3 ~~~~~~~~-~~~~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~-------------------------   56 (390)
T PRK06676          3 EEFEESLN-SVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHI-------------------------   56 (390)
T ss_pred             HHHHHHhh-hhhcccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccccc-------------------------
Confidence            46888887 888999999999999999999999999 889999999999863210                         


Q ss_pred             eeccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEE
Q 011538          236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT  314 (483)
Q Consensus       236 v~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV  314 (483)
                                   .+....+++|+.|.|+|+..+ .++++.||++++.....|+.+.++++.|++++|+|+++.++|++|
T Consensus        57 -------------~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V  123 (390)
T PRK06676         57 -------------EDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVV  123 (390)
T ss_pred             -------------cCcccccCCCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEE
Confidence                         011235889999999999964 567899999999888899999999999999999999999999999


Q ss_pred             EECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh----------hcCCCCCcEEEEEE
Q 011538          315 RIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGTV  383 (483)
Q Consensus       315 ~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e----------~~~l~vG~iv~G~V  383 (483)
                      +++|++||||.+++ +.+..++..   .+|+.+.|+|+++|++++++.+|+|....          ...+++|+++.|+|
T Consensus       124 ~~~G~~gflp~~el~~~~~~~~~~---~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V  200 (390)
T PRK06676        124 DVEGVRGFIPASLISTRFVEDFSD---FKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTV  200 (390)
T ss_pred             EECCEEEEEEHHHcCCccCCChHH---cCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEE
Confidence            99999999999999 555666554   48999999999999999999999997532          14689999999999


Q ss_pred             EEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccc
Q 011538          384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHI  462 (483)
Q Consensus       384 ~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~  462 (483)
                      ++++++|+||+++  +++|+||.++++|.++.++.+.|++||.|+|+|++++ ++++|.||+|++.++||+.+.+.++++
T Consensus       201 ~~v~~~G~fV~l~--~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G  278 (390)
T PRK06676        201 ARLTDFGAFVDIG--GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEG  278 (390)
T ss_pred             EEEecceEEEEeC--CeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCC
Confidence            9999999999996  5999999999999999999999999999999999998 689999999999999999998899999


Q ss_pred             eeeEEE
Q 011538          463 IFLFIL  468 (483)
Q Consensus       463 ~~~~~~  468 (483)
                      +.+.-.
T Consensus       279 ~~v~g~  284 (390)
T PRK06676        279 DVIEGT  284 (390)
T ss_pred             cEEEEE
Confidence            888333

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=2e-38  Score=340.64  Aligned_cols=275  Identities=24%  Similarity=0.292  Sum_probs=237.6

Q ss_pred             hhhhcccccccc----CCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhccc
Q 011538          157 KVGEDKVSVEYY----EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGK  232 (483)
Q Consensus       157 ~~~~~~~~~~~~----~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~  232 (483)
                      ++|+++++.+.+    .+++|++|+|+|+++++++++||+|++.+|+||.+|+....                       
T Consensus        15 ~~f~~~l~~~~~~~~~~~~~G~~v~G~V~~v~~~~v~Vdig~k~eg~ip~~e~~~~~-----------------------   71 (491)
T PRK13806         15 ESFAELLEAYEGERKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDAD-----------------------   71 (491)
T ss_pred             HHHHHHHHhhhhhccccCCCCCEEEEEEEEEECCEEEEEECCCcEEEEEHHHhcCcc-----------------------
Confidence            578888876653    39999999999999999999999999999999999985210                       


Q ss_pred             ceeeeccccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeE
Q 011538          233 MGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL  312 (483)
Q Consensus       233 v~vv~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~  312 (483)
                                        ....+++|+++++.|++.+ ++.+.||++.. ....|..+.++++.|++++|+|+++.++|+
T Consensus        72 ------------------~~~~~~~G~~i~~~Vi~~~-~~~~~lS~~~~-~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~  131 (491)
T PRK13806         72 ------------------GELTVAVGDEVELYVVSVN-GQEIRLSKALS-GQGGAAMLEEAYENGVPVEGKVTGTCKGGF  131 (491)
T ss_pred             ------------------ccccccCCCEEEEEEEEEc-CCEEEEEhHHh-hhhhHHHHHHHHhCCCEEEEEEEEEEcCCE
Confidence                              0123789999999999854 46799997754 567999999999999999999999999999


Q ss_pred             EEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh----------hcCCCCCcEEEE
Q 011538          313 LTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEG  381 (483)
Q Consensus       313 fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e----------~~~l~vG~iv~G  381 (483)
                      +|+++|++||||.|++ +....++..   .+|+++.|+|+++|++++++.+|+|+.++          ...+++|+++.|
T Consensus       132 ~V~i~g~~~flP~s~~~~~~~~~~~~---~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G  208 (491)
T PRK13806        132 NVEVLGRRAFCPVSQIDLRYVEDPES---YVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEG  208 (491)
T ss_pred             EEEECCEEEEEEHHHhccccCCChHH---cCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEE
Confidence            9999999999999999 555666654   48999999999999999999999997642          136999999999


Q ss_pred             EEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CC----CeEEEEEecCCCCcCcccc
Q 011538          382 TVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP----DKISLSIADLESEPGLFVS  456 (483)
Q Consensus       382 ~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek----~rI~LSLK~~~~dPw~~l~  456 (483)
                      +|+++.++|+||++++ |+.||||.++++|.++.++.+.|++||.|+|+|+++| ++    .||.||+|++.++||+.+.
T Consensus       209 ~V~~v~~~G~fV~l~~-gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~  287 (491)
T PRK13806        209 TVTRLAPFGAFVELAP-GVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVG  287 (491)
T ss_pred             EEEEEeCCeEEEEcCC-CcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhh
Confidence            9999999999999987 7999999999999999999999999999999999998 43    4899999999999999999


Q ss_pred             cccccceeeEEEEeecccceEE
Q 011538          457 DKEVHIIFLFILLFNKQYSVWF  478 (483)
Q Consensus       457 ~k~~V~~~~~~~~~~~~~~~~~  478 (483)
                      +++++++.+.-.+.+-...-.|
T Consensus       288 ~~~~~G~~v~G~V~~v~~~G~f  309 (491)
T PRK13806        288 DRLKAGDKVTGKVVRLAPFGAF  309 (491)
T ss_pred             ccCCCCCEEEEEEEEEeCceEE
Confidence            9999999995555444443333

>TIGR00717 rpsA ribosomal protein S1

Probab=100.00  E-value=1.3e-37  Score=335.50  Aligned_cols=273  Identities=26%  Similarity=0.364  Sum_probs=238.9

Q ss_pred             hhhcccccc--ccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhccccee
Q 011538          158 VGEDKVSVE--YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI  235 (483)
Q Consensus       158 ~~~~~~~~~--~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~v  235 (483)
                      +|+++++.+  ..++++|++|.|+|+++++++++||+|++.+|++|.+|+...                           
T Consensus         2 ~f~~~~~~~~~~~~~~~G~~v~g~V~~i~~~~~~v~~g~k~~g~i~~~E~~~~---------------------------   54 (516)
T TIGR00717         2 SFAQLLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDA---------------------------   54 (516)
T ss_pred             hHHHHHhhhcccccCCCCCEEEEEEEEEECCEEEEEcCCCcEEEEEHHHhcCC---------------------------
Confidence            578888665  346899999999999999999999999999999999988521                           


Q ss_pred             eeccccccccCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEE
Q 011538          236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT  314 (483)
Q Consensus       236 v~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV  314 (483)
                                      ...+++||++.+.|.+. +..|++.||+++......|..++++++.|++++|+|+++.++|++|
T Consensus        55 ----------------~~~~~vGd~i~~~V~~~~~~~g~i~lS~~~~~~~~~~~~l~~a~~~g~~v~g~V~~~~~~g~~V  118 (516)
T TIGR00717        55 ----------------PLEIQVGDEVEVYLDRVEDRFGETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIV  118 (516)
T ss_pred             ----------------ccCCCCCCEEEEEEEEEeCCCCcEEEEHHHhhhhHHHHHHHHHhhCCCeEEEEEEEEECCEEEE
Confidence                            13478999999999984 4679999999999888999999999999999999999999999999


Q ss_pred             EECCeEEEeeccccccc-cCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh----------hcCCCCCcEEEEEE
Q 011538          315 RIEGLRAFLPKAELLSR-VNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGTV  383 (483)
Q Consensus       315 ~I~Gi~gFVP~Sel~~r-v~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e----------~~~l~vG~iv~G~V  383 (483)
                      +++|++||||.+++..+ .++.   ...+|++++|+|+++|++++++++|+|+.+.          ...+++|++++|+|
T Consensus       119 ~i~g~~~flP~s~~~~~~~~~~---~~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V  195 (516)
T TIGR00717       119 DLNGVEAFLPGSQVDVKPIKDL---DSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVV  195 (516)
T ss_pred             EECCEEEEEeHHHhcCcccCch---hhhCCCEEEEEEEEEECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEE
Confidence            99999999999999533 2332   2369999999999999999999999997642          14799999999999


Q ss_pred             EEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccc
Q 011538          384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHI  462 (483)
Q Consensus       384 ~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~  462 (483)
                      +++.++|+||+++  |++||+|.++++|.+..++.+.|++||+|.|+|+++| +++++.||+|++.++||+.+.++++++
T Consensus       196 ~~i~~~G~~V~l~--g~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G  273 (516)
T TIGR00717       196 KNITDFGAFVDLG--GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVG  273 (516)
T ss_pred             EEEECCeEEEEEC--CEEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccCC
Confidence            9999999999996  6899999999999999999999999999999999998 778999999999999999998899999


Q ss_pred             eeeEEEEeecccceEE
Q 011538          463 IFLFILLFNKQYSVWF  478 (483)
Q Consensus       463 ~~~~~~~~~~~~~~~~  478 (483)
                      +.+.-.+.+-...-.|
T Consensus       274 ~i~~g~V~~v~~~G~f  289 (516)
T TIGR00717       274 DKITGRVTNLTDYGVF  289 (516)
T ss_pred             CEEEEEEEEeeCCcEE
Confidence            9995555444443344

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=2.8e-37  Score=347.68  Aligned_cols=271  Identities=16%  Similarity=0.232  Sum_probs=233.8

Q ss_pred             cccccccCCCCCcEEEEEEEEEe--CCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecc
Q 011538          162 KVSVEYYEPKPGDFVIGVVVSGN--ENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD  239 (483)
Q Consensus       162 ~~~~~~~~ik~GdiV~G~Vv~V~--~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~  239 (483)
                      .|+.....++.|++|+|+|++++  ++|++||+|++.+||||.+|+....           ..+                
T Consensus       388 ~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~-----------~~~----------------  440 (863)
T PRK12269        388 LKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQK-----------VDA----------------  440 (863)
T ss_pred             HHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhcccc-----------ccc----------------
Confidence            34444456789999999999985  4699999999999999999984210           000                


Q ss_pred             ccccccCCCCCCCCcccCCCEEEEEEEEEc------CCCcEEEEehHHHHHhhhHHHHHHh---hCCCeEEEEEEEEECC
Q 011538          240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRT------LSGRPLLSTRRLFRKMAWHRVRQIK---QLNEPIEVKFTEWNTG  310 (483)
Q Consensus       240 d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d------~~G~iiLS~k~~~~~~~w~~L~~~~---k~GeiV~GkV~~v~k~  310 (483)
                                   ....+|+.+++.|+..+      .++++++|+|++..+..|..+.+++   +.|++++|+|.++.++
T Consensus       441 -------------~~~~vG~~ie~~V~~~~~~~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~  507 (863)
T PRK12269        441 -------------PESLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSF  507 (863)
T ss_pred             -------------hHHhCCCeEEEEEEEEecccccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCC
Confidence                         11248999999998753      3468999999999888998887765   4789999999999999


Q ss_pred             eEEEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH----hhh--cCCCCCcEEEEEE
Q 011538          311 GLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTV  383 (483)
Q Consensus       311 G~fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~--~~l~vG~iv~G~V  383 (483)
                      |+||+++|++||||.|++ |.++.++.+.. ++||+++|+|+++|++++++.||+|+.    |..  ..+++|++++|+|
T Consensus       508 G~fVdl~Gv~Gfvp~SeiS~~~v~~~~~~~-kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V  586 (863)
T PRK12269        508 GAFIDLGGFDGLLHVNDMSWGHVARPREFV-KKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRV  586 (863)
T ss_pred             cEEEEECCEEEEEEchhccccccCCHHHhc-cCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEE
Confidence            999999999999999999 78888888765 899999999999999999999999964    432  3699999999999


Q ss_pred             EEEeCceEEEEECCCceEEEEeccCcCc-ccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCccccccccc
Q 011538          384 KKIYPYGAQIRIGDSNRSGLLHISNMSR-TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVH  461 (483)
Q Consensus       384 ~~I~~~GaFV~I~~~gi~GLlhiSels~-~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V  461 (483)
                      ++|++||+||++++ |++||+|+|+++| .++.+|.+.|++||+|+|+|+++| +++||+||+|++.+|||+.+.++|++
T Consensus       587 ~~I~~fG~fVeL~~-gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~v  665 (863)
T PRK12269        587 TKIADFGAFIELAE-GIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPV  665 (863)
T ss_pred             EEEeCCeEEEEecC-CceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHhCCC
Confidence            99999999999987 7999999999999 588999999999999999999998 78999999999999999999999999


Q ss_pred             ceeeEEEEeeccc
Q 011538          462 IIFLFILLFNKQY  474 (483)
Q Consensus       462 ~~~~~~~~~~~~~  474 (483)
                      |+.+.-.+.+-..
T Consensus       666 G~~v~G~V~~i~~  678 (863)
T PRK12269        666 GARFTRRIVKVTN  678 (863)
T ss_pred             CCEEEEEEEEEec
Confidence            9999655555443

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=2.5e-36  Score=340.09  Aligned_cols=298  Identities=21%  Similarity=0.275  Sum_probs=246.6

Q ss_pred             cCCCCChhhhhhhhhcccccCC--ChHHHhhhccccccccccccc--cchhhhcccccc-ccCCCCCcEEEEEEEEEeCC
Q 011538          112 KSEKPDEEEALAPFLKFFKPRD--SAEEVEEEGSEVGVSRESIDV--DDKVGEDKVSVE-YYEPKPGDFVIGVVVSGNEN  186 (483)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~-~~~ik~GdiV~G~Vv~V~~~  186 (483)
                      .+..++-+|.+.=.++..+.+.  .+|        ..+  ++.+|  ..---..+++.. +..+++|++|+|+|++++++
T Consensus       266 Dts~l~ieevv~~i~~~~~~~~~~~~~--------~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~G~iV~G~Vv~i~~~  335 (863)
T PRK12269        266 DTSCLTIEEVCERIAREAHRRALWGGE--------RSV--ENQEGKGTPLVPRQLQERYSFEAPEPGSVRMGTVVQVNAG  335 (863)
T ss_pred             ECCCCCHHHHHHHHHHHHHhccccccc--------ccc--ccccccCCCchhHHHHHhhccccCCCCCEEEEEEEEEECC
Confidence            3567888999998888888765  211        111  01111  001122444444 78899999999999999999


Q ss_pred             eEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCCCCCCCCcccCCCEEEEEEE
Q 011538          187 KLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVL  266 (483)
Q Consensus       187 gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi  266 (483)
                      ++|||+|++.+|++|.+|+..                                              .+++||+|+|.|+
T Consensus       336 ~v~VdiG~K~eGiI~~~E~~~----------------------------------------------~~kvGd~i~~~V~  369 (863)
T PRK12269        336 TVFVDIGGKSEGRVPVEEFEA----------------------------------------------PPKAGDGVRVYVE  369 (863)
T ss_pred             EEEEEeCCCceEEeEHHHhcc----------------------------------------------CCCCCCEEEEEEE
Confidence            999999999999999888731                                              1479999999999


Q ss_pred             EEcCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEE--CCeEEEEEC-CeEEEeeccccc-cccCChhhhhhhc
Q 011538          267 GRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN--TGGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKV  342 (483)
Q Consensus       267 ~~d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~--k~G~fV~I~-Gi~gFVP~Sel~-~rv~~~~~l~~~V  342 (483)
                      +.+.+| +.||++++...+.|+.+.++++.|++|+|+|+++.  ++|++|+++ |++||||.||+. ....++.   ..+
T Consensus       370 ~~~~~~-~~LS~~~~~~~~~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~~~~~~---~~v  445 (863)
T PRK12269        370 RVTPYG-PELSKTKADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPE---SLI  445 (863)
T ss_pred             EEcCCc-eEEEehHhhhhHHHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhccccccchH---HhC
Confidence            866566 89999999999999999999999999999999974  689999997 899999999994 3333433   358


Q ss_pred             CCEEEEEEEEEEC-----CCCceeechhhHhh----------hcCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEecc
Q 011538          343 GRRMYVQITRINE-----DTNDLILSEREAWA----------TLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHIS  407 (483)
Q Consensus       343 Gq~V~vkVl~ID~-----e~~rLiLS~K~~~e----------~~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiS  407 (483)
                      |++++|+|+++++     +++++++|+|+.++          ..++++|++|.|+|++++++|+||+++  |++||||.|
T Consensus       446 G~~ie~~V~~~~~~~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~--Gv~Gfvp~S  523 (863)
T PRK12269        446 GLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLG--GFDGLLHVN  523 (863)
T ss_pred             CCeEEEEEEEEecccccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEEC--CEEEEEEch
Confidence            9999999999975     34689999997532          147889999999999999999999996  699999999


Q ss_pred             CcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccceeeEEEEee
Q 011538          408 NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHIIFLFILLFN  471 (483)
Q Consensus       408 els~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~~~~~~~~  471 (483)
                      +++|.++.++.+.+++||+|+|+|+++| +++|+.||+|++.++||+.+.+++++|+.+.-.+.+
T Consensus       524 eiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~  588 (863)
T PRK12269        524 DMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTK  588 (863)
T ss_pred             hccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEE
Confidence            9999999999999999999999999998 689999999999999999999999999998444433

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

Probab=100.00  E-value=4.2e-36  Score=332.24  Aligned_cols=280  Identities=29%  Similarity=0.377  Sum_probs=244.4

Q ss_pred             hhhhccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceee
Q 011538          157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV  236 (483)
Q Consensus       157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv  236 (483)
                      .++.+.++.....+++|++|.|+|.+++++++||++|++.+|+||.+|++...           ..+             
T Consensus       287 ~~~~~~~~~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~-----------~~~-------------  342 (647)
T PRK00087        287 NEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDE-----------ISS-------------  342 (647)
T ss_pred             HHHHHHHHHHHhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccc-----------cCC-------------
Confidence            34455567788899999999999999999999999999999999999986321           001             


Q ss_pred             eccccccccCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEE
Q 011538          237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR  315 (483)
Q Consensus       237 ~~~d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~  315 (483)
                                    ....+++|+.+.++|++. +.+|++.||++++.....|+.+.++++.|+++.|+|+++.++|++|+
T Consensus       343 --------------~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~  408 (647)
T PRK00087        343 --------------LKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVD  408 (647)
T ss_pred             --------------hhhccCCCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEE
Confidence                          123488999999999995 46899999999998888999999999999999999999999999999


Q ss_pred             ECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCc-eeechhhHhh----------hcCCCCCcEEEEEE
Q 011538          316 IEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTND-LILSEREAWA----------TLNLREGTLLEGTV  383 (483)
Q Consensus       316 I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~r-LiLS~K~~~e----------~~~l~vG~iv~G~V  383 (483)
                      ++|++||||.+++ +.+..++..   .+|+.+.|+|+++|+++++ +.+|+|..+.          ..++++|+++.|+|
T Consensus       409 lggi~gfiP~sel~~~~~~d~~~---~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V  485 (647)
T PRK00087        409 YGGVRAFLPASHVELGYVEDLSE---YKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEV  485 (647)
T ss_pred             ECCEEEEEEHHHhCccccCCHHH---hCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEE
Confidence            9999999999999 555555543   4899999999999999888 9999998642          13689999999999


Q ss_pred             EEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccc
Q 011538          384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHI  462 (483)
Q Consensus       384 ~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~  462 (483)
                      ++++++|+||++ + +++||+|.++++|.++.++.+.|++||.|+|+|++++ ++++|.||+|++.++||..+.++++++
T Consensus       486 ~~v~~~G~fV~l-~-gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G  563 (647)
T PRK00087        486 KRLTDFGAFVDI-G-GVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVG  563 (647)
T ss_pred             EEEeCCcEEEEE-C-CEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCC
Confidence            999999999999 5 7999999999999999999999999999999999998 789999999999999999999999999


Q ss_pred             eeeEEEEeecccceEEE
Q 011538          463 IFLFILLFNKQYSVWFL  479 (483)
Q Consensus       463 ~~~~~~~~~~~~~~~~~  479 (483)
                      +.+.-.+.+-...-+|.
T Consensus       564 ~~v~g~V~~i~~~G~fV  580 (647)
T PRK00087        564 SIVLGKVVRIAPFGAFV  580 (647)
T ss_pred             eEEEEEEEEEECCeEEE
Confidence            98866666655555554

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=7.9e-36  Score=320.59  Aligned_cols=268  Identities=23%  Similarity=0.256  Sum_probs=229.9

Q ss_pred             ccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccc
Q 011538          163 VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAI  242 (483)
Q Consensus       163 ~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~  242 (483)
                      |......++.|++|+|+|.++.++|++|+++ +..||||.+++...+           ..++                  
T Consensus       106 ~~~l~~~~~~g~~v~g~V~~~~~~G~~V~i~-g~~~flP~s~~~~~~-----------~~~~------------------  155 (491)
T PRK13806        106 AAMLEEAYENGVPVEGKVTGTCKGGFNVEVL-GRRAFCPVSQIDLRY-----------VEDP------------------  155 (491)
T ss_pred             HHHHHHHHhCCCEEEEEEEEEEcCCEEEEEC-CEEEEEEHHHhcccc-----------CCCh------------------
Confidence            3444455679999999999999999999997 689999999985321           0011                  


Q ss_pred             cccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHH---HhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC-
Q 011538          243 AMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-  317 (483)
Q Consensus       243 ~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~---~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~-  317 (483)
                                . -.+|+++.|.|+..| .++++.||++....   ...|..+...++.|++++|+|+++.++|+||+++ 
T Consensus       156 ----------~-~~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~  224 (491)
T PRK13806        156 ----------E-SYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAP  224 (491)
T ss_pred             ----------H-HcCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCC
Confidence                      1 128999999999976 46789999998853   4688888788899999999999999999999995 


Q ss_pred             CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCC----CceeechhhH----hhh--cCCCCCcEEEEEEEEE
Q 011538          318 GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDT----NDLILSEREA----WAT--LNLREGTLLEGTVKKI  386 (483)
Q Consensus       318 Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~----~rLiLS~K~~----~e~--~~l~vG~iv~G~V~~I  386 (483)
                      |+.||||.+++ |.++.++.++. ++|+.|+|+|+++|+++    +++.||+|+.    |..  .++++|+++.|+|+++
T Consensus       225 gv~g~v~~sels~~~~~~~~~~~-~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v  303 (491)
T PRK13806        225 GVEGMVHISELSWSRVQKADEAV-SVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRL  303 (491)
T ss_pred             CcEEEEEHHHCCCccccChhHhc-CCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEE
Confidence            89999999999 77888887764 89999999999999875    4799999975    543  3789999999999999


Q ss_pred             eCceEEEEECCCceEEEEeccCcCc-ccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCccccccccccee
Q 011538          387 YPYGAQIRIGDSNRSGLLHISNMSR-TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHIIF  464 (483)
Q Consensus       387 ~~~GaFV~I~~~gi~GLlhiSels~-~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~  464 (483)
                      +++|+||++++ |++||+|.++++| .++.++.+.|++||.|+|+|+++| +++||.||+|++.++||+.+.+++++++.
T Consensus       304 ~~~G~fV~l~~-gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~  382 (491)
T PRK13806        304 APFGAFVEILP-GIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTT  382 (491)
T ss_pred             eCceEEEEeCC-CcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCE
Confidence            99999999987 7999999999999 578899999999999999999998 78999999999999999999999999998


Q ss_pred             eEEEEeecc
Q 011538          465 LFILLFNKQ  473 (483)
Q Consensus       465 ~~~~~~~~~  473 (483)
                      +.-.+.+..
T Consensus       383 v~G~V~~i~  391 (491)
T PRK13806        383 VTGTVEKRA  391 (491)
T ss_pred             EEEEEEEEe
Confidence            855544443

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1.1e-34  Score=316.49  Aligned_cols=270  Identities=21%  Similarity=0.305  Sum_probs=232.7

Q ss_pred             ccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccc
Q 011538          161 DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDD  240 (483)
Q Consensus       161 ~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d  240 (483)
                      ..+...+.++++|+++.|+|+++.+.|+||++| +.+|+||.+|++..+           ..+                 
T Consensus       190 ~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~-----------~~~-----------------  240 (565)
T PRK06299        190 EEREELLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKR-----------VNH-----------------  240 (565)
T ss_pred             hHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccc-----------cCC-----------------
Confidence            345556778999999999999999999999998 899999999986320           111                 


Q ss_pred             cccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC-C
Q 011538          241 AIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-G  318 (483)
Q Consensus       241 ~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~-G  318 (483)
                                ....+++||.|.|+|+..| .++++.||++.+.. .+|..+.+.++.|+++.|+|+++.++|+||+++ |
T Consensus       241 ----------~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~-~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~  309 (565)
T PRK06299        241 ----------PSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGE-DPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEG  309 (565)
T ss_pred             ----------HhhcCCCCCEEEEEEEEEeCCCCeEEEEEEeccc-ChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCC
Confidence                      1234899999999999976 47899999998764 689999888999999999999999999999995 8


Q ss_pred             eEEEeecccc-cc-ccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH----hhh--cCCCCCcEEEEEEEEEeCce
Q 011538          319 LRAFLPKAEL-LS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTVKKIYPYG  390 (483)
Q Consensus       319 i~gFVP~Sel-~~-rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~--~~l~vG~iv~G~V~~I~~~G  390 (483)
                      +.||+|.+++ |. +..++.... .+|+.|+|+|+++|++++++.||+|+.    |..  ..+++|+++.|+|++++++|
T Consensus       310 v~Glv~~sel~~~~~~~~~~~~~-~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G  388 (565)
T PRK06299        310 IEGLVHVSEMSWTKKNKHPSKVV-SVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFG  388 (565)
T ss_pred             CEEEEEHHHcCccccccCHHHhc-CCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecce
Confidence            9999999999 43 345565543 799999999999999999999999864    432  36789999999999999999


Q ss_pred             EEEEECCCceEEEEeccCcCcccc-cCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccceeeEEE
Q 011538          391 AQIRIGDSNRSGLLHISNMSRTRV-TSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHIIFLFIL  468 (483)
Q Consensus       391 aFV~I~~~gi~GLlhiSels~~~i-~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~~~~~  468 (483)
                      +||++++ +++|++|.++++|.+. .++.+.|++||.|+|+|+++| ++++|.||+|++..+||..+.+.+++++.+.-.
T Consensus       389 ~fV~l~~-~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV~G~  467 (565)
T PRK06299        389 AFVGLEG-GIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGT  467 (565)
T ss_pred             EEEECCC-CCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEEEEE
Confidence            9999987 7999999999999877 888999999999999999998 789999999999999999988889999988444


Q ss_pred             Eeec
Q 011538          469 LFNK  472 (483)
Q Consensus       469 ~~~~  472 (483)
                      +.+.
T Consensus       468 V~~v  471 (565)
T PRK06299        468 VTEV  471 (565)
T ss_pred             EEEE
Confidence            4433

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1.2e-34  Score=302.59  Aligned_cols=254  Identities=25%  Similarity=0.330  Sum_probs=219.7

Q ss_pred             cccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecccc
Q 011538          162 KVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA  241 (483)
Q Consensus       162 ~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~  241 (483)
                      .|......+++|+++.|+|+++.++|++|+++ +..||||.+|+...+           ..++                 
T Consensus        95 ~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~-G~~gflp~~el~~~~-----------~~~~-----------------  145 (390)
T PRK06676         95 AWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVE-GVRGFIPASLISTRF-----------VEDF-----------------  145 (390)
T ss_pred             hHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCcc-----------CCCh-----------------
Confidence            34444556789999999999999999999995 469999999986321           0011                 


Q ss_pred             ccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHH---hhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC
Q 011538          242 IAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRK---MAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE  317 (483)
Q Consensus       242 ~~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~~---~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~  317 (483)
                                 .. .+|+.+.|+|+..+ ..+++.||+|.+...   ..|..+...++.|++++|+|+++.++|+||+++
T Consensus       146 -----------~~-~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~  213 (390)
T PRK06676        146 -----------SD-FKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG  213 (390)
T ss_pred             -----------HH-cCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC
Confidence                       11 28999999999865 468899999987442   577877778899999999999999999999999


Q ss_pred             CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH----hhh--cCCCCCcEEEEEEEEEeCce
Q 011538          318 GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTVKKIYPYG  390 (483)
Q Consensus       318 Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~--~~l~vG~iv~G~V~~I~~~G  390 (483)
                      |++||||.+++ +.++.++.+.. ++|+.|+|+|+++|++++++.+|+|+.    |..  ..+++|+++.|+|++++++|
T Consensus       214 ~v~g~v~~sels~~~~~~~~~~~-~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~~G  292 (390)
T PRK06676        214 GVDGLVHISELSHERVEKPSEVV-SVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFG  292 (390)
T ss_pred             CeEEEEEHHHcCccccCCHHHhc-CCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeCce
Confidence            99999999999 67777777764 899999999999999999999999864    432  36899999999999999999


Q ss_pred             EEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccc
Q 011538          391 AQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDK  458 (483)
Q Consensus       391 aFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k  458 (483)
                      +||++.+ |+.||+|+++++|.++.++.+.|++||.|+|+|+++| ++++|.||+|++.++||+.+.++
T Consensus       293 ~fV~l~~-gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~~~~~~~  360 (390)
T PRK06676        293 AFVEVLP-GVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEEEDRR  360 (390)
T ss_pred             EEEEECC-CCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEecccChhhhhhhh
Confidence            9999987 7999999999999999999999999999999999998 78999999999999999988765

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1.9e-34  Score=308.16  Aligned_cols=247  Identities=20%  Similarity=0.268  Sum_probs=212.0

Q ss_pred             ccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccc
Q 011538          161 DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDD  240 (483)
Q Consensus       161 ~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d  240 (483)
                      +.|+..-...+.|++|+|+|+++.++|++|++|  ..||||.+++...+           ..+                 
T Consensus       111 ~~w~~ie~~~e~g~~V~G~V~~v~k~G~~VdlG--i~gflP~Sel~~~~-----------~~~-----------------  160 (486)
T PRK07899        111 RAWGTIEKIKEKDGVVTGTVIEVVKGGLILDIG--LRGFLPASLVEMRR-----------VRD-----------------  160 (486)
T ss_pred             chHHHHHHHhcCCCEEEEEEEEEECCeEEEEEC--CEEEEEhhHhcccc-----------cCC-----------------
Confidence            445533333458999999999999999999995  68999999874221           000                 


Q ss_pred             cccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHH---HhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEE
Q 011538          241 AIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI  316 (483)
Q Consensus       241 ~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~---~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I  316 (483)
                                  ..-.+|+.|.|+|+..+ ..++++||+|....   ...|..+...++.|++++|+|+++.++|+||++
T Consensus       161 ------------~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdl  228 (486)
T PRK07899        161 ------------LQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDL  228 (486)
T ss_pred             ------------hhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEE
Confidence                        01148999999999976 46789999997543   367888888889999999999999999999999


Q ss_pred             CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH----hhh--cCCCCCcEEEEEEEEEeCc
Q 011538          317 EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTVKKIYPY  389 (483)
Q Consensus       317 ~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~--~~l~vG~iv~G~V~~I~~~  389 (483)
                      +|++||||.+++ |.++.++.++. ++||.|+|+|+++|+++++|.||+|+.    |..  ..+.+|+++.|+|++|+++
T Consensus       229 ggv~Glv~~Sels~~~v~~~~~~~-kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~f  307 (486)
T PRK07899        229 GGVDGLVHVSELSWKHIDHPSEVV-EVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPF  307 (486)
T ss_pred             CCEEEEEEHHHCCCcccCCHHHhc-CCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEecc
Confidence            999999999999 78888887764 899999999999999999999999963    543  2577899999999999999


Q ss_pred             eEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCc
Q 011538          390 GAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEP  451 (483)
Q Consensus       390 GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dP  451 (483)
                      |+||++.+ |+.||+|++++++.++.++.+.|++||+|+|+|+++| +++||.||+|++.++-
T Consensus       308 GvFVeL~~-gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~~~  369 (486)
T PRK07899        308 GAFVRVEE-GIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQANEGV  369 (486)
T ss_pred             EEEEEeCC-CcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEEEcccCC
Confidence            99999987 7999999999999999999999999999999999998 8899999999998764

>TIGR00717 rpsA ribosomal protein S1

Probab=100.00  E-value=3.9e-34  Score=308.56  Aligned_cols=272  Identities=21%  Similarity=0.276  Sum_probs=230.6

Q ss_pred             hccccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecc
Q 011538          160 EDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD  239 (483)
Q Consensus       160 ~~~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~  239 (483)
                      +..+...+..+++|++++|+|.++.+.|+||++| +.+|+||.+|++...           ..++               
T Consensus       175 ~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~-g~~g~lp~~e~s~~~-----------~~~~---------------  227 (516)
T TIGR00717       175 SQAREELLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKR-----------VKHP---------------  227 (516)
T ss_pred             HHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCCC-----------CCCH---------------
Confidence            3455666778999999999999999999999997 589999999986321           1111               


Q ss_pred             ccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC-
Q 011538          240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-  317 (483)
Q Consensus       240 d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d-~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~-  317 (483)
                                  ...+++|+.+.|+|+..| .++++.||+|.+.. .+|+.+.+.++.|++++|+|+++.++|+||+++ 
T Consensus       228 ------------~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~-~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~  294 (516)
T TIGR00717       228 ------------SEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGE-DPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEE  294 (516)
T ss_pred             ------------HHhccCCCEEEEEEEEEECCCCcEEEEEEecch-hHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCC
Confidence                        124789999999999876 46889999998754 589998888899999999999999999999995 


Q ss_pred             CeEEEeecccc-cc-ccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH----hhh--cCCCCCcEEEEEEEEEeCc
Q 011538          318 GLRAFLPKAEL-LS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTVKKIYPY  389 (483)
Q Consensus       318 Gi~gFVP~Sel-~~-rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~--~~l~vG~iv~G~V~~I~~~  389 (483)
                      |+.||+|.+++ +. ...++.+.. .+|+.++|+|+++|++++++.||+|++    |..  ..+++|+++.|+|++++++
T Consensus       295 ~v~g~v~~sels~~~~~~~~~~~~-~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~  373 (516)
T TIGR00717       295 GIEGLVHVSEMSWVKKNSHPSKVV-KKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDF  373 (516)
T ss_pred             CCEEEEEHHHcCCccccCCHHHhc-cCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecc
Confidence            89999999999 43 344555443 799999999999999999999999864    432  3588999999999999999


Q ss_pred             eEEEEECCCceEEEEeccCcCcccc-cCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCcccccccccceeeEE
Q 011538          390 GAQIRIGDSNRSGLLHISNMSRTRV-TSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKEVHIIFLFI  467 (483)
Q Consensus       390 GaFV~I~~~gi~GLlhiSels~~~i-~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~~~~  467 (483)
                      |+||++++ +++||+|.++++|.+. .++...|++||.|.|+|+++| +++||.||+|++.+|||..+.+.+++++.+.-
T Consensus       374 G~fV~l~~-~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~g  452 (516)
T TIGR00717       374 GAFVELEG-GIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKG  452 (516)
T ss_pred             eEEEECCC-CCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEeeccccCCchhhhhhccCcceEEEE
Confidence            99999997 7999999999999754 456788999999999999998 78999999999999999999988999998855


Q ss_pred             EEeecc
Q 011538          468 LLFNKQ  473 (483)
Q Consensus       468 ~~~~~~  473 (483)
                      .+.+..
T Consensus       453 ~V~~v~  458 (516)
T TIGR00717       453 KVTEIK  458 (516)
T ss_pred             EEEEEe
Confidence            554443

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=9.3e-31  Score=289.74  Aligned_cols=247  Identities=24%  Similarity=0.335  Sum_probs=212.2

Q ss_pred             cccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecccc
Q 011538          162 KVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA  241 (483)
Q Consensus       162 ~~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~  241 (483)
                      .|......+++|+++.|+|+++.++|++|++|. .+||||.+|+...+-           .++                 
T Consensus       379 ~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lgg-i~gfiP~sel~~~~~-----------~d~-----------------  429 (647)
T PRK00087        379 AWKELEEAFENGEPVKGKVKEVVKGGLLVDYGG-VRAFLPASHVELGYV-----------EDL-----------------  429 (647)
T ss_pred             HHHHHHHHhhCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHhCcccc-----------CCH-----------------
Confidence            344444556899999999999999999999985 999999999864310           011                 


Q ss_pred             ccccCCCCCCCCcccCCCEEEEEEEEEcC-CCc-EEEEehHHHH---HhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEE
Q 011538          242 IAMSGGSGPGRPVVETGTVLFAEVLGRTL-SGR-PLLSTRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI  316 (483)
Q Consensus       242 ~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~-~G~-iiLS~k~~~~---~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I  316 (483)
                                 .. .+|+.+.|+|+..+. +++ +.+|+|....   ...|....+.++.|+++.|+|+++.++|+||++
T Consensus       430 -----------~~-~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l  497 (647)
T PRK00087        430 -----------SE-YKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI  497 (647)
T ss_pred             -----------HH-hCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEE
Confidence                       11 289999999998664 567 9999988753   345555666678999999999999999999999


Q ss_pred             CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH----hhh--cCCCCCcEEEEEEEEEeCc
Q 011538          317 EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTVKKIYPY  389 (483)
Q Consensus       317 ~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~----~e~--~~l~vG~iv~G~V~~I~~~  389 (483)
                      +|++||+|.+++ +.++.++.+.. .+|+.++++|+++|++++++.+|+|+.    |..  .++++|+++.|+|++++++
T Consensus       498 ~gv~Gll~~sels~~~~~~~~~~~-~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~  576 (647)
T PRK00087        498 GGVDGLLHVSEISWGRVEKPSDVL-KVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPF  576 (647)
T ss_pred             CCEEEEEEHHHcCccccCCHHHhc-CCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEECC
Confidence            999999999999 67777776654 899999999999999999999999964    432  3688999999999999999


Q ss_pred             eEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCc
Q 011538          390 GAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEP  451 (483)
Q Consensus       390 GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dP  451 (483)
                      |+||++.+ ++.||+|.+++++.++.++.+.|++||.|+|+|+++| +++|+.||+|++.++|
T Consensus       577 G~fV~l~~-~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~  638 (647)
T PRK00087        577 GAFVELEP-GVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP  638 (647)
T ss_pred             eEEEEECC-CCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence            99999988 7999999999999999999999999999999999998 7899999999999999

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.88  E-value=2.2e-21  Score=198.44  Aligned_cols=186  Identities=17%  Similarity=0.123  Sum_probs=150.1

Q ss_pred             HHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEECC-eEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCce
Q 011538          283 RKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEG-LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDL  360 (483)
Q Consensus       283 ~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~G-i~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rL  360 (483)
                      ....|+.+...++.|++++|+|+++.++|++|++++ .+||||.+++ +.+..++.+.. .+|+.++|+|++++++++++
T Consensus        18 f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~-~~G~~v~~~Vi~~~~~~~~i   96 (318)
T PRK07400         18 FAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVL-QPNETREFFILSDENEDGQL   96 (318)
T ss_pred             HHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHcc-CCCCEEEEEEEEEeCCCCeE
Confidence            344555555568999999999999999999999975 8999999999 67777777764 79999999999999999999


Q ss_pred             eechhhH-----hhh--cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEE
Q 011538          361 ILSEREA-----WAT--LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK  433 (483)
Q Consensus       361 iLS~K~~-----~e~--~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~  433 (483)
                      .||+|+.     |+.  .....|+++.|+|+++.++|+||+++  |++||||.|+++|.+..   +. .+|+.|+|+|++
T Consensus        97 ~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~--Gv~gfip~s~ls~~~~~---~~-~vG~~i~~kVl~  170 (318)
T PRK07400         97 TLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIE--GLRGFIPGSHISTRKPK---EE-LVGEELPLKFLE  170 (318)
T ss_pred             EEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC--CEEEEEEHHHcCccCCc---cc-cCCCEEEEEEEE
Confidence            9999863     543  24457999999999999999999996  69999999999986433   33 499999999999


Q ss_pred             Ee-CCCeEEEEEecCCCCcCcccccccccceeeEEEEeecccceEE
Q 011538          434 SM-FPDKISLSIADLESEPGLFVSDKEVHIIFLFILLFNKQYSVWF  478 (483)
Q Consensus       434 vd-ek~rI~LSLK~~~~dPw~~l~~k~~V~~~~~~~~~~~~~~~~~  478 (483)
                      +| +++||.||+|....++   ...++++|+.+.=.+.+-...-+|
T Consensus       171 id~~~~~i~lS~K~~~~~~---~~~~~k~G~vv~G~V~~I~~~G~f  213 (318)
T PRK07400        171 VDEERNRLVLSHRRALVER---KMNRLEVGEVVVGTVRGIKPYGAF  213 (318)
T ss_pred             EEcccCEEEEEhhHhhhhh---hhccCCCCCEEEEEEEEEECCeEE
Confidence            98 7799999999766543   345678888874333333333444

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

Probab=99.76  E-value=5.2e-17  Score=159.72  Aligned_cols=212  Identities=17%  Similarity=0.103  Sum_probs=169.2

Q ss_pred             CCCCCcEEEEEEEEEeCCeEEEEeCCcee-eEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          169 EPKPGDFVIGVVVSGNENKLDVNVGADLL-GTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       169 ~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~-G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      .+++|++..+.|++.++.|+|++-|.+.+ -++|.++..                                         
T Consensus         2 ~~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~-----------------------------------------   40 (287)
T COG2996           2 MIKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPE-----------------------------------------   40 (287)
T ss_pred             cccccceEEEEEEEeeceeEEEecCCCceEEeccccCCc-----------------------------------------
Confidence            46799999999999999999999876543 333333221                                         


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEE-CCeEEEEEC-CeEEEeec
Q 011538          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN-TGGLLTRIE-GLRAFLPK  325 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~-k~G~fV~I~-Gi~gFVP~  325 (483)
                          ...+++||+|.++++ .|.++++.+|.+.+..           ..|+.-.++|+.++ +-|+||++| .-+.+||.
T Consensus        41 ----~~e~evGdev~vFiY-~D~~~rl~aTt~~p~~-----------tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~  104 (287)
T COG2996          41 ----EDELEVGDEVTVFIY-VDSEDRLIATTREPKA-----------TVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPL  104 (287)
T ss_pred             ----CCccccCcEEEEEEE-ECCCCceeheeecceE-----------eecceeEEEEEEEcCCcceEEecCCCcceeeeh
Confidence                123679999999999 6889999999987753           68999999999999 679999996 46799999


Q ss_pred             cccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh--Hhhh--cCCC---CCcEEEEEEEEEeCceEEEEECCC
Q 011538          326 AELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE--AWAT--LNLR---EGTLLEGTVKKIYPYGAQIRIGDS  398 (483)
Q Consensus       326 Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~--~~e~--~~l~---vG~iv~G~V~~I~~~GaFV~I~~~  398 (483)
                      +++..    .++++..+|+++.|+ +.+|++ +|+....+.  .++.  ....   .|+.+.|+|+++...|.||-+.+ 
T Consensus       105 ~elp~----~~~~wpq~Gd~l~v~-l~~Dkk-~Ri~g~~a~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~-  177 (287)
T COG2996         105 DELPT----LKSLWPQKGDKLLVY-LYVDKK-GRIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITEN-  177 (287)
T ss_pred             hhccc----ccccCCCCCCEEEEE-EEEccC-CcEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcC-
Confidence            99842    223455799999999 588865 477776653  2221  1223   49999999999999999999977 


Q ss_pred             ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCCcC
Q 011538          399 NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPG  452 (483)
Q Consensus       399 gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~dPw  452 (483)
                      ++-||||.||..        ..++.|+++++||+.+.++++|.||++....+-.
T Consensus       178 ~~~GfIh~sEr~--------~~prlG~~l~~rVi~~reDg~lnLSl~p~~~E~l  223 (287)
T COG2996         178 GYLGFIHKSERF--------AEPRLGERLTARVIGVREDGKLNLSLRPRAHEML  223 (287)
T ss_pred             CeEEEEcchhhc--------ccccCCceEEEEEEEEccCCeeecccccccHHhh
Confidence            899999999975        5689999999999999999999999998766543

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

Probab=99.72  E-value=2.3e-17  Score=187.30  Aligned_cols=196  Identities=20%  Similarity=0.248  Sum_probs=168.6

Q ss_pred             CCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEE--CCeEEEeecccc
Q 011538          252 RPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAEL  328 (483)
Q Consensus       252 ~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I--~Gi~gFVP~Sel  328 (483)
                      -+.+++|.++.+++... +-+..+++|.++......+.++.+ ++.|+.|.|+|.++.+.|+.|.+  +.+.|++|.+|+
T Consensus       465 v~~~e~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~nD-I~iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hl  543 (1710)
T KOG1070|consen  465 VPIYEVGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVND-IEIGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHL  543 (1710)
T ss_pred             CCceecCCcccCccceecccCcEEEEEEehHhhccccccccc-ccccceeeeEEEEecCCcEEEEEecCceeeecChHhh
Confidence            35689999999999885 345556899988876666666655 79999999999999999999998  459999999999


Q ss_pred             ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh---------hcCCCCCcEEEEEEEEEeCceEEEEECCCc
Q 011538          329 LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA---------TLNLREGTLLEGTVKKIYPYGAQIRIGDSN  399 (483)
Q Consensus       329 ~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e---------~~~l~vG~iv~G~V~~I~~~GaFV~I~~~g  399 (483)
                      .+....+....+.+|..+++||+.++...+++.+++|..+-         ..++++|.++.|+|.++.++||||++.+ |
T Consensus       544 sd~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g-~  622 (1710)
T KOG1070|consen  544 SDHPLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGAFVTFTG-G  622 (1710)
T ss_pred             hhcccccccceeeeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCeEEEecC-c
Confidence            54333333344589999999999999999999999998642         2478899999999999999999999998 8


Q ss_pred             eEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCC
Q 011538          400 RSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (483)
Q Consensus       400 i~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~  449 (483)
                      ++||.|.++|+++++.++++.|.+||+|.|+|+++| +++||.|++|+...
T Consensus       623 lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~  673 (1710)
T KOG1070|consen  623 LSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSC  673 (1710)
T ss_pred             cccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhhh
Confidence            999999999999999999999999999999999997 88999999997653

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

Probab=99.71  E-value=6.2e-18  Score=148.50  Aligned_cols=82  Identities=38%  Similarity=0.576  Sum_probs=78.4

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCCc
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP  451 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~dP  451 (483)
                      .+++|++++|+|++|++|||||+|++ |-.||+|+||+++.+++++.+.+++||.|+|+|+++|++++|+||+|++++.|
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~-g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e~p   80 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEG-GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKLEEEP   80 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecC-CCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHHhhhCc
Confidence            47899999999999999999999998 79999999999999999999999999999999999999999999999999988


Q ss_pred             Ccc
Q 011538          452 GLF  454 (483)
Q Consensus       452 w~~  454 (483)
                      -..
T Consensus        81 e~~   83 (129)
T COG1098          81 EKQ   83 (129)
T ss_pred             ccc
Confidence            654

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

Probab=99.70  E-value=2.2e-16  Score=179.55  Aligned_cols=247  Identities=22%  Similarity=0.287  Sum_probs=196.6

Q ss_pred             ccccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeec-ccccccccchhhhhhhhhhhhhhHHhhcccceeeecccc
Q 011538          163 VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLT-KEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA  241 (483)
Q Consensus       163 ~~~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~-sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~  241 (483)
                      +....+...+|++..|+|..+++.++.|+.+.+.-|-++. .++.+.+  +         .+|                 
T Consensus      1058 ~~~~~k~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~--~---------~~P----------------- 1109 (1710)
T KOG1070|consen 1058 FSKSDKNPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSY--S---------MTP----------------- 1109 (1710)
T ss_pred             cccCCCCCCcchhhcceeeeeccceeEEecCCccccceEEeeehhccc--c---------CCh-----------------
Confidence            3344556669999999999999999999999888874332 2443321  0         011                 


Q ss_pred             ccccCCCCCCCCcccCCCEEEEEEEEEcC-CCcEEEEeh-------HHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEE
Q 011538          242 IAMSGGSGPGRPVVETGTVLFAEVLGRTL-SGRPLLSTR-------RLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLL  313 (483)
Q Consensus       242 ~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~-~G~iiLS~k-------~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~f  313 (483)
                                ...+..++.+.+.++..+. ++.+.||.+       .+.....--...+.++.|+++.|.|..+.+.|+|
T Consensus      1110 ----------~~~f~~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glf 1179 (1710)
T KOG1070|consen 1110 ----------VEHFTKIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLF 1179 (1710)
T ss_pred             ----------HHhcccccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEE
Confidence                      1235677888888888653 344899988       3332222222356779999999999999999999


Q ss_pred             EEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH---------hhhcCCCCCcEEEEE
Q 011538          314 TRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA---------WATLNLREGTLLEGT  382 (483)
Q Consensus       314 V~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~---------~e~~~l~vG~iv~G~  382 (483)
                      +.+. ++.||+|.+++ +...+.|+..+ .+|+.+.++|+.++...+|+.+|.|..         .....+++|+...|+
T Consensus      1180 i~ls~~v~a~v~is~~~ds~~k~w~k~~-~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~ 1258 (1710)
T KOG1070|consen 1180 IALSRKVEAFVPISGLSDSFEKEWEKHL-PVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGT 1258 (1710)
T ss_pred             EEEccceEEEEEccccccchhhhhhccC-CccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccce
Confidence            9996 79999999999 45555666554 899999999999999999999999852         123579999999999


Q ss_pred             EEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          383 VKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       383 V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      |..+.++|.||+++.+ ++.|++|+++..+++..+....+..|+.|+|.+++++ +++||.|++|..-
T Consensus      1259 v~~~~~~G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~~~V~a~~lk~~~ek~rIsl~~k~s~ 1326 (1710)
T KOG1070|consen 1259 VEVVDPFGLFIKLDVTVNMVGLCHISEEADDRGENITALYYAGDRVKACVLKEDSEKKRISLGLKSSY 1326 (1710)
T ss_pred             EEEecCCceEEEecCcceecccccceeecchhhhhcccceeccceeeeEeeeccchhhhhhhhhhhhc
Confidence            9999999999999875 4699999999999999999999999999999999998 8899999988653

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.66  E-value=3e-16  Score=159.68  Aligned_cols=98  Identities=20%  Similarity=0.255  Sum_probs=90.9

Q ss_pred             CCC-CCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          372 NLR-EGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       372 ~l~-vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      .+. +|++|.|+|++|.+||+||+|.++ |++||||+|++||.++.++++.+++||.|.|+|+++| ++++|.||+|++.
T Consensus        13 ~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~   92 (319)
T PTZ00248         13 KFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVS   92 (319)
T ss_pred             hCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecc
Confidence            455 899999999999999999999733 7999999999999999999999999999999999998 8899999999999


Q ss_pred             CCcCcccccccccceeeEEEE
Q 011538          449 SEPGLFVSDKEVHIIFLFILL  469 (483)
Q Consensus       449 ~dPw~~l~~k~~V~~~~~~~~  469 (483)
                      ++||..+.++|+.+..+.-++
T Consensus        93 ~~pw~~~~e~~~~g~~v~~~V  113 (319)
T PTZ00248         93 PEDIEACEEKFSKSKKVHSIM  113 (319)
T ss_pred             cchHHHHHHhCcCCCEEEEEE
Confidence            999999999999999884443

>PRK08582 hypothetical protein; Provisional

Probab=99.57  E-value=1.3e-14  Score=132.04  Aligned_cols=82  Identities=30%  Similarity=0.497  Sum_probs=77.8

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCCc
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP  451 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~dP  451 (483)
                      .+++|++|.|+|++|+++|+||+|++ +++||||+++++|.++.++.+.|++||.|+|+|++++.+++|.||+|++.++|
T Consensus         2 ~~kvG~iv~G~V~~I~~fG~fV~L~~-~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~~~   80 (139)
T PRK08582          2 SIEVGSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP   80 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEECC-CCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEecccCc
Confidence            37899999999999999999999998 79999999999999999999999999999999999986799999999999999


Q ss_pred             Ccc
Q 011538          452 GLF  454 (483)
Q Consensus       452 w~~  454 (483)
                      |..
T Consensus        81 ~~~   83 (139)
T PRK08582         81 KRQ   83 (139)
T ss_pred             hhh
Confidence            964

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.53  E-value=2.2e-15  Score=153.40  Aligned_cols=138  Identities=16%  Similarity=0.257  Sum_probs=121.2

Q ss_pred             hCCCeEEEEEEEEECCeEEEEE---CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh----
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----  366 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I---~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~----  366 (483)
                      +.|++|.|+|+++.++|+||++   +|++||||.|++ |.++.+++++. ++|+++.|+|+++|+++++|.||.|+    
T Consensus        16 ~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~v-kvGd~v~vkVl~VD~ekg~IdLS~K~v~~~   94 (319)
T PTZ00248         16 EEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLI-RVGRHEVVVVLRVDKEKGYIDLSKKRVSPE   94 (319)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhc-CCCCEEEEEEEEEeCCCCEEEEEeeecccc
Confidence            4799999999999999999999   489999999999 88999999986 89999999999999999999999996    


Q ss_pred             Hhhh--cCCCCCcEEEEEEEEEeC-ceEEEE------ECCCceEEEEeccCcCcccccCcccccC---CCCEEEEEEEEE
Q 011538          367 AWAT--LNLREGTLLEGTVKKIYP-YGAQIR------IGDSNRSGLLHISNMSRTRVTSVSDLLN---EGERVKVLVVKS  434 (483)
Q Consensus       367 ~~e~--~~l~vG~iv~G~V~~I~~-~GaFV~------I~~~gi~GLlhiSels~~~i~~~~~~~k---vGd~VkVkVi~v  434 (483)
                      +|..  ..++.|++++|+|..+.. +|++++      ... .+.++.|..++....+.++.+.|.   +++.++..++.+
T Consensus        95 pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~p-l~~~~gh~y~af~~~v~~~~evl~~l~i~~ev~~~l~~~  173 (319)
T PTZ00248         95 DIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWP-LYKKYGHALDALKEALTNPDNVFEGLDIPEEVKESLLQD  173 (319)
T ss_pred             hHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHH-HHHhcCCHHHHHHHHhcCchhhhccCCCCHHHHHHHHHH
Confidence            4643  478999999999999955 999998      344 689999999998888888877777   888887777654

>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=99.52  E-value=4.5e-14  Score=115.10  Aligned_cols=70  Identities=24%  Similarity=0.367  Sum_probs=64.6

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCc---ccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSV---SDLLNEGERVKVLVVKSM-FPDKISLS  443 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~---~~~~kvGd~VkVkVi~vd-ek~rI~LS  443 (483)
                      +++|+++.|+|++|+++|+||++++ +++|++|+++++|.++.++   .+.|++||.|+|+|+++| ++++|.||
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 IKEGQLLRGYVSSVTKQGVFFRLSS-SIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeCC-CCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            5799999999999999999999988 8999999999999987775   588999999999999998 77899886

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.

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

Probab=99.48  E-value=2.1e-13  Score=109.63  Aligned_cols=73  Identities=30%  Similarity=0.562  Sum_probs=68.9

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK  445 (483)
                      ++++|+++.|+|+++.++|+||++++ +++|+||.+++++.+..++...+++||+|+|+|++++ +++++.||+|
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 KLKEGDIVEGKVTSVEDFGVFVDLGN-GIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             -SSTTSEEEEEEEEEETTEEEEEEST-SSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECC-cEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            37899999999999999999999996 7999999999999999999999999999999999998 7889999986

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 ....

>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=99.48  E-value=1.3e-13  Score=111.49  Aligned_cols=71  Identities=24%  Similarity=0.386  Sum_probs=66.6

Q ss_pred             CCCCcEEEEEEEEEeC-ceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 011538          373 LREGTLLEGTVKKIYP-YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA  445 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~-~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK  445 (483)
                      +++|+++.|+|++|.+ +|+||++.+ +.+|++|+++++|++..++.+.|++||.|+|+|+++++ +|+.||+|
T Consensus         1 l~~G~iv~G~V~~i~~~~g~~v~l~~-~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LSl~   72 (72)
T cd05704           1 LEEGAVTLGMVTKVIPHSGLTVQLPF-GKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD-GKYQLSLR   72 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECCC-CCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC-CEEEEEeC
Confidence            5789999999999986 899999988 79999999999999999999999999999999999865 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.

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

Probab=99.46  E-value=3.3e-13  Score=109.23  Aligned_cols=71  Identities=34%  Similarity=0.534  Sum_probs=65.1

Q ss_pred             CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI  444 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSL  444 (483)
                      +.|+++.|+|++|++||+||++.+.+.+||+|+++++|.++.++.+.|++||+|+|+|++++..+|+.||+
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~   72 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL   72 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence            58999999999999999999996534799999999999999999999999999999999998555999987

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.

>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=99.45  E-value=5.5e-13  Score=108.80  Aligned_cols=72  Identities=25%  Similarity=0.285  Sum_probs=65.4

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~  449 (483)
                      ++++|+++.|+|++|+++|+||+++..|++||+|.++++|.      +.+++||.+.|+|++++ +++++.||+|++.+
T Consensus         1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~   73 (74)
T cd05694           1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV   73 (74)
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            47899999999999999999999972279999999999976      77999999999999998 78999999998765

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=99.43  E-value=5.5e-13  Score=108.32  Aligned_cols=70  Identities=17%  Similarity=0.161  Sum_probs=65.6

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccc--ccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR--VTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD  446 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~--i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~  446 (483)
                      |+++.|+|+++.++|+||++.+ +++|+||.++++|.+  ..++.+.|++||.|+|+|+++| +++||.||+|.
T Consensus         1 G~~V~g~V~~i~~~g~~V~l~~-~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k~   73 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTISP-DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG   73 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCC-CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEecC
Confidence            7899999999999999999988 799999999999874  8899999999999999999998 78999999973

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.

>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=4.9e-13  Score=110.55  Aligned_cols=73  Identities=27%  Similarity=0.346  Sum_probs=69.1

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL  444 (483)
                      .++++|+++.|+|++|.++|+||++++ +++||+|.++++++++.++.+.|++||.|+|+|++++ ++++|.|||
T Consensus        10 ~~~~~G~i~~g~V~~v~~~G~fv~l~~-~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461          10 SDLKPGMVVHGYVRNITPYGVFVEFLG-GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             HhCCCCCEEEEEEEEEeeceEEEEcCC-CCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence            368999999999999999999999988 7999999999999999999999999999999999998 689999986

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=6.7e-13  Score=105.75  Aligned_cols=69  Identities=26%  Similarity=0.352  Sum_probs=65.5

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK  445 (483)
                      |+++.|+|+++.++|+||++++ +++||+|.+++++++..++.+.|++||.++|+|++++ +++++.||+|
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~~-~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k   70 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFYN-NVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECC-CCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            7899999999999999999988 7999999999999999999999999999999999998 6789999986

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK07252 hypothetical protein; Provisional

Probab=99.42  E-value=1.1e-12  Score=116.75  Aligned_cols=77  Identities=38%  Similarity=0.592  Sum_probs=72.6

Q ss_pred             CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCc
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEP  451 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dP  451 (483)
                      ++|+++.|+|++|+++|+||+|.+ ++.||+|++++++.++.++.+.|++||.|+|+|+++| +++++.||+|++.+++
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~-~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~   79 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALEN-GTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEK   79 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECC-CCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence            589999999999999999999988 7999999999999999999999999999999999998 6899999999998843

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.42  E-value=2.7e-13  Score=153.10  Aligned_cols=85  Identities=28%  Similarity=0.392  Sum_probs=80.5

Q ss_pred             CCCCCcEEE-EEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCC
Q 011538          372 NLREGTLLE-GTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESE  450 (483)
Q Consensus       372 ~l~vG~iv~-G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~d  450 (483)
                      ..++|+++. |+|++|++||+||+|.+ |++||||+|+|+|+++.++.+.|++||.|+|+|+++|.++||.||+|++.+|
T Consensus       750 ~~~vG~iy~~g~V~~I~~FGaFVeL~~-g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~~grI~LSlK~l~~~  828 (891)
T PLN00207        750 VPTVGDIYRNCEIKSIAPYGAFVEIAP-GREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRALLPE  828 (891)
T ss_pred             CcCCCcEEECcEEEEEeccEEEEEeCC-CCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECCCCcEEEEEeccccC
Confidence            578999995 69999999999999988 7999999999999999999999999999999999998889999999999999


Q ss_pred             cCccccc
Q 011538          451 PGLFVSD  457 (483)
Q Consensus       451 Pw~~l~~  457 (483)
                      ||+....
T Consensus       829 Pw~~~~~  835 (891)
T PLN00207        829 ANSEKSS  835 (891)
T ss_pred             chhhhhh
Confidence            9997766

>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=99.41  E-value=1.7e-12  Score=104.37  Aligned_cols=72  Identities=21%  Similarity=0.309  Sum_probs=67.5

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK  445 (483)
                      +++|+++.|+|++++++|+||++++ +++|++|.+++++++..++.+.|++||.|+|+|++++ +++++.||+|
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 LKVGDILPGRVTKVNDRYVLVQLGN-KVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCC-CcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            4789999999999999999999998 7999999999999988888899999999999999998 6789999985

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.

>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=99.40  E-value=1.7e-12  Score=106.23  Aligned_cols=75  Identities=32%  Similarity=0.573  Sum_probs=69.5

Q ss_pred             CcEEEEEEEEEeCceEEEEECCC--ceEEEEeccCcCcccc-cCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCCc
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDS--NRSGLLHISNMSRTRV-TSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP  451 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~--gi~GLlhiSels~~~i-~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~dP  451 (483)
                      |+++.|+|++|+++|+||++++.  +.+||+|.++++|.++ .++.+.|++||.|+|+|++++ ++++.+|+|+++++.
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k~~~~~~   78 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSMKDVDQDT   78 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe-CCEEEEEEEecccCC
Confidence            78999999999999999999842  5899999999999986 899999999999999999999 999999999998864

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.

>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=99.39  E-value=1.4e-12  Score=103.93  Aligned_cols=68  Identities=22%  Similarity=0.449  Sum_probs=64.5

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL  444 (483)
                      |+++.|+|++|.++|+||++++ +++|++|.++++|.+..++.+.|++||.++|+|+++| +++++.|||
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 GQVVKGTIRKLRPSGIFVKLSD-HIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecC-CcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            7899999999999999999987 7999999999999999999999999999999999998 689999985

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.

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

Probab=99.39  E-value=2.4e-12  Score=103.91  Aligned_cols=74  Identities=31%  Similarity=0.395  Sum_probs=68.1

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD  446 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~  446 (483)
                      +++|+++.|+|.++.++|+||++.+. +++||+|.++++++++.++.+.|++||.|+|+|++++ +++++.||+|+
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~   76 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence            36899999999999999999999743 5899999999999999999999999999999999998 67899999985

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

>PRK05807 hypothetical protein; Provisional

Probab=99.38  E-value=2.7e-12  Score=116.55  Aligned_cols=75  Identities=39%  Similarity=0.582  Sum_probs=70.8

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLE  448 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~  448 (483)
                      .+++|+++.|+|+.|+++|+||++.  +..||||++++++.++.++.+.|++||.|+|+|++++++++|.||+|.+.
T Consensus         2 ~~~vG~vv~G~Vt~i~~~GafV~L~--~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~   76 (136)
T PRK05807          2 TLKAGSILEGTVVNITNFGAFVEVE--GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAM   76 (136)
T ss_pred             CccCCCEEEEEEEEEECCeEEEEEC--CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence            3679999999999999999999994  58999999999999999999999999999999999987799999999987

>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=99.38  E-value=1.7e-12  Score=104.73  Aligned_cols=68  Identities=25%  Similarity=0.403  Sum_probs=64.0

Q ss_pred             CcEEE-EEEEEE-eCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538          376 GTLLE-GTVKKI-YPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (483)
Q Consensus       376 G~iv~-G~V~~I-~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL  444 (483)
                      |++++ |+|+++ .++|+||++.+ |++||+|.|++++.+..++.+.|++||.++|+|+++| .+++|.||+
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 GAVVDSVKVTKVEPDLGAVFELKD-GLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCC-CCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            78999 999999 69999999988 7999999999999999999999999999999999998 778999985

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.

>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=99.37  E-value=3.5e-12  Score=102.79  Aligned_cols=74  Identities=35%  Similarity=0.542  Sum_probs=68.5

Q ss_pred             CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecC
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADL  447 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~  447 (483)
                      ++|+++.|+|++++++|+||++.+.+++|++|.+++++++..++.+.|++||.|+|+|++++ +++++.||+|+.
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 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            46999999999999999999998546899999999999999899999999999999999998 689999999974

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=99.36  E-value=3.6e-12  Score=101.78  Aligned_cols=72  Identities=31%  Similarity=0.527  Sum_probs=67.7

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      |+++.|+|+++.++|+||++.+ +++|++|.++++++++.++.+.|++||.++|+|++++ +++++.||+|+++
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 GSIVTGKVTEVDAKGATVKLGD-GVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE   73 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCC-CCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEcC
Confidence            7899999999999999999988 7999999999999999999999999999999999998 5689999999864

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.

>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=99.35  E-value=2.9e-12  Score=101.79  Aligned_cols=67  Identities=21%  Similarity=0.311  Sum_probs=63.4

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS  443 (483)
                      |+++.|+|++|.++|+||++.+ +++||+|.+++++++..++.+.|++||.|+|+|+++| ++++|.||
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 GDVVRGFVKNIANNGVFVTLGR-GVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCC-CCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            7899999999999999999998 7999999999999999999999999999999999998 67898876

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.

>PRK08059 general stress protein 13; Validated

Probab=99.34  E-value=6.1e-12  Score=112.20  Aligned_cols=79  Identities=37%  Similarity=0.586  Sum_probs=75.3

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE  450 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~d  450 (483)
                      ++++|+++.|+|++|+++|+||++.+ ++.|++|.++++++++.++.+.|++||.|+|+|++++ +++++.||+|.+..+
T Consensus         4 ~~k~G~iv~G~V~~i~~~G~fV~i~~-~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~~   82 (123)
T PRK08059          4 QYEVGSVVTGKVTGIQPYGAFVALDE-ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEA   82 (123)
T ss_pred             cCCCCCEEEEEEEEEecceEEEEECC-CCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEcccC
Confidence            58899999999999999999999998 7999999999999999999999999999999999997 789999999999998


Q ss_pred             c
Q 011538          451 P  451 (483)
Q Consensus       451 P  451 (483)
                      |
T Consensus        83 ~   83 (123)
T PRK08059         83 P   83 (123)
T ss_pred             c
Confidence            8

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

Probab=99.33  E-value=3.6e-12  Score=100.98  Aligned_cols=67  Identities=31%  Similarity=0.560  Sum_probs=62.0

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCc-ccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR-TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~-~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS  443 (483)
                      |+++.|+|++|+++|+||++.+ +++||+|.++++| .+..++.+.|++||+|+|+|+++| ++++|.||
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~-~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCC-CCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence            7899999999999999999988 7999999999997 577888899999999999999998 77898875

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.

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

Probab=99.31  E-value=1e-11  Score=97.28  Aligned_cols=69  Identities=45%  Similarity=0.755  Sum_probs=65.1

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA  445 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK  445 (483)
                      |+++.|+|++++++|+||++++ ++.||+|.++++++++.++.+.|++||.|+|+|++++.++++.||+|
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 GSVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECC-CCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence            7899999999999999999987 79999999999999999999999999999999999977789999986

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

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

Probab=99.28  E-value=1.8e-11  Score=97.53  Aligned_cols=69  Identities=25%  Similarity=0.379  Sum_probs=65.3

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK  445 (483)
                      |+++.|+|.++.++|+||+++. +.+|++|.+++++.+..++.+.|++||.++|+|++++ +++++.||+|
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGY-KSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCC-CceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            7899999999999999999987 7999999999999999999999999999999999998 6789999986

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.

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

Probab=99.25  E-value=2.7e-11  Score=97.12  Aligned_cols=70  Identities=31%  Similarity=0.488  Sum_probs=62.6

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc-cccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~-~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS  443 (483)
                      +.+|+++.|+|++|+++|+||++.+ +++||+|.++++|. +..++.+.|++||.|+|+|+++| +++++.||
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~~-~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELEE-GVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcCC-CCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence            4689999999999999999999988 79999999999975 55577788999999999999998 77888764

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.

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

Probab=99.25  E-value=3.7e-11  Score=96.57  Aligned_cols=71  Identities=23%  Similarity=0.450  Sum_probs=63.2

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      ++.|++++|+|+++.++|+||+++ |+.||||.+++ +.+..++.... .+||++.|+|+++|++++++.+|+|
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 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVY-KIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTC-ETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCcccccccccc-CCCCEEEEEEEEEECCCCeEEEEEC
Confidence            478999999999999999999998 89999999999 45455555544 8999999999999999999999986

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 ....

>PHA02945 interferon resistance protein; Provisional

Probab=99.23  E-value=4.8e-11  Score=99.56  Aligned_cols=75  Identities=23%  Similarity=0.227  Sum_probs=68.9

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCc--CcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNM--SRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSel--s~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      .++|+++.|+|+. .+||+||.+.++ |.+||+|.|+.  +..++++ ++.+ +||+|.|+|+++| .++.|.||||+..
T Consensus         9 P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~V~   85 (88)
T PHA02945          9 PNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKRMC   85 (88)
T ss_pred             CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeEcc
Confidence            4689999999999 999999999776 89999999955  9999999 9999 9999999999998 7899999999986


Q ss_pred             CC
Q 011538          449 SE  450 (483)
Q Consensus       449 ~d  450 (483)
                      ++
T Consensus        86 ~~   87 (88)
T PHA02945         86 RH   87 (88)
T ss_pred             cC
Confidence            54

>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=99.21  E-value=2.4e-11  Score=104.76  Aligned_cols=74  Identities=30%  Similarity=0.405  Sum_probs=66.6

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc-------------------cCcccccCCCCEEEEEEEE
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-------------------TSVSDLLNEGERVKVLVVK  433 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i-------------------~~~~~~~kvGd~VkVkVi~  433 (483)
                      |++|++|.|+|++|.++|+||.+.+ ++.|++|.++++|.+.                   .++.+.|++||.|+|+|++
T Consensus         1 L~~G~vV~G~V~~v~~~gl~v~L~~-g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~   79 (100)
T cd05693           1 LSEGMLVLGQVKEITKLDLVISLPN-GLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVS   79 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECCC-CcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEE
Confidence            5789999999999999999999988 8999999999998752                   3477899999999999999


Q ss_pred             EeC----CCeEEEEEecC
Q 011538          434 SMF----PDKISLSIADL  447 (483)
Q Consensus       434 vde----k~rI~LSLK~~  447 (483)
                      ++.    +++|.||+|..
T Consensus        80 ~d~~~~~~~~i~LSlr~~   97 (100)
T cd05693          80 LDKSKSGKKRIELSLEPE   97 (100)
T ss_pred             ccCCcCCCcEEEEEecHH
Confidence            984    68999999864

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.

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

Probab=99.21  E-value=2.6e-11  Score=107.06  Aligned_cols=75  Identities=21%  Similarity=0.297  Sum_probs=69.2

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhhh
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWAT  370 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e~  370 (483)
                      ++.|.+++|+|+++.++|+||.++ |-+||||+|++ ...++++.++. .+||+|.|+|+.+|. ++++.||.|.+.+.
T Consensus         3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L-~vG~eV~vKVl~ide-~GKisLSIr~~~e~   79 (129)
T COG1098           3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHL-KVGQEVKVKVLDIDE-NGKISLSIRKLEEE   79 (129)
T ss_pred             ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHh-cCCCEEEEEEEeecc-CCCcceehHHhhhC
Confidence            578999999999999999999995 69999999999 78899999987 899999999999997 89999999987653

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

Probab=99.20  E-value=5.6e-11  Score=98.70  Aligned_cols=74  Identities=18%  Similarity=0.199  Sum_probs=67.1

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCc----ccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR----TRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~----~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~  447 (483)
                      +++|++|.|+|+++.++|++|+++. +++|++|.+++++    .+..++.+.+++||.|+|+|+++++++++.||+|+.
T Consensus         4 p~~GdiV~g~V~~i~~~g~~v~i~~-~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~   81 (86)
T cd05789           4 PEVGDVVIGRVTEVGFKRWKVDINS-PYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSL   81 (86)
T ss_pred             CCCCCEEEEEEEEECCCEEEEECCC-CeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence            5799999999999999999999987 7999999999996    455677888999999999999997669999999975

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".

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

Probab=99.20  E-value=9.6e-11  Score=92.90  Aligned_cols=66  Identities=41%  Similarity=0.700  Sum_probs=59.0

Q ss_pred             CCeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          297 NEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      |++++|+|+++.++|++|+++|++||||.+++ +.+..++.+   .+|+.+.|+|+++|++++++.+|+|
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 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDE---YVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCChHH---hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            78999999999999999999999999999999 455555444   4899999999999999999999985

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.

>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=99.20  E-value=4.9e-11  Score=93.24  Aligned_cols=67  Identities=39%  Similarity=0.583  Sum_probs=62.6

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS  443 (483)
                      |+++.|+|++++++|+||++.. +..|++|.+++++.++.++.+.|++||.|+|+|++++ +++++.||
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~-~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGV-KQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCC-CCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            7899999999999999999987 7999999999999988899999999999999999998 67888876

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

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

Probab=99.20  E-value=6.8e-11  Score=94.15  Aligned_cols=65  Identities=18%  Similarity=0.328  Sum_probs=58.7

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS  443 (483)
                      |+++.|+|+++.++|+||++.+ +++|++|.++++..+..  .+.|++||+|+|+|+.+| ++++|.||
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~~-~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~~~i~LS   66 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFLS-SFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcC-CceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            7899999999999999999987 79999999999866544  778999999999999998 67888876

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.

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

Probab=99.17  E-value=1.1e-10  Score=91.75  Aligned_cols=68  Identities=43%  Similarity=0.605  Sum_probs=63.4

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI  444 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSL  444 (483)
                      |+++.|+|.++.++|+||++++ +..||+|.+++++.++.++.+.|++||.|+|+|++++.++++.||+
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 GKIYEGKVVKIKDFGAFVEILP-GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCC-CCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECCCCcEEeeC
Confidence            6899999999999999999987 6999999999999999888999999999999999997777998884

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=99.15  E-value=1.9e-10  Score=91.26  Aligned_cols=66  Identities=21%  Similarity=0.302  Sum_probs=60.0

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK  445 (483)
                      |+++.|+|+++.++|++|++ + |++||||.+++++.+..++.+  .+||.++|+|+++| ++++|.||+|
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-E-GVRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-C-CEEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            78999999999999999999 5 799999999999988777766  38999999999998 6789999976

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.

>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=99.15  E-value=1.7e-10  Score=94.00  Aligned_cols=69  Identities=12%  Similarity=0.124  Sum_probs=60.1

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChh---hhhhhcCCEEEEEEEEEECCCCceeec
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFT---ELKEKVGRRMYVQITRINEDTNDLILS  363 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~---~l~~~VGq~V~vkVl~ID~e~~rLiLS  363 (483)
                      ++.|+++.|+|+++.++|+||+++ +++||+|.+++ +.++.+++   +. +++|+.++|+|+++|++++++.||
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 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKY-LPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcc-cCCCCEEEEEEEEEECCCCEEecC
Confidence            368999999999999999999995 89999999999 66655543   44 389999999999999999999886

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.

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

Probab=99.14  E-value=1.7e-10  Score=90.39  Aligned_cols=67  Identities=46%  Similarity=0.671  Sum_probs=62.3

Q ss_pred             CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (483)
Q Consensus       375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS  443 (483)
                      +|+++.|+|.++.++|+||+++  +++|++|.+++++.++.++.+.|++||.|+|+|++++ +++++.||
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~--~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLG--GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC--CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence            4899999999999999999997  5899999999999999899999999999999999998 67888876

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

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

Probab=99.14  E-value=2.6e-10  Score=89.00  Aligned_cols=71  Identities=37%  Similarity=0.597  Sum_probs=65.6

Q ss_pred             CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK  445 (483)
                      ++|+++.|+|.+++++|+||++++ ++.|++|.+++++.+..++.+.|++||.|+|+|++++ +++++.||++
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~~-~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeCC-CCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            479999999999999999999997 7999999999999888888889999999999999998 5699999985

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

Probab=99.14  E-value=1.7e-10  Score=115.46  Aligned_cols=79  Identities=28%  Similarity=0.507  Sum_probs=73.3

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCC
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE  450 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~d  450 (483)
                      .++|+++.|+|++|.++|+||++.++ |++||+|.|+++++++.++.+.|++||.|.|+|+++| ++++|.||+|++.++
T Consensus         6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~~   85 (262)
T PRK03987          6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNEH   85 (262)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEecccc
Confidence            57899999999999999999999754 7999999999999999999999999999999999998 678999999988865


Q ss_pred             c
Q 011538          451 P  451 (483)
Q Consensus       451 P  451 (483)
                      -
T Consensus        86 e   86 (262)
T PRK03987         86 Q   86 (262)
T ss_pred             h
Confidence            4

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

Probab=99.13  E-value=4.2e-11  Score=117.76  Aligned_cols=79  Identities=28%  Similarity=0.517  Sum_probs=74.0

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCC
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE  450 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~d  450 (483)
                      .++|++|-|+|.+|.+||+||.|..+ |++||+|+||++.++++++++.+++||.+-|+||++| .++.|.||||...++
T Consensus         9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~~   88 (269)
T COG1093           9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTEH   88 (269)
T ss_pred             CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCCHH
Confidence            46899999999999999999999655 7999999999999999999999999999999999998 789999999999876


Q ss_pred             c
Q 011538          451 P  451 (483)
Q Consensus       451 P  451 (483)
                      -
T Consensus        89 q   89 (269)
T COG1093          89 Q   89 (269)
T ss_pred             H
Confidence            3

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

Probab=99.13  E-value=1.1e-09  Score=108.51  Aligned_cols=145  Identities=17%  Similarity=0.141  Sum_probs=114.0

Q ss_pred             cCCCCCcEEEEEEEEEe-CCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccC
Q 011538          168 YEPKPGDFVIGVVVSGN-ENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~-~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~  246 (483)
                      ..+.+|+.-.++|+.++ +.|+|||.|...+-++|.+|+...  +++                                 
T Consensus        69 p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~--~~~---------------------------------  113 (287)
T COG2996          69 PKATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTL--KSL---------------------------------  113 (287)
T ss_pred             ceEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccc--ccc---------------------------------
Confidence            55678999999999999 789999999988999999987532  111                                 


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhHHHHHHhh--CCCeEEEEEEEEECCeEEEEE-CCeEEEe
Q 011538          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQ--LNEPIEVKFTEWNTGGLLTRI-EGLRAFL  323 (483)
Q Consensus       247 ~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~~L~~~~k--~GeiV~GkV~~v~k~G~fV~I-~Gi~gFV  323 (483)
                             =+++||.+-+.++ .|+.||+..+++....  .++....+..  .|+.+.|+|.+....|.||-+ ++..|||
T Consensus       114 -------wpq~Gd~l~v~l~-~Dkk~Ri~g~~a~~~~--l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfI  183 (287)
T COG2996         114 -------WPQKGDKLLVYLY-VDKKGRIWGTLAIEKI--LENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFI  183 (287)
T ss_pred             -------CCCCCCEEEEEEE-EccCCcEEEEecchhH--HHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEE
Confidence                   1679999999887 7888899777654321  1111111222  589999999999999999999 4799999


Q ss_pred             eccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538          324 PKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (483)
Q Consensus       324 P~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~  366 (483)
                      |.||....+        .+|++++++|+.+.. .++|.||.+.
T Consensus       184 h~sEr~~~p--------rlG~~l~~rVi~~re-Dg~lnLSl~p  217 (287)
T COG2996         184 HKSERFAEP--------RLGERLTARVIGVRE-DGKLNLSLRP  217 (287)
T ss_pred             cchhhcccc--------cCCceEEEEEEEEcc-CCeeeccccc
Confidence            999985332        589999999999965 8999999985

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

Probab=99.12  E-value=2.6e-10  Score=96.13  Aligned_cols=73  Identities=32%  Similarity=0.442  Sum_probs=62.7

Q ss_pred             CCCCCcEEEEEEEEEeCc--eEEEEECCCceEEEEeccCcCc---ccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 011538          372 NLREGTLLEGTVKKIYPY--GAQIRIGDSNRSGLLHISNMSR---TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~--GaFV~I~~~gi~GLlhiSels~---~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK  445 (483)
                      .+++|+++.|+|++|.++  ||||++++ +.+||||.++++|   .++.++.+.+++||.|.|+|++.. ..+-..|+.+
T Consensus         4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~   82 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTN   82 (88)
T ss_pred             cCCCCCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEE
Confidence            468999999999999997  99999998 7999999999999   678888999999999999999875 3343444443

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

>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=99.11  E-value=3.7e-10  Score=91.75  Aligned_cols=68  Identities=12%  Similarity=0.170  Sum_probs=60.6

Q ss_pred             CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-cc--ccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LS--RVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~--rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      |++++|+|+++.++|+||.++ +++||||.+++ +.  +.+++.+.+ ++|+.++|+|+++|+++++|.||.|
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 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKF-PIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhC-CCCCEEEEEEEEEeCCCCEEEEEec
Confidence            789999999999999999995 89999999999 43  366666654 8999999999999999999999975

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.11  E-value=1.1e-10  Score=129.71  Aligned_cols=71  Identities=32%  Similarity=0.456  Sum_probs=66.3

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcC----cccccCcccccCCCCEEEEEEEEEeCCCeEEEE
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS----RTRVTSVSDLLNEGERVKVLVVKSMFPDKISLS  443 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels----~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LS  443 (483)
                      .+++|++|.|+|++|++||+||+|.+ |++||||+|+++    |.++.++.+.+++||+|+|+|+++|+++||+|+
T Consensus       644 ~~~vG~i~~GkV~~I~dfGaFVel~~-G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gKI~L~  718 (719)
T TIGR02696       644 MPEVGERFLGTVVKTTAFGAFVSLLP-GKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSLV  718 (719)
T ss_pred             cCCCCCEEEEEEEEEECceEEEEecC-CceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCCeeec
Confidence            47899999999999999999999987 799999999996    468999999999999999999999988899886

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.

>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=99.10  E-value=3.5e-10  Score=90.02  Aligned_cols=68  Identities=21%  Similarity=0.328  Sum_probs=60.6

Q ss_pred             CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      |+++.|+|+++.++|+||+++ ++.||+|.+++ +.+..++.+.. ++||.++|+|+++|++++++.||+|
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 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHF-RVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcc-cCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            789999999999999999995 79999999999 55666666643 8999999999999999999999975

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.

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

Probab=99.09  E-value=6.4e-10  Score=90.94  Aligned_cols=71  Identities=21%  Similarity=0.416  Sum_probs=61.9

Q ss_pred             CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc-----------CcccccCCCCEEEEEEEEEe-CCCeEEE
Q 011538          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FPDKISL  442 (483)
Q Consensus       375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~-----------~~~~~~kvGd~VkVkVi~vd-ek~rI~L  442 (483)
                      +|+++.|+|++|+++|+||+++..+++|++|.++++++++.           +....|++||.|+|+|++++ +++++.+
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            48999999999999999999987569999999999876432           44578999999999999998 6889999


Q ss_pred             EEe
Q 011538          443 SIA  445 (483)
Q Consensus       443 SLK  445 (483)
                      ++.
T Consensus        81 ~l~   83 (83)
T cd04471          81 ELV   83 (83)
T ss_pred             EEC
Confidence            863

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=99.07  E-value=6.6e-10  Score=124.82  Aligned_cols=76  Identities=36%  Similarity=0.533  Sum_probs=71.9

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~  447 (483)
                      ..+++|+++.|+|++|.+||+||+|.+ +.+||+|+|+++|.++.++.+.|++||.|+|+|+++|..++|.||+|.+
T Consensus       617 ~~~~vG~v~~G~V~~I~~fGafVei~~-~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~~  692 (693)
T PRK11824        617 AEPEVGEIYEGKVVRIVDFGAFVEILP-GKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV  692 (693)
T ss_pred             ccCcCCeEEEEEEEEEECCeEEEEECC-CCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCCCcEEEEEEec
Confidence            368999999999999999999999988 7999999999999999999999999999999999998559999999976

>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=99.05  E-value=9e-10  Score=87.71  Aligned_cols=67  Identities=12%  Similarity=0.325  Sum_probs=59.0

Q ss_pred             CCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~  364 (483)
                      |++++|+|+++.++|++|++ +|++||+|.+++ +.+..++.+.. .+||.++|+|+++|++++++.||+
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 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKF-KPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcC-CCCCEEEEEEEEEECCCCEEEEEC
Confidence            78999999999999999999 479999999999 55566665543 899999999999999999999874

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=99.04  E-value=8.5e-10  Score=90.02  Aligned_cols=68  Identities=21%  Similarity=0.290  Sum_probs=59.4

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC--CeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      ++.|+++.|+|+++.++|+||+++  |++||||.+++...    ..+  ++||.+.|+|+++|++++++.||.|+.
T Consensus         2 l~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~----~~~--~~Gq~v~~~V~~vd~~~~~v~ls~k~~   71 (74)
T cd05694           2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF----SKL--KVGQLLLCVVEKVKDDGRVVSLSADPS   71 (74)
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc----ccc--CCCCEEEEEEEEEECCCCEEEEEEeec
Confidence            468999999999999999999996  89999999999422    122  699999999999999999999998753

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=99.04  E-value=7.7e-10  Score=118.87  Aligned_cols=108  Identities=20%  Similarity=0.281  Sum_probs=85.7

Q ss_pred             CcccCCCEEEEEEEEEcCCCcEEEEehHHHH-----HhhhHHHHHHhh--CCCeEEEEEEEEECCeEEEEECCeEEEeec
Q 011538          253 PVVETGTVLFAEVLGRTLSGRPLLSTRRLFR-----KMAWHRVRQIKQ--LNEPIEVKFTEWNTGGLLTRIEGLRAFLPK  325 (483)
Q Consensus       253 ~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~-----~~~w~~L~~~~k--~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~  325 (483)
                      +.+++||.+.+.|...+ -||+.++..+...     +..++.+.+.++  .|++|+|+|.++.++|++|+++|+.||||.
T Consensus        85 ~~~~vGD~ie~~I~~~~-fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLggvea~LP~  163 (470)
T PRK09202         85 PDAEVGDYIEEEIESVD-FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGRAEAILPR  163 (470)
T ss_pred             ccccCCCeEEEEEcccc-CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEECCeEEEecH
Confidence            34789999999987655 5556544443332     334447777776  999999999999999999999999999999


Q ss_pred             cccccccCChhhhhhhcCCEEEEEEEEEECCCC--ceeechhhH
Q 011538          326 AELLSRVNNFTELKEKVGRRMYVQITRINEDTN--DLILSEREA  367 (483)
Q Consensus       326 Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~--rLiLS~K~~  367 (483)
                      +++..     .+. +++|++++|+|++++++++  +|+|||+.+
T Consensus       164 sE~ip-----~E~-~~~GdrIka~I~~Vd~~~kg~qIilSRt~p  201 (470)
T PRK09202        164 KEQIP-----REN-FRPGDRVRAYVYEVRKEARGPQIILSRTHP  201 (470)
T ss_pred             HHcCC-----Ccc-CCCCCEEEEEEEEEecCCCCCeEEEEeCcH
Confidence            99941     122 2799999999999998777  999999975

>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=99.03  E-value=1.1e-09  Score=90.46  Aligned_cols=70  Identities=17%  Similarity=0.210  Sum_probs=63.2

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~  364 (483)
                      ++.|+++.|+|+++.++|+||++ +|+.||+|.+++ +.+..++.+.. .+||.++|+|+++|++++++.+|+
T Consensus        12 ~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~-~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461          12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGF-KKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhc-CCCCEEEEEEEEEcCCCCEEEEeC
Confidence            58999999999999999999999 479999999999 66677777654 899999999999999999999884

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.

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

Probab=99.03  E-value=1.3e-09  Score=89.93  Aligned_cols=73  Identities=16%  Similarity=0.145  Sum_probs=68.0

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEec
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIAD  446 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~  446 (483)
                      .++|++|.|+|+++.+.|++|+++. ..+|++|.++++..+..++.+.|++||.+.|+|+++++.+++.||++.
T Consensus         4 p~~GdiV~G~V~~v~~~~~~V~i~~-~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~   76 (82)
T cd04454           4 PDVGDIVIGIVTEVNSRFWKVDILS-RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD   76 (82)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEeCC-CceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence            4799999999999999999999987 799999999999888888899999999999999999755899999987

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".

>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=99.00  E-value=1.5e-09  Score=87.62  Aligned_cols=67  Identities=24%  Similarity=0.204  Sum_probs=58.1

Q ss_pred             CCeEE-EEEEEE-ECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538          297 NEPIE-VKFTEW-NTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (483)
Q Consensus       297 GeiV~-GkV~~v-~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~  364 (483)
                      |++++ |+|+++ .++|+||++ +|++||+|.|++ +.+..++.+.. ++|+.++++|+.+|+.++++.||.
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 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPF-KAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCccccc-CCCCEEEEEEEEEeCCCCEEEEeC
Confidence            68889 999999 699999999 489999999999 56665555543 799999999999999999999984

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.

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=98.99  E-value=6.3e-10  Score=123.37  Aligned_cols=80  Identities=35%  Similarity=0.545  Sum_probs=75.2

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~  449 (483)
                      .+|++|+++.|+|+++.+||+||+|+- ..+|++|+|+++..++.+|.+++++||.|+|+|+++| .++||.|||+....
T Consensus       654 ~dLk~Gm~leg~Vrnv~~fgafVdIgv-~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~  732 (780)
T COG2183         654 TDLKPGMILEGTVRNVVDFGAFVDIGV-HQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEE  732 (780)
T ss_pred             hhccCCCEEEEEEEEeeeccceEEecc-ccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccCC
Confidence            489999999999999999999999998 6999999999999999999999999999999999999 78999999997765


Q ss_pred             Cc
Q 011538          450 EP  451 (483)
Q Consensus       450 dP  451 (483)
                      .+
T Consensus       733 ~~  734 (780)
T COG2183         733 EG  734 (780)
T ss_pred             cc
Confidence            43

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

Probab=98.98  E-value=3.9e-09  Score=86.39  Aligned_cols=65  Identities=29%  Similarity=0.394  Sum_probs=59.5

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI  444 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSL  444 (483)
                      .+++.|+.+.|+|++++++|+||++.+ +..||+|.+++.        +.+++||+++++|+++.+++++.+|+
T Consensus        12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~-~~~Glv~~se~~--------~~~~iGd~v~v~I~~i~e~~~i~l~~   76 (77)
T cd04473          12 EDLEVGKLYKGKVNGVAKYGVFVDLND-HVRGLIHRSNLL--------RDYEVGDEVIVQVTDIPENGNIDLIP   76 (77)
T ss_pred             hhCCCCCEEEEEEEeEecceEEEEECC-CcEEEEEchhcc--------CcCCCCCEEEEEEEEECCCCcEEEEE
Confidence            468899999999999999999999998 699999999974        56999999999999997789999986

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.

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

Probab=98.97  E-value=2.6e-09  Score=84.80  Aligned_cols=66  Identities=18%  Similarity=0.282  Sum_probs=58.6

Q ss_pred             CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS  363 (483)
                      |+++.|+|+++.++|+||++. ++.||+|.+++ +.+..++.+.. .+||.++++|+++|++++++.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRF-KVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhcc-CCCCEEEEEEEEEeCCCCEEecC
Confidence            789999999999999999995 79999999999 56666666654 89999999999999999999876

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.

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

Probab=98.97  E-value=3.1e-09  Score=84.62  Aligned_cols=68  Identities=19%  Similarity=0.339  Sum_probs=61.2

Q ss_pred             CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      |+++.|+|.++.++|++|+++ +.+|++|.+++ +.+..++.+.. ++|+.++|+|+++|++++++.||+|
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~-~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEV-KVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcC-CCCCEEEEEEEEEECCCCeEEEEeC
Confidence            789999999999999999996 69999999999 66677776654 8999999999999988889999985

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.

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

Probab=98.96  E-value=3e-09  Score=84.70  Aligned_cols=64  Identities=14%  Similarity=0.173  Sum_probs=54.9

Q ss_pred             CCeEEEEEEEEECCeEEEEE-CCeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS  363 (483)
                      |++++|+|+++.++|++|++ ++++||+|.+|+. .+.. .+.  +++|++++|+|+.+|++++++.||
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 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS-KST--YKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc-ccC--cCCCCEEEEEEEEEeCCCCEEecC
Confidence            78999999999999999999 5799999999994 2322 222  379999999999999999998887

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.

>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=98.96  E-value=2.2e-09  Score=85.92  Aligned_cols=62  Identities=21%  Similarity=0.350  Sum_probs=57.0

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccc--ccCcccccCCCCEEEEEEEEEeCCC
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR--VTSVSDLLNEGERVKVLVVKSMFPD  438 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~--i~~~~~~~kvGd~VkVkVi~vdek~  438 (483)
                      |+++.|+|+++.++|+||++++ +++|++|.+++++++  ..++.+.|++||.|+|+|++++..+
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~-~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~   64 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLAD-NVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK   64 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCC-CcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence            7899999999999999999988 799999999999884  7888899999999999999997443

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.

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=98.95  E-value=3.5e-09  Score=101.12  Aligned_cols=90  Identities=23%  Similarity=0.352  Sum_probs=75.6

Q ss_pred             EEECCCCceeechhhHhhh--cCCCCCcEEEEEEEEEeCceEEEEECC---------CceEEEEeccCcCcccccCcccc
Q 011538          352 RINEDTNDLILSEREAWAT--LNLREGTLLEGTVKKIYPYGAQIRIGD---------SNRSGLLHISNMSRTRVTSVSDL  420 (483)
Q Consensus       352 ~ID~e~~rLiLS~K~~~e~--~~l~vG~iv~G~V~~I~~~GaFV~I~~---------~gi~GLlhiSels~~~i~~~~~~  420 (483)
                      ++|.+++++.+.   +|..  ..+++|++|.|+|++|.++|+||+|++         .++.|++|.+++++.+..++.+.
T Consensus        42 ~id~~~~~Isv~---P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~  118 (189)
T PRK09521         42 FIDDINRKISVI---PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDA  118 (189)
T ss_pred             EEcCCCCEEEEe---cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhc
Confidence            346556666664   4432  357899999999999999999999952         15789999999999988899999


Q ss_pred             cCCCCEEEEEEEEEeCCCeEEEEEec
Q 011538          421 LNEGERVKVLVVKSMFPDKISLSIAD  446 (483)
Q Consensus       421 ~kvGd~VkVkVi~vdek~rI~LSLK~  446 (483)
                      |++||.|.|+|++++  +++.||+|+
T Consensus       119 ~~~GD~V~akV~~i~--~~i~LS~k~  142 (189)
T PRK09521        119 FKIGDIVRAKVISYT--DPLQLSTKG  142 (189)
T ss_pred             cCCCCEEEEEEEecC--CcEEEEEec
Confidence            999999999999987  899999996

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

Probab=98.95  E-value=3.4e-09  Score=85.70  Aligned_cols=68  Identities=19%  Similarity=0.324  Sum_probs=60.4

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECC--eEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEG--LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~G--i~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~  364 (483)
                      +.|++++|+|+++.++|+||++.|  .+||+|.+++ +.++.++.+.. .+||+++++|+++|.++ ++.||+
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~-~~Gd~v~vkv~~vd~~~-ki~ls~   72 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVV-DVGEKVWVKVIGREMKD-KMKLSL   72 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEE-CCCCEEEEEEEEECCCC-cEEEEe
Confidence            479999999999999999999977  5999999999 77777777764 89999999999999865 888875

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.

>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.95  E-value=3.6e-09  Score=84.96  Aligned_cols=70  Identities=10%  Similarity=0.037  Sum_probs=60.8

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      +.|+++.|+|+++.++|++|+++ +++||+|.+++ +++..++.+.. ++||.++++|+++|++++++.||.|
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 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKF-KKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCcccccccccc-CCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            58999999999999999999996 79999999999 55444444543 8999999999999998999999864

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.

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

Probab=98.94  E-value=1.7e-09  Score=118.45  Aligned_cols=77  Identities=36%  Similarity=0.578  Sum_probs=73.8

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLE  448 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~  448 (483)
                      ..+++|+++.|+|++|.+||+||.+.+ |-+||+|+|++++.|+.+..+.+++||.|.|||+.+|+++|+.||+|...
T Consensus       615 ~e~evg~iy~G~V~ri~~fGaFv~l~~-gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~~~  691 (692)
T COG1185         615 REVEVGEVYEGTVVRIVDFGAFVELLP-GKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIKAVL  691 (692)
T ss_pred             hhcccccEEEEEEEEEeecceEEEecC-CcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccceehhcc
Confidence            479999999999999999999999998 89999999999999999999999999999999999999999999999764

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

Probab=98.93  E-value=5.3e-09  Score=84.32  Aligned_cols=71  Identities=21%  Similarity=0.353  Sum_probs=63.0

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC---CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~---Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~  366 (483)
                      +.|+++.|+|+++.++|+||++.   |+.||+|.+++ +.+..++.+.. .+||.++++|+++|..++++.+|+|+
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 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLV-KVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHee-CCCCEEEEEEEEEECCCCEEEEEEcC
Confidence            47999999999999999999994   59999999999 66677776654 89999999999999988999999863

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

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

Probab=98.90  E-value=4e-09  Score=80.74  Aligned_cols=64  Identities=33%  Similarity=0.497  Sum_probs=58.4

Q ss_pred             EEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538          379 LEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (483)
Q Consensus       379 v~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS  443 (483)
                      +.|+|.++.++|+||+++. ++.|++|.+++++.+..++.+.|++||.|+|+|++++ +++++.||
T Consensus         1 v~g~V~~v~~~g~~v~l~~-~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           1 VTGKVVSITKFGVFVELED-GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             CEEEEEEEEeeeEEEEecC-CCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            4799999999999999997 7999999999999888888899999999999999997 57788775

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.

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

Probab=98.89  E-value=7.4e-09  Score=83.31  Aligned_cols=71  Identities=17%  Similarity=0.354  Sum_probs=62.3

Q ss_pred             CCCeEEEEEEEEECCeEEEEEC--CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          296 LNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       296 ~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      .|+++.|+|+++.++|+||++.  ++.|++|.+++ +.+..++.+.. .+||.|+|+|+++|.+++++.+|+|++
T Consensus         2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~-~~Gd~v~v~i~~vd~~~~~i~ls~k~~   75 (77)
T cd05708           2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLF-RVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHee-cCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            6899999999999999999996  59999999999 55655555543 899999999999999999999998754

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.

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

Probab=98.89  E-value=6.4e-09  Score=84.13  Aligned_cols=68  Identities=21%  Similarity=0.095  Sum_probs=60.2

Q ss_pred             hCCCeEEEEEEEEEC-CeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          295 QLNEPIEVKFTEWNT-GGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       295 k~GeiV~GkV~~v~k-~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      +.|+++.|+|+++.+ +|+||++. |.+|++|.+++ +++..++.+.. .+||.++|+|+++|.  +++.||+|
T Consensus         2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~-~~Gd~v~~kV~~~~~--~~i~LSl~   72 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGF-KPGKIVRCCILSKKD--GKYQLSLR   72 (72)
T ss_pred             CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhC-CCCCEEEEEEEEecC--CEEEEEeC
Confidence            589999999999986 89999994 89999999999 67777777754 899999999999984  88999875

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.

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

Probab=98.89  E-value=6.7e-09  Score=88.85  Aligned_cols=80  Identities=26%  Similarity=0.433  Sum_probs=69.5

Q ss_pred             cEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccC-----------cccccCCCCEEEEEEEEEe-C-----CCe
Q 011538          377 TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTS-----------VSDLLNEGERVKVLVVKSM-F-----PDK  439 (483)
Q Consensus       377 ~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~-----------~~~~~kvGd~VkVkVi~vd-e-----k~r  439 (483)
                      +++.|+|++|.++|+||++.  +++|++|.++++++++..           ....|++||.|+|+|++++ +     ..+
T Consensus         1 ~vv~g~V~~i~~~GifV~l~--~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~   78 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIG--PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESK   78 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEc--CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCce
Confidence            47899999999999999997  489999999999887653           3478999999999999998 3     258


Q ss_pred             EEEEEecCCCCcCcccccc
Q 011538          440 ISLSIADLESEPGLFVSDK  458 (483)
Q Consensus       440 I~LSLK~~~~dPw~~l~~k  458 (483)
                      +.||+|+....||+.+++.
T Consensus        79 i~ls~k~~~~g~~~~~~~~   97 (99)
T cd04460          79 IGLTMRQPGLGKLEWIEEE   97 (99)
T ss_pred             EEEEEecCCCCcHHHhhhh
Confidence            9999999999999887653

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.

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

Probab=98.89  E-value=7.7e-09  Score=82.48  Aligned_cols=69  Identities=30%  Similarity=0.439  Sum_probs=61.2

Q ss_pred             CCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~  366 (483)
                      |+++.|+|+++.++|++|++ ++++||+|.+++ +.+..++.+.. .+|+.++|+|+++|++++++.+|+|.
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 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERF-KVGDEVEAKITNVDRKNRKISLSIKA   71 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHcc-CCCCEEEEEEEEEeCCCCEEEEEEEE
Confidence            78999999999999999999 479999999999 56666666654 89999999999999988999999875

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

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

Probab=98.85  E-value=1.3e-08  Score=80.53  Aligned_cols=66  Identities=15%  Similarity=0.318  Sum_probs=57.4

Q ss_pred             CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-c-cccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-L-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS  363 (483)
                      |+++.|+|+++.++|+||+++ ++.||+|.+++ | .+..++.+.. .+||.++++|+++|.+++++.+|
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~-~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIY-KKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEE-CCCCEEEEEEEEEECCcCEEeCC
Confidence            689999999999999999995 79999999999 4 4555665543 89999999999999999988775

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.

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

Probab=98.83  E-value=1.7e-08  Score=78.86  Aligned_cols=67  Identities=18%  Similarity=0.337  Sum_probs=59.1

Q ss_pred             CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      |+++.|+|+++.++|+||+++ +..||+|.+++ +.+..++.+.. .+|+.+.++|+++|+ ++++.+|+|
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVL-KEGDKVKVKVLSIDA-RGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHcc-CCCCEEEEEEEEECC-CCcEEEEEC
Confidence            789999999999999999996 79999999999 56666666554 899999999999998 889999865

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=98.83  E-value=2e-08  Score=78.61  Aligned_cols=67  Identities=18%  Similarity=0.346  Sum_probs=59.0

Q ss_pred             CCCeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (483)
Q Consensus       296 ~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS  363 (483)
                      .|+++.|+|+++.++|++|+++++.||+|.+++ +.+..++.+.. .+||.++|+|+++|+.++++.+|
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 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVV-NVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccccCHhHEE-CCCCEEEEEEEEEECCCCEEecC
Confidence            488999999999999999999999999999999 55565555543 89999999999999988888876

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.

>PRK07252 hypothetical protein; Provisional

Probab=98.83  E-value=1.3e-08  Score=90.66  Aligned_cols=73  Identities=23%  Similarity=0.339  Sum_probs=64.4

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHh
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAW  368 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~  368 (483)
                      +.|+++.|+|+++.++|+||+++ ++.||+|.+++ +.++.++.+.. .+||.|.|+|+++|.+++++.+|++..-
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~-~vGD~V~VkI~~iD~~~~ri~lSlk~~~   76 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLL-KVGEEVLVQVVDFDEYTGKASLSLRTLE   76 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhcc-CCCCEEEEEEEEEeCCCCEEEEEEeecc
Confidence            57999999999999999999995 79999999999 66666665543 8999999999999999999999998653

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

Probab=98.83  E-value=2.8e-08  Score=81.94  Aligned_cols=76  Identities=24%  Similarity=0.296  Sum_probs=62.5

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      |-+++||+|.|+|+++.+++++|+++.+.+|++|.+++...+.+           +.                       
T Consensus         2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~-----------~~-----------------------   47 (82)
T cd04454           2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKK-----------EI-----------------------   47 (82)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchH-----------HH-----------------------
Confidence            45789999999999999999999999999999999998643100           01                       


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~  281 (483)
                          ...+++||.+.|+|++.+.++++.||++..
T Consensus        48 ----~~~~~~GD~i~~~V~~~~~~~~i~LS~~~~   77 (82)
T cd04454          48 ----RKSLQPGDLILAKVISLGDDMNVLLTTADN   77 (82)
T ss_pred             ----HhcCCCCCEEEEEEEEeCCCCCEEEEECCC
Confidence                234789999999999977668999998753

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".

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

Probab=98.81  E-value=2.7e-08  Score=82.59  Aligned_cols=80  Identities=28%  Similarity=0.337  Sum_probs=62.9

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      |.+++|++|.|+|+++.+++++|+++.+.+|++|.+|+....   .       .....+                     
T Consensus         2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~---~-------~~~~~~---------------------   50 (86)
T cd05789           2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPR---T-------DEDELN---------------------   50 (86)
T ss_pred             CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCC---C-------ccchHH---------------------
Confidence            457899999999999999999999999999999999985210   0       000000                     


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~  281 (483)
                         ....+++||.+.|+|++.+.++++.||++..
T Consensus        51 ---~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~   81 (86)
T cd05789          51 ---MRSYLDEGDLIVAEVQSVDSDGSVSLHTRSL   81 (86)
T ss_pred             ---HHhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence               0234789999999999987779999999875

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".

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

Probab=98.81  E-value=2.6e-08  Score=77.60  Aligned_cols=70  Identities=27%  Similarity=0.464  Sum_probs=59.8

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC-CeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      +.|+++.|+|+++.++|++|+++ ++.||+|.+++. .+..+..+. +.+|+.+.++|+++++.++++.+|++
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~-~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEV-LKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHe-ecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            36999999999999999999997 899999999994 434444443 38999999999999998899999864

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.79  E-value=9e-09  Score=115.55  Aligned_cols=70  Identities=37%  Similarity=0.593  Sum_probs=65.7

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL  442 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~L  442 (483)
                      .+++|+++.|+|++|.+||+||++.+ +.+||+|+|+++|.++.++.+.|++||.|+|+|++++.++||.|
T Consensus       615 ~~~~G~i~~G~V~~I~~~GafVei~~-g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~~gki~L  684 (684)
T TIGR03591       615 EPEVGKIYEGKVVRIMDFGAFVEILP-GKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQGRIKL  684 (684)
T ss_pred             ccccCcEEEEEEEEEeCCEEEEEECC-CcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECCCCCccC
Confidence            57899999999999999999999988 79999999999999999999999999999999999987777754

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).

>PRK08582 hypothetical protein; Provisional

Probab=98.79  E-value=1.5e-08  Score=92.51  Aligned_cols=72  Identities=18%  Similarity=0.280  Sum_probs=63.5

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      ++.|+++.|+|+++.++|+||+++ ++.||||.+++ +.++.++.+.. .+||.|+|+|+++|. .++|.||++++
T Consensus         3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l-~vGD~VkvkV~~id~-~gkI~LSlk~~   76 (139)
T PRK08582          3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHL-KVGDEVEVKVLNVED-DGKIGLSIKKA   76 (139)
T ss_pred             CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCccccccccccc-CCCCEEEEEEEEECC-CCcEEEEEEec
Confidence            468999999999999999999995 79999999999 66666665554 899999999999996 48999999875

>PRK05807 hypothetical protein; Provisional

Probab=98.76  E-value=2.5e-08  Score=90.69  Aligned_cols=73  Identities=18%  Similarity=0.245  Sum_probs=64.9

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHh
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAW  368 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~  368 (483)
                      ++.|++++|+|+++.++|+||++++..||||.+++ +.++.++.+.. .+||.|+|+|+++|. +++|.||+|...
T Consensus         3 ~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~~~~~-kvGd~V~VkV~~id~-~gkI~LSlk~~~   76 (136)
T PRK05807          3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHL-KEQDKVKVKVISIDD-NGKISLSIKQAM   76 (136)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCccccC-CCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence            46899999999999999999999989999999999 66676666654 899999999999997 789999998753

>TIGR01953 NusA transcription termination factor NusA

Probab=98.76  E-value=3.2e-08  Score=102.57  Aligned_cols=108  Identities=23%  Similarity=0.280  Sum_probs=83.8

Q ss_pred             CcccCCCEEEEEEEEEcCCCcEEEEehHH-----HHHhhhHHHHHHh--hCCCeEEEEEEEEECCe-EEEEECCeEEEee
Q 011538          253 PVVETGTVLFAEVLGRTLSGRPLLSTRRL-----FRKMAWHRVRQIK--QLNEPIEVKFTEWNTGG-LLTRIEGLRAFLP  324 (483)
Q Consensus       253 ~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~-----~~~~~w~~L~~~~--k~GeiV~GkV~~v~k~G-~fV~I~Gi~gFVP  324 (483)
                      +.+++||.+.+.+... .-|++.++..+.     ..+..++.+.+.+  +.|++|+|+|.++.++| ++|+++|+.||||
T Consensus        82 ~~~~vGD~I~~~I~~~-~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP  160 (341)
T TIGR01953        82 PDVQIGDEVKKEIPPE-NFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGILP  160 (341)
T ss_pred             cccccCCEEEEEeccc-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEECCeEEEec
Confidence            4578999999887533 345555444433     3466777787777  49999999999999988 6999999999999


Q ss_pred             ccccccccCChhhhhhhcCCEEEEEEEEEECC--CCceeechhhH
Q 011538          325 KAELLSRVNNFTELKEKVGRRMYVQITRINED--TNDLILSEREA  367 (483)
Q Consensus       325 ~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e--~~rLiLS~K~~  367 (483)
                      .+++...     +. +.+|++++|.|++++..  +..++|||+.+
T Consensus       161 ~~E~ip~-----E~-~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~  199 (341)
T TIGR01953       161 KKEQIPG-----EK-FRIGDRIKAYVYEVRKTAKGPQIILSRTHP  199 (341)
T ss_pred             HHHcCCC-----cC-CCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence            9999421     11 26999999999999954  45899999975

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.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.76  E-value=4.4e-08  Score=96.78  Aligned_cols=75  Identities=19%  Similarity=0.225  Sum_probs=68.7

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc----cCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----TSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i----~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~  447 (483)
                      ..++||+|.|+|++++++|+||+|+. ...|+||.++++|.++    .++++.|++||.|.|+|++++..+++.||+|+.
T Consensus        60 ~P~vGDiViG~V~~i~~~~~~vdI~~-~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~  138 (235)
T PRK04163         60 IPKVGDLVIGKVTDVTFSGWEVDINS-PYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGK  138 (235)
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEeCC-CceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCC
Confidence            35899999999999999999999987 6899999999999987    888999999999999999998666799999864

>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=98.73  E-value=5.9e-08  Score=75.65  Aligned_cols=66  Identities=18%  Similarity=0.206  Sum_probs=57.4

Q ss_pred             CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS  363 (483)
                      |+.+.|+|+++.++|+||+++ +..||+|.+++ +.+..++.+.. .+||.+.|+|+++|++++++.+|
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~-~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVV-SVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhc-CCCCEEEEEEEEEECCCCEEecC
Confidence            678999999999999999995 68999999999 55565665543 89999999999999988888876

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.

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

Probab=98.72  E-value=3.6e-08  Score=85.05  Aligned_cols=72  Identities=14%  Similarity=0.248  Sum_probs=61.4

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccc-------------------cCChhhhhhhcCCEEEEEEEEE
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSR-------------------VNNFTELKEKVGRRMYVQITRI  353 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~r-------------------v~~~~~l~~~VGq~V~vkVl~I  353 (483)
                      +.|++|.|+|+++.+.|++|.+. |+.||+|.+++ +.+                   ..++.+.+ ++||.|+|+|+++
T Consensus         2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f-~vGd~V~~kVi~~   80 (100)
T cd05693           2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLF-SVGQLVRCKVVSL   80 (100)
T ss_pred             CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhc-cCCCEEEEEEEEc
Confidence            68999999999999999999995 89999999999 432                   12344554 8999999999999


Q ss_pred             ECC---CCceeechhhH
Q 011538          354 NED---TNDLILSEREA  367 (483)
Q Consensus       354 D~e---~~rLiLS~K~~  367 (483)
                      |++   +++|.||.|..
T Consensus        81 d~~~~~~~~i~LSlr~~   97 (100)
T cd05693          81 DKSKSGKKRIELSLEPE   97 (100)
T ss_pred             cCCcCCCcEEEEEecHH
Confidence            987   78999999865

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=98.71  E-value=5.1e-08  Score=79.72  Aligned_cols=68  Identities=18%  Similarity=0.256  Sum_probs=59.3

Q ss_pred             CCeEEEEEEEEECCeEEEEEC----CeEEEeecccc-cccc-CChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE----GLRAFLPKAEL-LSRV-NNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~----Gi~gFVP~Sel-~~rv-~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      |+++.|+|+++.++|+||+++    +..||+|.+++ +.+. .++.+.. .+||.|+++|+++|  ++++.+|+|..
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~-~~Gd~v~v~v~~vd--~~~i~~s~k~~   74 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVV-KRGQKVKVKVISIQ--NGKISLSMKDV   74 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhhee-CCCCEEEEEEEEEe--CCEEEEEEEec
Confidence            689999999999999999997    68999999999 6654 6666553 89999999999999  78999998763

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.

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

Probab=98.69  E-value=7.4e-08  Score=77.08  Aligned_cols=68  Identities=16%  Similarity=0.265  Sum_probs=56.6

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-cc-ccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~-rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS  363 (483)
                      ..|+++.|+|+++.++|+||+++ |+.||+|.+++ +. +..++... +.+||.++|+|+++|.+++++.+|
T Consensus         2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~-~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKV-VSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccE-eCCCCEEEEEEEEeeCCcCEEeCC
Confidence            57999999999999999999994 79999999999 43 32233333 379999999999999988888764

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.

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

Probab=98.66  E-value=3.5e-08  Score=105.51  Aligned_cols=84  Identities=26%  Similarity=0.362  Sum_probs=79.8

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCCc
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP  451 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~dP  451 (483)
                      ++..|-++.|+|+.+.++|+||++.+ +..||+|+|+++..++.+|++.+.+||.|.|+.+..|.++.+.+|.|.+.++|
T Consensus       665 ~l~~g~vy~~tIt~~rd~G~~V~l~p-~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~~~ls~ralLp~p  743 (760)
T KOG1067|consen  665 DLEFGGVYTATITEIRDTGVMVELYP-MQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSSRALLPDP  743 (760)
T ss_pred             ceEeeeEEEEEEeeecccceEEEecC-CchhhccchhcccccccChHHHHhhcceeEEEEEeecCccceeehhhhhcCCc
Confidence            78899999999999999999999999 89999999999999999999999999999999999999999999999999999


Q ss_pred             Ccccc
Q 011538          452 GLFVS  456 (483)
Q Consensus       452 w~~l~  456 (483)
                      -....
T Consensus       744 ~~~~~  748 (760)
T KOG1067|consen  744 ATKES  748 (760)
T ss_pred             ccCCc
Confidence            76544

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

Probab=98.65  E-value=5.1e-08  Score=96.27  Aligned_cols=71  Identities=17%  Similarity=0.272  Sum_probs=66.8

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEE---CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I---~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      -..|++|-|+|.++.++|+||.+   +|++||+|.||+ ..++++++++. ++||++-|+|+++|++++.|-||+|
T Consensus         9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~v-kegqkvV~kVlrVd~~rg~IDLSlk   83 (269)
T COG1093           9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYV-KEGQKVVAKVLRVDPKRGHIDLSLK   83 (269)
T ss_pred             CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHh-hcCCeEEEEEEEEcCCCCeEeeehh
Confidence            36899999999999999999998   689999999999 67889999987 9999999999999999999999997

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

Probab=98.65  E-value=1.4e-07  Score=73.89  Aligned_cols=66  Identities=23%  Similarity=0.327  Sum_probs=57.2

Q ss_pred             CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~  364 (483)
                      |+++.|+|+++.++|+||+++ +..||+|.+++ +.+..++.+.. .+||.+.++|+++|+ ++++.+|+
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVL-KVGDEVKVKVIEVDD-RGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHcc-CCCCEEEEEEEEECC-CCcEEeeC
Confidence            678999999999999999995 69999999999 55555555543 899999999999998 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.

>PRK08059 general stress protein 13; Validated

Probab=98.64  E-value=1e-07  Score=85.03  Aligned_cols=74  Identities=16%  Similarity=0.270  Sum_probs=65.0

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHh
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAW  368 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~  368 (483)
                      ++.|+++.|+|+++.++|++|+++ ++.|++|.+++ +.+..++.+.. .+|+.|.|+|+++|++++++.+|++..-
T Consensus         5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~-~vGD~I~vkI~~id~~~~~i~lslk~~~   80 (123)
T PRK08059          5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFL-SVGDEVKVKVLSVDEEKGKISLSIRATE   80 (123)
T ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcC-CCCCEEEEEEEEEECCCCeEEEEEEEcc
Confidence            578999999999999999999995 79999999999 55666655543 7999999999999999999999998763

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

Probab=98.63  E-value=1.7e-07  Score=74.60  Aligned_cols=62  Identities=24%  Similarity=0.391  Sum_probs=53.6

Q ss_pred             CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeC-C--CeEEEE
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMF-P--DKISLS  443 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vde-k--~rI~LS  443 (483)
                      ..|+++.|+|.++.++|+||+++  +.+|+||.++++.      .+.|++||.|+|.|+++++ +  ..|.||
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig--~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS   66 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLG--KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILS   66 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcC--CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence            47999999999999999999996  4899999999873      4678999999999999972 2  467777

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

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

Probab=98.62  E-value=1.5e-07  Score=74.93  Aligned_cols=64  Identities=20%  Similarity=0.341  Sum_probs=54.1

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCC--Cceeech
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDT--NDLILSE  364 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~--~rLiLS~  364 (483)
                      ..|++++|+|.++.++|++|++++++||||.+++..     .+. +.+|+++++.|++++..+  .+|.|||
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~-----~~~-~~~Gd~v~v~v~~v~~~~~~~~i~lSr   67 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIP-----GES-YRPGDRIKAYVLEVRKTSKGPQIILSR   67 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCC-----CCc-CCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence            479999999999999999999988999999999942     111 279999999999998643  4688886

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.

>PHA02945 interferon resistance protein; Provisional

Probab=98.62  E-value=9.4e-08  Score=80.00  Aligned_cols=69  Identities=14%  Similarity=0.176  Sum_probs=60.9

Q ss_pred             hCCCeEEEEEEEEECCeEEEEE---CCeEEEeecccc---ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL---LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I---~Gi~gFVP~Sel---~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      +.|+++-|+|.. .++|+||.+   +|.+||+|.|+.   ..++++ ++..  +||++-|+|+++|+.++.|-||+|..
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 NVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL--VGKTVKVKVIRVDYTKGYIDVNYKRM   84 (88)
T ss_pred             CCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe--cCCEEEEEEEEECCCCCEEEeEeeEc
Confidence            689999999999 999999999   589999999955   456666 6664  99999999999999999999998853

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.61  E-value=2.7e-07  Score=103.18  Aligned_cols=95  Identities=18%  Similarity=0.246  Sum_probs=74.7

Q ss_pred             EEcCCCcEEEEehH-HHHHhhhHHHHHH-----hhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc----c-cccCC
Q 011538          267 GRTLSGRPLLSTRR-LFRKMAWHRVRQI-----KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL----L-SRVNN  334 (483)
Q Consensus       267 ~~d~~G~iiLS~k~-~~~~~~w~~L~~~-----~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel----~-~rv~~  334 (483)
                      .++.+|.+.++... ....++...+...     .+.|++++|+|+++.++|+||++ .|++||||.|++    | .++.+
T Consensus       612 di~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~  691 (719)
T TIGR02696       612 SIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVEN  691 (719)
T ss_pred             EEecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCC
Confidence            34568888766533 3334444444433     46999999999999999999999 489999999998    3 57888


Q ss_pred             hhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538          335 FTELKEKVGRRMYVQITRINEDTNDLILS  363 (483)
Q Consensus       335 ~~~l~~~VGq~V~vkVl~ID~e~~rLiLS  363 (483)
                      +.++. ++||+|+|+|+++|+ ++|+.|+
T Consensus       692 ~~dv~-kvGd~V~VKVl~ID~-~gKI~L~  718 (719)
T TIGR02696       692 VEDVL-SVGQKIQVEIADIDD-RGKLSLV  718 (719)
T ss_pred             HHHcC-CCCCEEEEEEEEECC-CCCeeec
Confidence            88865 899999999999995 6788775

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.56  E-value=2.3e-07  Score=96.97  Aligned_cols=109  Identities=17%  Similarity=0.258  Sum_probs=79.3

Q ss_pred             CcccCCCEEEEEEEEEcCCCcEEEEehHHH----HHhhhHHHHHHh--hCCCeEEEEEEEEECCeEEEEECCeEEEeecc
Q 011538          253 PVVETGTVLFAEVLGRTLSGRPLLSTRRLF----RKMAWHRVRQIK--QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKA  326 (483)
Q Consensus       253 ~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~----~~~~w~~L~~~~--k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~S  326 (483)
                      +..++||.+...+...+.++....+.|+..    .+...+.+.+.+  +.|++++|+|.++.++|++|+++|++||||.+
T Consensus        85 ~~~~vGD~i~~~I~~~~fgR~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP~~  164 (362)
T PRK12327         85 PAYELGDVIEIEVTPKDFGRIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLGKIEAVLPPA  164 (362)
T ss_pred             ccccCCCEEEEecCcCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeCCeEEEecHH
Confidence            347899999888754333333333333332    233444555555  79999999999999999999999999999988


Q ss_pred             ccccccCChhhhhhhcCCEEEEEEEEEECCCC--ceeechhhH
Q 011538          327 ELLSRVNNFTELKEKVGRRMYVQITRINEDTN--DLILSEREA  367 (483)
Q Consensus       327 el~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~--rLiLS~K~~  367 (483)
                      ++...     +. +.+|++++|+|++++...+  .|+|||..+
T Consensus       165 E~ip~-----e~-~~~Gd~Ika~V~~V~~~~kgp~IivSRt~p  201 (362)
T PRK12327        165 EQIPG-----ET-YKHGDRIKVYVVKVEKTTKGPQIFVSRTHP  201 (362)
T ss_pred             HcCCC-----CC-CCCCCEEEEEEEEEecCCCCCeEEEEeCCH
Confidence            88321     11 2699999999999995443  799999864

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.55  E-value=2.2e-07  Score=100.17  Aligned_cols=112  Identities=15%  Similarity=0.207  Sum_probs=85.0

Q ss_pred             EEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeec-hhhH----hh-------hcCCC--CCcEEEEEEEE
Q 011538          320 RAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS-EREA----WA-------TLNLR--EGTLLEGTVKK  385 (483)
Q Consensus       320 ~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS-~K~~----~e-------~~~l~--vG~iv~G~V~~  385 (483)
                      .++||.++.-..  ++.   ..+|+.+.+.|...+  .+|+.++ .|+.    |.       ...++  .|+++.|+|++
T Consensus        72 ~~eI~L~eAk~~--~~~---~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~r  144 (470)
T PRK09202         72 TKEISLEEARKI--DPD---AEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKR  144 (470)
T ss_pred             cceeeHHHHhhh--Ccc---ccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEE
Confidence            467787777321  221   259999999998876  3444333 3332    22       13454  99999999999


Q ss_pred             EeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCC--eEEEEEec
Q 011538          386 IYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD--KISLSIAD  446 (483)
Q Consensus       386 I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~--rI~LSLK~  446 (483)
                      +.++|+||+++  +++||||.++++      |++.|++||+|+|+|++++ +++  +|.||.+.
T Consensus       145 i~~~giiVDLg--gvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~  200 (470)
T PRK09202        145 VERGNIIVDLG--RAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH  200 (470)
T ss_pred             EecCCEEEEEC--CeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence            99999999996  689999999985      6788999999999999997 444  78888774

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=98.54  E-value=2.8e-07  Score=105.11  Aligned_cols=71  Identities=21%  Similarity=0.300  Sum_probs=64.7

Q ss_pred             hhCCCeEE-EEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538          294 KQLNEPIE-VKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (483)
Q Consensus       294 ~k~GeiV~-GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~  366 (483)
                      .+.|++++ |+|+++.++|+||++. |++||||.|++ +.++.++++.. ++||.|+|+|+++|+ +++|.||+|.
T Consensus       751 ~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~-kvGD~V~VkVi~ID~-~grI~LSlK~  824 (891)
T PLN00207        751 PTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAF-KVGDRIDVKLIEVND-KGQLRLSRRA  824 (891)
T ss_pred             cCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhc-CCCCEEEEEEEEECC-CCcEEEEEec
Confidence            57999996 6999999999999995 89999999999 78888888765 899999999999997 7899999986

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

Probab=98.53  E-value=5e-07  Score=85.59  Aligned_cols=81  Identities=25%  Similarity=0.415  Sum_probs=68.9

Q ss_pred             CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc-----------CcccccCCCCEEEEEEEEEe------C
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM------F  436 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~-----------~~~~~~kvGd~VkVkVi~vd------e  436 (483)
                      .+|++++|+|++++++|+||+++  .++|++|.+++.+++..           +....++.||.|++||++++      +
T Consensus        80 ~~gEvv~G~V~~v~~~GifV~lg--~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~  157 (179)
T TIGR00448        80 ELGEIVEGEVIEIVEFGAFVSLG--PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPE  157 (179)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEeC--CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCC
Confidence            47999999999999999999996  48999999999866432           23467999999999999996      2


Q ss_pred             CCeEEEEEecCCCCcCcccc
Q 011538          437 PDKISLSIADLESEPGLFVS  456 (483)
Q Consensus       437 k~rI~LSLK~~~~dPw~~l~  456 (483)
                      ..+|.||+|+....|++.++
T Consensus       158 ~~~I~lt~k~~~LG~~~w~~  177 (179)
T TIGR00448       158 GSKIGLTMRQPLLGKLEWIE  177 (179)
T ss_pred             cceEEEEeccCcCCcccccc
Confidence            46999999998888887764

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

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

Probab=98.50  E-value=4.2e-07  Score=77.32  Aligned_cols=74  Identities=19%  Similarity=0.259  Sum_probs=65.5

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEE--------CCCceEEEEeccCcCccccc--CcccccCCCCEEEEEEEEEeCCCeEEE
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRI--------GDSNRSGLLHISNMSRTRVT--SVSDLLNEGERVKVLVVKSMFPDKISL  442 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I--------~~~gi~GLlhiSels~~~i~--~~~~~~kvGd~VkVkVi~vdek~rI~L  442 (483)
                      .++|++|.|+|++++...+.|+|        .. ...|++|++++...+..  ++.+.|++||.|+|+|+++.+...+.|
T Consensus         4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~L   82 (92)
T cd05791           4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKE-SFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYYL   82 (92)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCC-CcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcEE
Confidence            47999999999999999999999        55 58999999999877666  788999999999999999876677999


Q ss_pred             EEecC
Q 011538          443 SIADL  447 (483)
Q Consensus       443 SLK~~  447 (483)
                      |+++-
T Consensus        83 st~~~   87 (92)
T cd05791          83 STAEN   87 (92)
T ss_pred             EecCC
Confidence            99863

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".

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

Probab=98.49  E-value=4.4e-07  Score=69.29  Aligned_cols=63  Identities=22%  Similarity=0.350  Sum_probs=52.9

Q ss_pred             EEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538          300 IEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (483)
Q Consensus       300 V~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS  363 (483)
                      +.|+|+++.++|++|+++ +++||+|.+++ +.+..++.+.. .+|+.+.++|+++|++++++.+|
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~-~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVF-KVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEe-CCCCEEEEEEEEEcCCcCEEecC
Confidence            479999999999999997 89999999999 44444444443 79999999999999988888776

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=98.48  E-value=4.3e-07  Score=91.13  Aligned_cols=71  Identities=18%  Similarity=0.295  Sum_probs=64.3

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC---CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~---Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      .+.|+++.|+|+++.++|+||++.   |+.||+|.+++ +.++.++.+.. .+||.+.|+|+++|++++++.||+|
T Consensus         6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~-kvGd~V~vkVi~VD~~k~~I~LSlK   80 (262)
T PRK03987          6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHV-KEGQKVVCKVIRVDPRKGHIDLSLK   80 (262)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhC-CCCCEEEEEEEEEecccCeEEEEEE
Confidence            468999999999999999999994   79999999999 66777777664 8999999999999999999999987

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

Probab=98.48  E-value=5.4e-07  Score=75.96  Aligned_cols=70  Identities=17%  Similarity=0.234  Sum_probs=58.0

Q ss_pred             hhCCCeEEEEEEEEECC--eEEEEEC-CeEEEeecccc-c---cccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538          294 KQLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAEL-L---SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~--G~fV~I~-Gi~gFVP~Sel-~---~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~  364 (483)
                      .+.|+++.|+|+++.++  |+||+++ |.+||||.+++ +   .++.++.+.. ++||.|.|+|++.....+-..+|.
T Consensus         5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~-~~Gd~v~VqV~~~~~~~K~~~lt~   81 (88)
T cd04453           5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLL-KEGQEILVQVVKEPIGTKGPRLTT   81 (88)
T ss_pred             CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcC-CCCCEEEEEEEEecCCCCCceEEE
Confidence            46899999999999996  9999996 79999999999 5   4566666654 899999999999876665555554

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

>TIGR02063 RNase_R ribonuclease R

Probab=98.46  E-value=5.7e-07  Score=101.70  Aligned_cols=73  Identities=26%  Similarity=0.446  Sum_probs=63.9

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc-----------cCcccccCCCCEEEEEEEEEe-CCCe
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDK  439 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i-----------~~~~~~~kvGd~VkVkVi~vd-ek~r  439 (483)
                      .-++|++++|+|++|+++|+||++.+.+++||+|+++++++++           .+....|++||+|+|+|+++| ++++
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            4578999999999999999999998656999999999997643           344578999999999999998 7899


Q ss_pred             EEEEE
Q 011538          440 ISLSI  444 (483)
Q Consensus       440 I~LSL  444 (483)
                      |.+++
T Consensus       704 I~~~l  708 (709)
T TIGR02063       704 IDFEL  708 (709)
T ss_pred             EEEEE
Confidence            99986

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=98.39  E-value=1.2e-06  Score=98.86  Aligned_cols=97  Identities=19%  Similarity=0.217  Sum_probs=75.9

Q ss_pred             cCCCcEEEEehH-HHHHhhhHHHH---HHhhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhc
Q 011538          269 TLSGRPLLSTRR-LFRKMAWHRVR---QIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKV  342 (483)
Q Consensus       269 d~~G~iiLS~k~-~~~~~~w~~L~---~~~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~V  342 (483)
                      +.+|.+.++... ...+++...+.   ...+.|+++.|+|+++.++|+||++. |.+||+|.|++ +.++.++.+.. ++
T Consensus       590 ~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~-kv  668 (693)
T PRK11824        590 EDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVL-KE  668 (693)
T ss_pred             CCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCcccee-CC
Confidence            457888655432 22222333332   33579999999999999999999995 79999999999 67787777764 89


Q ss_pred             CCEEEEEEEEEECCCCceeechhhH
Q 011538          343 GRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       343 Gq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      ||.|+|+|+++|++ +++.||+|..
T Consensus       669 GD~V~VkV~~iD~~-grI~LS~k~~  692 (693)
T PRK11824        669 GDEVKVKVLEIDKR-GRIRLSRKAV  692 (693)
T ss_pred             CCEEEEEEEEECCC-CcEEEEEEec
Confidence            99999999999987 9999998753

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

Probab=98.35  E-value=1.5e-06  Score=70.87  Aligned_cols=67  Identities=12%  Similarity=0.234  Sum_probs=54.4

Q ss_pred             CCeEEEEEEEEECCeEEEEEC--CeEEEeecccc-ccccC-----------ChhhhhhhcCCEEEEEEEEEECCCCceee
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRVN-----------NFTELKEKVGRRMYVQITRINEDTNDLIL  362 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel-~~rv~-----------~~~~l~~~VGq~V~vkVl~ID~e~~rLiL  362 (483)
                      |++++|+|+++.++|+||+++  |+.|++|.+++ +.++.           +.... ..+||.|+++|+++|.+++++.+
T Consensus         2 g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~-~~~gd~v~v~v~~vd~~~~~i~~   80 (83)
T cd04471           2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKV-FRLGDKVKVRVVRVDLDRRKIDF   80 (83)
T ss_pred             CCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCE-EcCCCEEEEEEEEeccccCEEEE
Confidence            889999999999999999997  69999999998 33211           11122 27899999999999988888887


Q ss_pred             ch
Q 011538          363 SE  364 (483)
Q Consensus       363 S~  364 (483)
                      +.
T Consensus        81 ~l   82 (83)
T cd04471          81 EL   82 (83)
T ss_pred             EE
Confidence            64

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.

>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=98.35  E-value=2.3e-06  Score=68.50  Aligned_cols=61  Identities=10%  Similarity=0.134  Sum_probs=51.6

Q ss_pred             CCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-cc--ccCChhhhhhhcCCEEEEEEEEEECCCC
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LS--RVNNFTELKEKVGRRMYVQITRINEDTN  358 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~--rv~~~~~l~~~VGq~V~vkVl~ID~e~~  358 (483)
                      |+++.|+|+++.+.|++|.++ |++|++|.+++ +.  ...++.+.. .+||.+.|+|+++|.++.
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~-~~Gd~i~~kVl~~d~~~~   65 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKF-KIGQKIKARVIGGHDAKT   65 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhC-CCCCEEEEEEEEEeCccc
Confidence            789999999999999999995 89999999999 44  255555543 799999999999987543

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.

>PRK11642 exoribonuclease R; Provisional

Probab=98.34  E-value=1.6e-06  Score=99.23  Aligned_cols=76  Identities=25%  Similarity=0.388  Sum_probs=65.5

Q ss_pred             CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc-----------CcccccCCCCEEEEEEEEEe-CCCeEE
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FPDKIS  441 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~-----------~~~~~~kvGd~VkVkVi~vd-ek~rI~  441 (483)
                      ++|+++.|+|++|+++|+||+|.+.+++||+|++++.++++.           +....|++||.|+|+|+++| ++++|.
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            689999999999999999999987569999999999977432           33577999999999999998 789999


Q ss_pred             EEEecCCC
Q 011538          442 LSIADLES  449 (483)
Q Consensus       442 LSLK~~~~  449 (483)
                      |++-....
T Consensus       722 f~l~~~~~  729 (813)
T PRK11642        722 FSLISSER  729 (813)
T ss_pred             EEEecccc
Confidence            99864443

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

Probab=98.32  E-value=1.7e-06  Score=81.94  Aligned_cols=79  Identities=25%  Similarity=0.407  Sum_probs=64.8

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc----------C-cccccCCCCEEEEEEEEEe--CC--
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT----------S-VSDLLNEGERVKVLVVKSM--FP--  437 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~----------~-~~~~~kvGd~VkVkVi~vd--ek--  437 (483)
                      ...|++|.|.|+++.++|+||.|+.  .+||+|++++.++++.          + -...+++||.|+|||+...  +.  
T Consensus        79 P~~gEVV~GeVv~~~~~G~fV~igp--~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~  156 (183)
T COG1095          79 PFRGEVVEGEVVEVVEFGAFVRIGP--LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRP  156 (183)
T ss_pred             eccccEEEEEEEEEeecceEEEecc--ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcc
Confidence            3469999999999999999999996  7999999999988431          2 3347999999999999885  32  


Q ss_pred             --CeEEEEEecCCCCcCc
Q 011538          438 --DKISLSIADLESEPGL  453 (483)
Q Consensus       438 --~rI~LSLK~~~~dPw~  453 (483)
                        .+|.|+||+.-..+.+
T Consensus       157 ~~~~I~lTmrq~~LGkle  174 (183)
T COG1095         157 RESKIGLTMRQPGLGKLE  174 (183)
T ss_pred             ccceEEEEeccccCCcch
Confidence              6899999987655443

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=98.32  E-value=2e-06  Score=82.25  Aligned_cols=104  Identities=15%  Similarity=0.234  Sum_probs=78.8

Q ss_pred             CCCcccCCCEEEEEEEEE---cCCC-cEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC---------
Q 011538          251 GRPVVETGTVLFAEVLGR---TLSG-RPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE---------  317 (483)
Q Consensus       251 ~~~~~kVGd~V~v~Vi~~---d~~G-~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~---------  317 (483)
                      +...+..+..+.+.+.+.   |.++ ++.+.        +|.......+.|++|.|+|+++.+.|++|+++         
T Consensus        23 G~Gty~~~~~i~as~~G~~~id~~~~~Isv~--------P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l   94 (189)
T PRK09521         23 GEGTYEDNGEVYASVVGKVFIDDINRKISVI--------PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSEREL   94 (189)
T ss_pred             CCCEEeeCCEEEEEeeEEEEEcCCCCEEEEe--------cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEeccccccc
Confidence            345577788888888873   4333 34342        45443345679999999999999999999994         


Q ss_pred             --CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538          318 --GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (483)
Q Consensus       318 --Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~  366 (483)
                        ++.||+|.+++ +.+..+..+.. ++||.|.|+|++++   +++.||.|.
T Consensus        95 ~~~~~G~l~~s~i~~~~~~~~~~~~-~~GD~V~akV~~i~---~~i~LS~k~  142 (189)
T PRK09521         95 ATSKLAYIHISQVSDGYVESLTDAF-KIGDIVRAKVISYT---DPLQLSTKG  142 (189)
T ss_pred             CCCceeeEEhhHcChhhhhhHHhcc-CCCCEEEEEEEecC---CcEEEEEec
Confidence              57899999999 55555555544 89999999999997   689999874

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

Probab=98.28  E-value=2.7e-06  Score=95.51  Aligned_cols=72  Identities=22%  Similarity=0.405  Sum_probs=63.1

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc-----------cCcccccCCCCEEEEEEEEEe-CCCeE
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDKI  440 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i-----------~~~~~~~kvGd~VkVkVi~vd-ek~rI  440 (483)
                      -++|++++|+|++|+++|+||++.+.+++||+|++++.|+++           .+....|++||+|+|+|+++| ++++|
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            367999999999999999999998558999999999998742           234577999999999999998 88899


Q ss_pred             EEEE
Q 011538          441 SLSI  444 (483)
Q Consensus       441 ~LSL  444 (483)
                      .+++
T Consensus       650 ~f~l  653 (654)
T TIGR00358       650 IFEL  653 (654)
T ss_pred             EEEE
Confidence            9886

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.

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

Probab=98.26  E-value=6e-06  Score=67.52  Aligned_cols=62  Identities=19%  Similarity=0.326  Sum_probs=54.3

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~  364 (483)
                      ++.|+.+.|+|+++.++|+||+++ ++.||+|.+++...        .++||.++++|.++ .+++++.+|.
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--------YEVGDEVIVQVTDI-PENGNIDLIP   76 (77)
T ss_pred             CCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhccCc--------CCCCCEEEEEEEEE-CCCCcEEEEE
Confidence            578999999999999999999995 59999999997432        26999999999999 7888888763

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.

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=98.23  E-value=2.8e-06  Score=70.58  Aligned_cols=70  Identities=13%  Similarity=0.149  Sum_probs=65.7

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEe-ccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLH-ISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlh-iSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL  444 (483)
                      .++|+++. .|+.|.+.|++|.+.++|++|++. .+|++.+++.++++.+ +|..+.|+|+.+| +++.|.||.
T Consensus        14 P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         14 PNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             CCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence            56899999 899999999999998888999999 9999999999999999 9999999999998 889999984

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=98.21  E-value=2.8e-06  Score=94.91  Aligned_cols=82  Identities=16%  Similarity=0.097  Sum_probs=71.7

Q ss_pred             hhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceee
Q 011538          285 MAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLIL  362 (483)
Q Consensus       285 ~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiL  362 (483)
                      .....+. .++.|+++.|+|.++..+|+||+|| ..+|+||+|++ ...+++|.++. .+|+.|+++|+++|..+++|.|
T Consensus       648 ~~v~~i~-dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv-~vGdiV~v~V~~vD~~r~rI~L  725 (780)
T COG2183         648 EGVESIT-DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVV-KVGDIVKVKVIEVDTARKRIAL  725 (780)
T ss_pred             hhhhhHh-hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhc-ccCCEEEEEEEEEecccCeeee
Confidence            3344443 5689999999999999999999997 58999999999 56788888876 8999999999999999999999


Q ss_pred             chhhHh
Q 011538          363 SEREAW  368 (483)
Q Consensus       363 S~K~~~  368 (483)
                      |++..-
T Consensus       726 smr~~~  731 (780)
T COG2183         726 SMRLDE  731 (780)
T ss_pred             EeeccC
Confidence            998753

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

Probab=98.20  E-value=5.7e-06  Score=78.72  Aligned_cols=83  Identities=25%  Similarity=0.396  Sum_probs=67.0

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc-----------CcccccCCCCEEEEEEEEEe-CC---
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FP---  437 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~-----------~~~~~~kvGd~VkVkVi~vd-ek---  437 (483)
                      ..+|+++.|+|++++++|+||+++.  ++|++|.+++.+++..           +....+++||.|+++|++++ +.   
T Consensus        79 P~~GEVv~g~V~~v~~~Gi~V~lg~--~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~  156 (187)
T PRK08563         79 PELQEVVEGEVVEVVEFGAFVRIGP--VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP  156 (187)
T ss_pred             ccCCCEEEEEEEEEEccEEEEEEeC--ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCC
Confidence            3479999999999999999999974  8999999999876432           34567999999999999997 32   


Q ss_pred             --CeEEEEEecCCCCcCccccc
Q 011538          438 --DKISLSIADLESEPGLFVSD  457 (483)
Q Consensus       438 --~rI~LSLK~~~~dPw~~l~~  457 (483)
                        .+|.+|+++..--+.+.+.+
T Consensus       157 ~~~~I~ls~~~~~LG~~~w~~~  178 (187)
T PRK08563        157 RGSKIGLTMRQPGLGKLEWIEE  178 (187)
T ss_pred             CCCEEEEEecCCCCCcHHHHHH
Confidence              48999999866555444443

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.19  E-value=9.1e-06  Score=91.66  Aligned_cols=92  Identities=15%  Similarity=0.173  Sum_probs=70.4

Q ss_pred             EcCCCcEEEEeh-HHHHHhhhH---HHHHHhhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhh
Q 011538          268 RTLSGRPLLSTR-RLFRKMAWH---RVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEK  341 (483)
Q Consensus       268 ~d~~G~iiLS~k-~~~~~~~w~---~L~~~~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~  341 (483)
                      ++.+|++.++.. ....+++..   .+....+.|+++.|+|+++.++|+||++ +|.+||+|.|++ +.++.++.+.. +
T Consensus       586 i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~-k  664 (684)
T TIGR03591       586 IEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVL-K  664 (684)
T ss_pred             EecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhcc-C
Confidence            445788865542 222222322   2333457899999999999999999999 579999999999 77788887765 8


Q ss_pred             cCCEEEEEEEEEECCCCcee
Q 011538          342 VGRRMYVQITRINEDTNDLI  361 (483)
Q Consensus       342 VGq~V~vkVl~ID~e~~rLi  361 (483)
                      +||.|.|+|+++|+ ++++.
T Consensus       665 vGD~V~VkVi~id~-~gki~  683 (684)
T TIGR03591       665 EGDEVKVKVLEIDK-QGRIK  683 (684)
T ss_pred             CCCEEEEEEEEECC-CCCcc
Confidence            99999999999997 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).

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.11  E-value=1.3e-05  Score=79.34  Aligned_cols=79  Identities=23%  Similarity=0.274  Sum_probs=63.0

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      |.+++||+|.|+|+++.+++++||++....|+||.+++...+. +                          .|.      
T Consensus        59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~-~--------------------------~d~------  105 (235)
T PRK04163         59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPV-N--------------------------VEG------  105 (235)
T ss_pred             ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCcc-c--------------------------cch------
Confidence            7789999999999999999999999988999999999864310 0                          000      


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 011538          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~  280 (483)
                       .+..+.+++||.|.|+|+..+.++.+.||++.
T Consensus       106 -~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~  137 (235)
T PRK04163        106 -TDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKG  137 (235)
T ss_pred             -hhhHhhCCCCCEEEEEEEEECCCCcEEEEEcC
Confidence             01134589999999999998877789999864

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

Probab=98.11  E-value=1.1e-05  Score=89.09  Aligned_cols=98  Identities=16%  Similarity=0.178  Sum_probs=78.0

Q ss_pred             EcCCCcEEEEehHH-HHHhhh---HHHHHHhhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhh
Q 011538          268 RTLSGRPLLSTRRL-FRKMAW---HRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEK  341 (483)
Q Consensus       268 ~d~~G~iiLS~k~~-~~~~~w---~~L~~~~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~  341 (483)
                      ++.+|++.++.... ....+.   ..+....+.|+++.|+|+++.++|+||.+ +|-.|++|.|++ +.++....+.. +
T Consensus       587 ieddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvl-k  665 (692)
T COG1185         587 IEDDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVL-K  665 (692)
T ss_pred             ecCCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhccccee-e
Confidence            45789886665443 223333   33445578999999999999999999999 689999999999 66777777766 8


Q ss_pred             cCCEEEEEEEEEECCCCceeechhhH
Q 011538          342 VGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       342 VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      +||.+.++|+.+|+ ++++.+|++..
T Consensus       666 ~Gd~v~Vkv~~iD~-~Gri~ls~~~~  690 (692)
T COG1185         666 EGDEVKVKVIEIDK-QGRIRLSIKAV  690 (692)
T ss_pred             cCceEEEEEeeecc-cCCccceehhc
Confidence            99999999999984 68899998754

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

Probab=98.04  E-value=1.1e-05  Score=68.99  Aligned_cols=69  Identities=19%  Similarity=0.213  Sum_probs=55.6

Q ss_pred             CeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccCCh-----------hhhhhhcCCEEEEEEEEEECCC-----Cce
Q 011538          298 EPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNF-----------TELKEKVGRRMYVQITRINEDT-----NDL  360 (483)
Q Consensus       298 eiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~~~-----------~~l~~~VGq~V~vkVl~ID~e~-----~rL  360 (483)
                      +++.|+|+++.++|+||+++++.||+|.+++ +++....           ... +.+|+.+.++|.++|.+.     +++
T Consensus         1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~Gd~v~vkI~~vd~~~~~~~~~~i   79 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRV-LKVGDVVRARIVAVSLKERRPRESKI   79 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCE-ECCCCEEEEEEEEEeHHHCcCCCceE
Confidence            4789999999999999999889999999999 4433211           122 379999999999999764     478


Q ss_pred             eechhhH
Q 011538          361 ILSEREA  367 (483)
Q Consensus       361 iLS~K~~  367 (483)
                      .||.|..
T Consensus        80 ~ls~k~~   86 (99)
T cd04460          80 GLTMRQP   86 (99)
T ss_pred             EEEEecC
Confidence            9999864

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.

>TIGR01953 NusA transcription termination factor NusA

Probab=98.01  E-value=2.9e-05  Score=80.82  Aligned_cols=97  Identities=20%  Similarity=0.324  Sum_probs=73.3

Q ss_pred             hcCCEEEEEEEEEECCCCceeech-hhHh----h-------hcCC--CCCcEEEEEEEEEeCce-EEEEECCCceEEEEe
Q 011538          341 KVGRRMYVQITRINEDTNDLILSE-REAW----A-------TLNL--REGTLLEGTVKKIYPYG-AQIRIGDSNRSGLLH  405 (483)
Q Consensus       341 ~VGq~V~vkVl~ID~e~~rLiLS~-K~~~----e-------~~~l--~vG~iv~G~V~~I~~~G-aFV~I~~~gi~GLlh  405 (483)
                      .+|+.+++.|..-  +.+|+.++. |+.+    .       ...+  +.|+++.|+|.++.+.| ++|+++  +++|+||
T Consensus        85 ~vGD~I~~~I~~~--~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG--~~ea~LP  160 (341)
T TIGR01953        85 QIGDEVKKEIPPE--NFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG--KTEGILP  160 (341)
T ss_pred             ccCCEEEEEeccc--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC--CeEEEec
Confidence            6999999987543  234444443 3321    0       0234  69999999999999988 699996  6899999


Q ss_pred             ccCcCcccccCcccccCCCCEEEEEEEEEeC---CCeEEEEEecC
Q 011538          406 ISNMSRTRVTSVSDLLNEGERVKVLVVKSMF---PDKISLSIADL  447 (483)
Q Consensus       406 iSels~~~i~~~~~~~kvGd~VkVkVi~vde---k~rI~LSLK~~  447 (483)
                      .+++.      +.+.|++||+++|.|++++.   ...|.||.+..
T Consensus       161 ~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~  199 (341)
T TIGR01953       161 KKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP  199 (341)
T ss_pred             HHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence            99987      45679999999999999972   24788888753

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=97.99  E-value=1.4e-05  Score=83.63  Aligned_cols=96  Identities=19%  Similarity=0.262  Sum_probs=70.9

Q ss_pred             hcCCEEEEEEEEEECCCCceeechhhHhh-----------hcCC--CCCcEEEEEEEEEeCceEEEEECCCceEEEEecc
Q 011538          341 KVGRRMYVQITRINEDTNDLILSEREAWA-----------TLNL--REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHIS  407 (483)
Q Consensus       341 ~VGq~V~vkVl~ID~e~~rLiLS~K~~~e-----------~~~l--~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiS  407 (483)
                      .+|+.+.+.+...+-.+. ...+.|+.+.           ...+  +.|+++.|+|.++.+.|+||+++  +++|+||.+
T Consensus        88 ~vGD~i~~~I~~~~fgR~-aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg--~vEa~LP~~  164 (362)
T PRK12327         88 ELGDVIEIEVTPKDFGRI-AAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG--KIEAVLPPA  164 (362)
T ss_pred             cCCCEEEEecCcCCCChH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC--CeEEEecHH
Confidence            589999998765443222 2222222210           1244  89999999999999999999997  589999998


Q ss_pred             CcCcccccCcccccCCCCEEEEEEEEEe-CCC--eEEEEEe
Q 011538          408 NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD--KISLSIA  445 (483)
Q Consensus       408 els~~~i~~~~~~~kvGd~VkVkVi~vd-ek~--rI~LSLK  445 (483)
                      ++.      +++.|++||+++|.|++++ +++  .|.||..
T Consensus       165 E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt  199 (362)
T PRK12327        165 EQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT  199 (362)
T ss_pred             HcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence            875      3688999999999999997 332  5776654

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.91  E-value=4.2e-05  Score=80.09  Aligned_cols=108  Identities=20%  Similarity=0.243  Sum_probs=74.8

Q ss_pred             CcccCCCEEEEEEEEEcCCCcE-EEEehHHH----HHhhhHHHHHH--hhCCCeEEEEEEEEEC-CeEEEEECCeEEEee
Q 011538          253 PVVETGTVLFAEVLGRTLSGRP-LLSTRRLF----RKMAWHRVRQI--KQLNEPIEVKFTEWNT-GGLLTRIEGLRAFLP  324 (483)
Q Consensus       253 ~~~kVGd~V~v~Vi~~d~~G~i-iLS~k~~~----~~~~w~~L~~~--~k~GeiV~GkV~~v~k-~G~fV~I~Gi~gFVP  324 (483)
                      +.+++||.+...+--.+ =||+ .-+.++..    .+...+.+.+.  -+.|+++.|+|.++.. ++++|++++..|+||
T Consensus        89 ~~~~vGd~i~~~i~~~~-fgRiaaq~akq~i~Qkir~~er~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdlg~~ea~LP  167 (374)
T PRK12328         89 PSVEIGDELTYELSLEN-MGRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEIDEIRAVLP  167 (374)
T ss_pred             CCCCCCCEEEEecChhh-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEcCCeEEEeC
Confidence            45789999987654322 2333 22333332    11222223332  2699999999999996 569999999999999


Q ss_pred             ccccccccCChhhhhhhcCCEEEEEEEEEECCCC---ceeechhhH
Q 011538          325 KAELLSRVNNFTELKEKVGRRMYVQITRINEDTN---DLILSEREA  367 (483)
Q Consensus       325 ~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~---rLiLS~K~~  367 (483)
                      .+++...    +.  +.+|+.++|.|.+|+...+   .++|||..+
T Consensus       168 ~~eqip~----E~--~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p  207 (374)
T PRK12328        168 MKNRIKG----EK--FKVGDVVKAVLKRVKIDKNNGILIELSRTSP  207 (374)
T ss_pred             HHHcCCC----Cc--CCCCCEEEEEEEEEecCCCCCCEEEEEcCCH
Confidence            9998421    11  2699999999999987654   899999864

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=97.91  E-value=5.2e-05  Score=59.66  Aligned_cols=61  Identities=21%  Similarity=0.115  Sum_probs=37.8

Q ss_pred             CCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCCCCCC
Q 011538          172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPG  251 (483)
Q Consensus       172 ~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~~~~~  251 (483)
                      +|++...+|+++++.|+|++.|...+-+||.+|+.                                             
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~---------------------------------------------   35 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP---------------------------------------------   35 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG-----------------------------------------------
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC---------------------------------------------
Confidence            48999999999999999999988788888888863                                             


Q ss_pred             CCcccCCCEEEEEEEEEcCCCcEEEEeh
Q 011538          252 RPVVETGTVLFAEVLGRTLSGRPLLSTR  279 (483)
Q Consensus       252 ~~~~kVGd~V~v~Vi~~d~~G~iiLS~k  279 (483)
                       ..+++||.|.++|+ .|.++++++|++
T Consensus        36 -~~~~~Gd~v~VFvY-~D~~~rl~AT~k   61 (61)
T PF13509_consen   36 -EPLKVGDEVEVFVY-LDKEGRLVATTK   61 (61)
T ss_dssp             -----TTSEEEEEEE-E-TTS-EEEE--
T ss_pred             -CCCCCCCEEEEEEE-ECCCCCEEEecC
Confidence             12679999999999 578889999864

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

Probab=97.89  E-value=9.4e-06  Score=76.88  Aligned_cols=74  Identities=19%  Similarity=0.212  Sum_probs=58.7

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccC----------ChhhhhhhcCCEEEEEEEEEECCC-----
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVN----------NFTELKEKVGRRMYVQITRINEDT-----  357 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~----------~~~~l~~~VGq~V~vkVl~ID~e~-----  357 (483)
                      ...|++|.|.|+++.++|+||.++..+||+|.+++ ++++.          .-.+....+|+.|++||+.+....     
T Consensus        79 P~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~  158 (183)
T COG1095          79 PFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRE  158 (183)
T ss_pred             eccccEEEEEEEEEeecceEEEeccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcccc
Confidence            45899999999999999999999999999999999 43221          011222368999999999997554     


Q ss_pred             CceeechhhH
Q 011538          358 NDLILSEREA  367 (483)
Q Consensus       358 ~rLiLS~K~~  367 (483)
                      .++.+++|++
T Consensus       159 ~~I~lTmrq~  168 (183)
T COG1095         159 SKIGLTMRQP  168 (183)
T ss_pred             ceEEEEeccc
Confidence            4788888876

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

Probab=97.86  E-value=8.6e-05  Score=63.16  Aligned_cols=78  Identities=21%  Similarity=0.241  Sum_probs=59.6

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEe--------CCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecc
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNV--------GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD  239 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~Vdi--------G~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~  239 (483)
                      +-+++||+|.|+|+++....+.|+|        .....|++|.+++.+.+-.+                           
T Consensus         2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~---------------------------   54 (92)
T cd05791           2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDK---------------------------   54 (92)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccch---------------------------
Confidence            4568999999999999999999999        67778999998886431000                           


Q ss_pred             ccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538          240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (483)
Q Consensus       240 d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~  281 (483)
                        ..+       ...|++||.|.|+|++.+....+.||++..
T Consensus        55 --~~~-------~~~f~~GDiV~AkVis~~~~~~~~Lst~~~   87 (92)
T cd05791          55 --VEM-------YKCFRPGDIVRAKVISLGDASSYYLSTAEN   87 (92)
T ss_pred             --HHH-------HhhcCCCCEEEEEEEEcCCCCCcEEEecCC
Confidence              001       234899999999999866556788998653

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".

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

Probab=97.82  E-value=4.5e-05  Score=72.34  Aligned_cols=73  Identities=14%  Similarity=0.183  Sum_probs=59.0

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccc-cccC-Ch---------hhhhhhcCCEEEEEEEEEE-----CCCC
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL-SRVN-NF---------TELKEKVGRRMYVQITRIN-----EDTN  358 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~-~rv~-~~---------~~l~~~VGq~V~vkVl~ID-----~e~~  358 (483)
                      ..|++++|+|++++++|+||+++.++|++|.+++. +... +.         ......+|+.|+++|.++|     ++..
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            47999999999999999999998899999999983 3221 11         1123479999999999998     5567


Q ss_pred             ceeechhhH
Q 011538          359 DLILSEREA  367 (483)
Q Consensus       359 rLiLS~K~~  367 (483)
                      ++.+|+|++
T Consensus       160 ~I~lt~k~~  168 (179)
T TIGR00448       160 KIGLTMRQP  168 (179)
T ss_pred             eEEEEeccC
Confidence            899999976

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

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

Probab=97.82  E-value=5.8e-06  Score=81.83  Aligned_cols=88  Identities=22%  Similarity=0.283  Sum_probs=78.6

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~  449 (483)
                      -.+++++|-+.|.+|.+.|+||.+..+ +++|++-.||||..|+.++....++|..=.|.|+.+| +++.|.||.+...+
T Consensus        13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~   92 (304)
T KOG2916|consen   13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP   92 (304)
T ss_pred             CCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCCH
Confidence            457899999999999999999999543 7999999999999999999999999999999999998 89999999999988


Q ss_pred             CcCccccccc
Q 011538          450 EPGLFVSDKE  459 (483)
Q Consensus       450 dPw~~l~~k~  459 (483)
                      +--...++++
T Consensus        93 ed~~kC~Er~  102 (304)
T KOG2916|consen   93 EDKEKCEERF  102 (304)
T ss_pred             HHHHHHHHHH
Confidence            7665555443

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

Probab=97.64  E-value=0.00037  Score=58.77  Aligned_cols=74  Identities=26%  Similarity=0.409  Sum_probs=59.1

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      |.+++||+|-|+|+.+..+...|||+....|+||..++...                                       
T Consensus         2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga---------------------------------------   42 (86)
T cd05790           2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA---------------------------------------   42 (86)
T ss_pred             CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc---------------------------------------
Confidence            56789999999999999999999999888999887654211                                       


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 011538          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~  280 (483)
                      ..+.++.+++||.|.|+|...+.+..+.||...
T Consensus        43 tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~   75 (86)
T cd05790          43 TKRNRPNLNVGDLVYARVVKANRDMEPELSCVD   75 (86)
T ss_pred             cccccccCCCCCEEEEEEEecCCCCCeEEEEeC
Confidence            011246789999999999987777778888754

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".

>PRK05054 exoribonuclease II; Provisional

Probab=97.60  E-value=0.00024  Score=79.88  Aligned_cols=71  Identities=14%  Similarity=0.202  Sum_probs=58.3

Q ss_pred             CCC--cEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccc--c--c--------CcccccCCCCEEEEEEEEEe-CCC
Q 011538          374 REG--TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR--V--T--------SVSDLLNEGERVKVLVVKSM-FPD  438 (483)
Q Consensus       374 ~vG--~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~--i--~--------~~~~~~kvGd~VkVkVi~vd-ek~  438 (483)
                      ++|  +.+.|.|++|+++|+||+|.+.+++||||.+.+..++  +  .        .-...|+.||+|+|+|.++| +++
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  5999999999999999999877899999999996531  1  0        11247999999999999998 788


Q ss_pred             eEEEEE
Q 011538          439 KISLSI  444 (483)
Q Consensus       439 rI~LSL  444 (483)
                      +|.+++
T Consensus       638 ~i~~~~  643 (644)
T PRK05054        638 SIIARP  643 (644)
T ss_pred             eEEEEE
Confidence            888764

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

Probab=97.57  E-value=0.00042  Score=65.95  Aligned_cols=73  Identities=25%  Similarity=0.331  Sum_probs=62.0

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCC---------ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDS---------NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL  442 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~---------gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~L  442 (483)
                      -++.|++|-|+|+++....+.|++.+.         -..|-+|+|+.+..++.++++.|++||.|+|+|++.-  ..+.|
T Consensus        61 ~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~~~L  138 (188)
T COG1096          61 LPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DPIQL  138 (188)
T ss_pred             CCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--CCeEE
Confidence            578899999999999999999998431         1467899999999999999999999999999999853  45667


Q ss_pred             EEec
Q 011538          443 SIAD  446 (483)
Q Consensus       443 SLK~  446 (483)
                      |++.
T Consensus       139 st~~  142 (188)
T COG1096         139 STKG  142 (188)
T ss_pred             EecC
Confidence            7653

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.55  E-value=0.00022  Score=76.16  Aligned_cols=62  Identities=35%  Similarity=0.568  Sum_probs=53.3

Q ss_pred             CCCCCcEEEEEEEEEeCc--eEEEEECCCceEEEEeccCcCcc------------cccCcccccCCCCEEEEEEEEE
Q 011538          372 NLREGTLLEGTVKKIYPY--GAQIRIGDSNRSGLLHISNMSRT------------RVTSVSDLLNEGERVKVLVVKS  434 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~--GaFV~I~~~gi~GLlhiSels~~------------~i~~~~~~~kvGd~VkVkVi~v  434 (483)
                      ...+|++|.|+|.+|.+.  ||||+|+. +..||||.+++.+.            +..++.+.+++||.|.|.|++-
T Consensus        22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~-~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke   97 (414)
T TIGR00757        22 RQLKGNIYKGRVTRILPSLQAAFVDIGL-EKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKE   97 (414)
T ss_pred             cCCCCCEEEEEEeeecCCCceEEEEcCC-CceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeC
Confidence            356899999999999998  99999998 79999999998753            2345567899999999999974

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.

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

Probab=97.53  E-value=0.00059  Score=57.63  Aligned_cols=59  Identities=10%  Similarity=0.182  Sum_probs=48.0

Q ss_pred             CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc-----------CcccccCCCCEEEEEEEEEe
Q 011538          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM  435 (483)
Q Consensus       375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~-----------~~~~~~kvGd~VkVkVi~vd  435 (483)
                      +|++++|+|++++++|+||.+++  +++|+|.+.+..+..-           +-...+..|+.|++||+.+.
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gp--l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~   70 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGP--LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTR   70 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcC--ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEE
Confidence            58999999999999999999986  7899988877544221           22455899999999999885

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.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=97.52  E-value=0.00046  Score=54.26  Aligned_cols=61  Identities=20%  Similarity=0.235  Sum_probs=37.6

Q ss_pred             CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 011538          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA  445 (483)
Q Consensus       375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK  445 (483)
                      +|++...+|.+++++|+|++.+. +-+-+||.+++.        ..+++||.|.|-|- .|.++|+..++|
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~-~~~vlLp~~e~~--------~~~~~Gd~v~VFvY-~D~~~rl~AT~k   61 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGE-GKEVLLPKSEVP--------EPLKVGDEVEVFVY-LDKEGRLVATTK   61 (61)
T ss_dssp             --------EEEE-SSEEEEEETT--EEEEEEGGG--------------TTSEEEEEEE-E-TTS-EEEE--
T ss_pred             CCCCcceEEEEEeCCEEEEECCC-CCEEEechHHcC--------CCCCCCCEEEEEEE-ECCCCCEEEecC
Confidence            48899999999999999999887 689999999985        45999999999886 577789988876

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

Probab=97.49  E-value=0.0004  Score=68.53  Aligned_cols=76  Identities=24%  Similarity=0.360  Sum_probs=67.4

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc----cCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----TSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i----~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~  447 (483)
                      ..++||+|-|+|..+...+..|+|+. -+.+++|.|++.+..+    .+++..|++||.|.|+|.+++......|++|+.
T Consensus        61 iP~~gD~VIG~I~~v~~~~W~VDI~s-p~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~  139 (239)
T COG1097          61 IPEVGDVVIGKIIEVGPSGWKVDIGS-PYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDE  139 (239)
T ss_pred             cCCCCCEEEEEEEEEcccceEEEcCC-ccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeecC
Confidence            35789999999999999999999997 4899999999966653    577889999999999999999999999999764


Q ss_pred             C
Q 011538          448 E  448 (483)
Q Consensus       448 ~  448 (483)
                      .
T Consensus       140 ~  140 (239)
T COG1097         140 G  140 (239)
T ss_pred             C
Confidence            3

>TIGR02063 RNase_R ribonuclease R

Probab=97.48  E-value=0.00038  Score=79.07  Aligned_cols=70  Identities=16%  Similarity=0.265  Sum_probs=56.8

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC--CeEEEeeccccc-ccc-----------CChhhhhhhcCCEEEEEEEEEECCCCc
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL-SRV-----------NNFTELKEKVGRRMYVQITRINEDTND  359 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel~-~rv-----------~~~~~l~~~VGq~V~vkVl~ID~e~~r  359 (483)
                      .+.|++++|+|+++.++|+||++.  |+.|++|.+++. +++           ++.... +.+||+|+|+|.++|..+++
T Consensus       625 ~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~-~~lGd~V~Vkv~~vd~~~~~  703 (709)
T TIGR02063       625 EKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKV-FRLGDRVKVRVVKADLDTGK  703 (709)
T ss_pred             ccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcE-ECCCCEEEEEEEEEecccCe
Confidence            368999999999999999999996  699999999993 322           111122 37999999999999998899


Q ss_pred             eeech
Q 011538          360 LILSE  364 (483)
Q Consensus       360 LiLS~  364 (483)
                      +.++.
T Consensus       704 I~~~l  708 (709)
T TIGR02063       704 IDFEL  708 (709)
T ss_pred             EEEEE
Confidence            88763

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.

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

Probab=97.45  E-value=0.0008  Score=56.79  Aligned_cols=73  Identities=22%  Similarity=0.116  Sum_probs=62.3

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~  447 (483)
                      .++||.|-|+|+.+...+.+|+|+. -..|+||..++... .++.+..+++||-|-|||.+++......||+.+.
T Consensus         4 P~~gD~VIG~V~~~~~~~~~VdI~s-~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~   76 (86)
T cd05790           4 PAKGDHVIGIVVAKAGDFFKVDIGG-SEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRDMEPELSCVDS   76 (86)
T ss_pred             CCCCCEEEEEEEEEcCCeEEEEcCC-CcceEechHHcccc-cccccccCCCCCEEEEEEEecCCCCCeEEEEeCC
Confidence            4689999999999999999999988 48999999886432 4455678999999999999988767889999873

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".

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

Probab=97.44  E-value=0.00049  Score=56.09  Aligned_cols=67  Identities=21%  Similarity=0.341  Sum_probs=56.5

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc---CcccccCCCCEE-EEEEEEEe-CCCeEEEEEe
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT---SVSDLLNEGERV-KVLVVKSM-FPDKISLSIA  445 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~---~~~~~~kvGd~V-kVkVi~vd-ek~rI~LSLK  445 (483)
                      |++|+|+|..-++.+++|++.+.|+.|++|..++|+ +..   ..-..+++||++ .+.|+  + ..+.|.||.|
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-HVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence            789999999999999999999889999999999998 443   234559999999 89998  4 5567778765

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.

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

Probab=97.44  E-value=0.00048  Score=56.16  Aligned_cols=65  Identities=23%  Similarity=0.390  Sum_probs=53.4

Q ss_pred             CCeEEEEEEEEECCeEEEEEC--CeEEEeeccccccccCC----hhhhhhhcCCEE-EEEEEEEECCCCceeechh
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLSRVNN----FTELKEKVGRRM-YVQITRINEDTNDLILSER  365 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel~~rv~~----~~~l~~~VGq~V-~vkVl~ID~e~~rLiLS~K  365 (483)
                      |++|+|+|....+.+++|+++  |++|++|..|+.+++.+    ++.+  .+|+++ .+-|+  +...+.+.+|.|
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~~~k~~~~~~kl--rvG~~L~~~lvL--~~~~r~i~lt~K   72 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCL--QEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhh--hcCCCccceEEE--eccccEEEEecC
Confidence            689999999999999999994  69999999999544432    2334  599999 88888  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.

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

Probab=97.43  E-value=0.00072  Score=66.73  Aligned_cols=80  Identities=21%  Similarity=0.383  Sum_probs=64.8

Q ss_pred             ccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccC
Q 011538          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (483)
Q Consensus       167 ~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~  246 (483)
                      -|.++.||+|-|+|+.+...+..||||+...+++|++++..+.   +                               ..
T Consensus        59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~---~-------------------------------~~  104 (239)
T COG1097          59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRK---F-------------------------------EN  104 (239)
T ss_pred             cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhccc---c-------------------------------cc
Confidence            4788999999999999999999999999999999999984321   0                               00


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 011538          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (483)
Q Consensus       247 ~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~  280 (483)
                      ...+.++.+.+||.|.|+|...+.++.+.|++|.
T Consensus       105 ~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~  138 (239)
T COG1097         105 AEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD  138 (239)
T ss_pred             cccccccccccCCEEEEEEEEccCCCceEEEeec
Confidence            0112356799999999999999999999998844

>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=97.40  E-value=0.00035  Score=58.41  Aligned_cols=61  Identities=18%  Similarity=0.310  Sum_probs=42.2

Q ss_pred             CCCcEEEEEEEEEeCceEEEEECCC-----------------ceEEEEeccCcCccccc--CcccccCCCCEEEEEEEEE
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIGDS-----------------NRSGLLHISNMSRTRVT--SVSDLLNEGERVKVLVVKS  434 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~~~-----------------gi~GLlhiSels~~~i~--~~~~~~kvGd~VkVkVi~v  434 (483)
                      ++|++|.|+|++|++.-|+++|-..                 ...|++|.+++......  ++.+.|++||.|+|+|+++
T Consensus         3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViSl   82 (82)
T PF10447_consen    3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVISL   82 (82)
T ss_dssp             -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEEE
T ss_pred             CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEeeC
Confidence            5899999999999998888887422                 46899999998766544  4588899999999999974

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

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

Probab=97.40  E-value=0.00024  Score=67.61  Aligned_cols=72  Identities=19%  Similarity=0.252  Sum_probs=57.1

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccc-cccC-----------ChhhhhhhcCCEEEEEEEEEECCCC----
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL-SRVN-----------NFTELKEKVGRRMYVQITRINEDTN----  358 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~-~rv~-----------~~~~l~~~VGq~V~vkVl~ID~e~~----  358 (483)
                      ..|+++.|+|+++++.|++|+++.+.||++.+++. ++..           +.. ....+|+.|+++|.+++...+    
T Consensus        80 ~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~-~~i~~Gd~VrvrV~~v~~~~~~~~~  158 (187)
T PRK08563         80 ELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESK-RVLKVGDVVRARIVAVSLKERRPRG  158 (187)
T ss_pred             cCCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCC-eEEcCCCEEEEEEEEEEcccCCCCC
Confidence            58999999999999999999998899999999983 3221           111 123789999999999986543    


Q ss_pred             -ceeechhhH
Q 011538          359 -DLILSEREA  367 (483)
Q Consensus       359 -rLiLS~K~~  367 (483)
                       ++.+|++.+
T Consensus       159 ~~I~ls~~~~  168 (187)
T PRK08563        159 SKIGLTMRQP  168 (187)
T ss_pred             CEEEEEecCC
Confidence             678888863

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=97.37  E-value=0.00075  Score=72.02  Aligned_cols=109  Identities=16%  Similarity=0.241  Sum_probs=74.4

Q ss_pred             CcccCCCEEEEEEEEE-cCCCcEE-EEehHH----HHHhhhHHHHHHh--hCCCeEEEEEEEEECCeEEEEE----CC--
Q 011538          253 PVVETGTVLFAEVLGR-TLSGRPL-LSTRRL----FRKMAWHRVRQIK--QLNEPIEVKFTEWNTGGLLTRI----EG--  318 (483)
Q Consensus       253 ~~~kVGd~V~v~Vi~~-d~~G~ii-LS~k~~----~~~~~w~~L~~~~--k~GeiV~GkV~~v~k~G~fV~I----~G--  318 (483)
                      +.+++||.+...+.-. ..=||+. .+.|+.    ..+...+.+.+.+  +.|+++.|+|.++.+++++|++    |.  
T Consensus       101 ~~~~iGD~v~~~v~~~~~~fgRiAAq~aKQvi~Qkire~ER~~i~~ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~  180 (449)
T PRK12329        101 DEAQLGDTVVLDVTPEQEDFGRMAAIQTKQVLAQKLRDQQRKMIQEEFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPE  180 (449)
T ss_pred             CCCcCCCEEEEecCccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcc
Confidence            4478999998766421 1235553 223332    1222233333333  6999999999999999999998    42  


Q ss_pred             eEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCC---CceeechhhH
Q 011538          319 LRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDT---NDLILSEREA  367 (483)
Q Consensus       319 i~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~---~rLiLS~K~~  367 (483)
                      +.|+||.+++...     +. +.+|+.++|.|.+|....   -+|+|||..+
T Consensus       181 ~EaiLP~~Eqip~-----E~-y~~Gdrika~i~~V~~~~~kGpqIilSRt~p  226 (449)
T PRK12329        181 VEAELPKREQLPN-----DN-YRANATFKVFLKEVSEGPRRGPQLFVSRANA  226 (449)
T ss_pred             eEEEecHHHcCCC-----Cc-CCCCCEEEEEEEEeecCCCCCCEEEEEcCCH
Confidence            8999999998321     11 269999999999997652   3799999864

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

Probab=97.34  E-value=0.0011  Score=63.12  Aligned_cols=73  Identities=10%  Similarity=0.041  Sum_probs=56.3

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc-----------cc-cCcccccCCCCEEEEEEEEEe--C-C
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-----------RV-TSVSDLLNEGERVKVLVVKSM--F-P  437 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~-----------~i-~~~~~~~kvGd~VkVkVi~vd--e-k  437 (483)
                      .-.|++++|+|++++++|+||.++.  .++|+|.+.|...           +. .+-...+..|+.|++||+.+.  + +
T Consensus        79 Pf~gEVv~g~V~~v~~~G~~v~~Gp--~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~  156 (176)
T PTZ00162         79 PFKDEVLDAIVTDVNKLGFFAQAGP--LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASN  156 (176)
T ss_pred             cCCCCEEEEEEEEEecceEEEEeeC--eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCC
Confidence            4579999999999999999999986  6799999998733           11 122456999999999999885  2 2


Q ss_pred             CeEEEEEecC
Q 011538          438 DKISLSIADL  447 (483)
Q Consensus       438 ~rI~LSLK~~  447 (483)
                      .+...|||+-
T Consensus       157 ~~~i~T~~~~  166 (176)
T PTZ00162        157 LFAIATINSD  166 (176)
T ss_pred             cEEEEEecCC
Confidence            3455677753

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

Probab=97.23  E-value=0.0014  Score=55.39  Aligned_cols=34  Identities=18%  Similarity=0.315  Sum_probs=31.7

Q ss_pred             CCCeEEEEEEEEECCeEEEEECCeEEEeeccccc
Q 011538          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL  329 (483)
Q Consensus       296 ~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~  329 (483)
                      .|++++|+|+++++.|++|.+|.+++|++.+++.
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip   34 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIP   34 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecC
Confidence            4899999999999999999999999999998883

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.

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

Probab=97.14  E-value=0.0019  Score=72.82  Aligned_cols=68  Identities=16%  Similarity=0.352  Sum_probs=55.7

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC--CeEEEeecccc-cccc-----------CChhhhhhhcCCEEEEEEEEEECCCCce
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRV-----------NNFTELKEKVGRRMYVQITRINEDTNDL  360 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel-~~rv-----------~~~~~l~~~VGq~V~vkVl~ID~e~~rL  360 (483)
                      +.|+.++|+|+++.++|+||++.  |++|++|.+++ ++++           ++... .+.+|++|+|+|.++|..+++|
T Consensus       571 ~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~-~~~lGD~V~Vki~~vd~~~~~I  649 (654)
T TIGR00358       571 KVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGK-VYRIGDRVTVKLTEVNMETRSI  649 (654)
T ss_pred             CCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCc-EECCCCEEEEEEEEEecccCeE
Confidence            57999999999999999999995  69999999999 4321           11111 2379999999999999999988


Q ss_pred             eec
Q 011538          361 ILS  363 (483)
Q Consensus       361 iLS  363 (483)
                      .++
T Consensus       650 ~f~  652 (654)
T TIGR00358       650 IFE  652 (654)
T ss_pred             EEE
Confidence            776

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

>PRK11642 exoribonuclease R; Provisional

Probab=97.13  E-value=0.0014  Score=75.45  Aligned_cols=70  Identities=14%  Similarity=0.205  Sum_probs=57.4

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC--CeEEEeecccc-ccccC-C----------hhhhhhhcCCEEEEEEEEEECCCCce
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRVN-N----------FTELKEKVGRRMYVQITRINEDTNDL  360 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel-~~rv~-~----------~~~l~~~VGq~V~vkVl~ID~e~~rL  360 (483)
                      +.|++++|+|+++.++|+||++.  +++|+||.+++ ++++. +          ... .+.+||.|+|+|.++|..+++|
T Consensus       642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~-~~~lGD~V~VkV~~vD~~~rkI  720 (813)
T PRK11642        642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQ-TYRLGDRVEVRVEAVNMDERKI  720 (813)
T ss_pred             cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCc-EECCCCEEEEEEEEeecCCCeE
Confidence            58999999999999999999995  49999999999 33211 1          011 2379999999999999999999


Q ss_pred             eechh
Q 011538          361 ILSER  365 (483)
Q Consensus       361 iLS~K  365 (483)
                      .++.-
T Consensus       721 ~f~l~  725 (813)
T PRK11642        721 DFSLI  725 (813)
T ss_pred             EEEEe
Confidence            98874

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

Probab=97.09  E-value=0.0022  Score=69.67  Aligned_cols=73  Identities=16%  Similarity=0.306  Sum_probs=61.7

Q ss_pred             hCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA  369 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e  369 (483)
                      ..|-+.+++|+++.+.|+||.+ .+..|++|.+|+ .+++.++.++. .+||+|.++.++.|+.. .+.+|.|+.+.
T Consensus       667 ~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~l-evGq~I~vk~ie~d~~g-~~~ls~ralLp  741 (760)
T KOG1067|consen  667 EFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLL-EVGQEIQVKYIERDPRG-GIMLSSRALLP  741 (760)
T ss_pred             EeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHH-hhcceeEEEEEeecCcc-ceeehhhhhcC
Confidence            4677889999999999999999 468899999999 57788999885 89999999999999765 46666666543

>TIGR02062 RNase_B exoribonuclease II

Probab=97.07  E-value=0.0016  Score=73.25  Aligned_cols=68  Identities=10%  Similarity=0.198  Sum_probs=55.0

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCc--ccc-----c---Cc--ccccCCCCEEEEEEEEEe-CCCeEEE
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR--TRV-----T---SV--SDLLNEGERVKVLVVKSM-FPDKISL  442 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~--~~i-----~---~~--~~~~kvGd~VkVkVi~vd-ek~rI~L  442 (483)
                      |+.+.|+|+.++++|+||++...+++||+|.+.+..  +++     .   .+  ...|+.||+|+|+|.++| ++++|.+
T Consensus       558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~  637 (639)
T TIGR02062       558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIA  637 (639)
T ss_pred             CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEee
Confidence            459999999999999999997668999999999965  221     1   11  126999999999999998 7778765


Q ss_pred             E
Q 011538          443 S  443 (483)
Q Consensus       443 S  443 (483)
                      .
T Consensus       638 ~  638 (639)
T TIGR02062       638 R  638 (639)
T ss_pred             e
Confidence            3

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.

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=97.06  E-value=0.0018  Score=54.09  Aligned_cols=67  Identities=16%  Similarity=0.255  Sum_probs=58.1

Q ss_pred             hCCCeEEEEEEEEECCeEEEEE--CCeEEEee-cccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeech
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRI--EGLRAFLP-KAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I--~Gi~gFVP-~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~  364 (483)
                      +.|+.+. .|+.+.+.|++|.+  -|++|+|+ .+++ .++++...++.  +|....++|+++|+.+|-|-||.
T Consensus        15 ~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll--VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         15 NINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL--VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             CCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh--cCCeeEEEEEEECCCCCEEEeEc
Confidence            6889998 89999999999998  25999988 9999 56777777764  99999999999999999887763

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=97.03  E-value=0.0019  Score=73.54  Aligned_cols=74  Identities=23%  Similarity=0.363  Sum_probs=63.1

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc-----------cCcccccCCCCEEEEEEEEEe-CCCe
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDK  439 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i-----------~~~~~~~kvGd~VkVkVi~vd-ek~r  439 (483)
                      .-++|+...|+|++++.+|+||.+.+.+++|++|.+.+..+++           .+....++.||.|+|++++++ ..++
T Consensus       619 ~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~  698 (706)
T COG0557         619 KKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERK  698 (706)
T ss_pred             HHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccc
Confidence            5578999999999999999999998877999999999986432           234557999999999999997 7788


Q ss_pred             EEEEEe
Q 011538          440 ISLSIA  445 (483)
Q Consensus       440 I~LSLK  445 (483)
                      |.+++-
T Consensus       699 i~~~~v  704 (706)
T COG0557         699 IDFELV  704 (706)
T ss_pred             eEEEec
Confidence            887764

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.01  E-value=0.0038  Score=65.60  Aligned_cols=88  Identities=16%  Similarity=0.114  Sum_probs=64.1

Q ss_pred             cCCCCCcEEEEEEEEEeC-CeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccC
Q 011538          168 YEPKPGDFVIGVVVSGNE-NKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~-~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~  246 (483)
                      +.-+.|++|.|+|.+++. +.++|++| +.+|+||.+|..|.                                      
T Consensus       134 y~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eqip~--------------------------------------  174 (374)
T PRK12328        134 YKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNRIKG--------------------------------------  174 (374)
T ss_pred             HHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHcCCC--------------------------------------
Confidence            455689999999999996 46999998 69999999887653                                      


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEc--CC--CcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEE
Q 011538          247 GSGPGRPVVETGTVLFAEVLGRT--LS--GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKF  304 (483)
Q Consensus       247 ~~~~~~~~~kVGd~V~v~Vi~~d--~~--G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV  304 (483)
                            ..|++||.+.|.|....  ..  -.++||+..+..-   .+|.+ .+.=++.+|.|
T Consensus       175 ------E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p~~v---~~Lfe-~EVPEI~dG~V  226 (374)
T PRK12328        175 ------EKFKVGDVVKAVLKRVKIDKNNGILIELSRTSPKFL---EALLE-LEVPEIKDGEV  226 (374)
T ss_pred             ------CcCCCCCEEEEEEEEEecCCCCCCEEEEEcCCHHHH---HHHHH-HhCccccCCeE
Confidence                  24789999999999843  22  3678998877532   22222 24556666654

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

Probab=96.84  E-value=0.0037  Score=59.38  Aligned_cols=73  Identities=14%  Similarity=0.233  Sum_probs=50.2

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccccccC-C-------h----hhhhhhcCCEEEEEEEEEECCC--Cce
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVN-N-------F----TELKEKVGRRMYVQITRINEDT--NDL  360 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~~rv~-~-------~----~~l~~~VGq~V~vkVl~ID~e~--~rL  360 (483)
                      -.|++++|+|+++++.|++|.+|-+++|+|.++|.+... +       +    .+.....|+.|++||..+..+.  ...
T Consensus        80 f~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~  159 (176)
T PTZ00162         80 FKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFA  159 (176)
T ss_pred             CCCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEE
Confidence            489999999999999999999988999999999942210 0       0    1122256777777776664332  234


Q ss_pred             eechhhH
Q 011538          361 ILSEREA  367 (483)
Q Consensus       361 iLS~K~~  367 (483)
                      +.|+|++
T Consensus       160 i~T~~~~  166 (176)
T PTZ00162        160 IATINSD  166 (176)
T ss_pred             EEEecCC
Confidence            5555543

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

Probab=96.68  E-value=0.0022  Score=74.39  Aligned_cols=76  Identities=21%  Similarity=0.256  Sum_probs=66.6

Q ss_pred             CCCCCcEEEEEEEEEeCce---EEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecC
Q 011538          372 NLREGTLLEGTVKKIYPYG---AQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADL  447 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~G---aFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~  447 (483)
                      .+.+|.+|.++|++|+..-   +-|.+.+ |+.|+|+.+++|...+.+|...+++||+|.+||++++ ++=.+.||+|..
T Consensus       982 t~~~g~iV~~~V~~vt~rr~~Cv~v~ld~-G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~s 1060 (1299)
T KOG1856|consen  982 TFYEGAIVPVTVTKVTHRRGICVRVRLDC-GVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred             HhccCceEEEeeeEEEecccceeEEEecC-CCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence            5889999999999998754   4567777 8999999999999999999999999999999999998 666777888765


Q ss_pred             C
Q 011538          448 E  448 (483)
Q Consensus       448 ~  448 (483)
                      .
T Consensus      1061 d 1061 (1299)
T KOG1856|consen 1061 D 1061 (1299)
T ss_pred             H
Confidence            3

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.65  E-value=0.0082  Score=64.29  Aligned_cols=89  Identities=10%  Similarity=0.034  Sum_probs=64.0

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEe----CC-ceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccc
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNV----GA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAI  242 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~Vdi----G~-k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~  242 (483)
                      +.-+.|++|.|+|.+++.++++|++    |. +.+|+||.+|..|.                                  
T Consensus       148 f~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~----------------------------------  193 (449)
T PRK12329        148 FQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPN----------------------------------  193 (449)
T ss_pred             HHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCC----------------------------------
Confidence            4556899999999999999999998    33 48999998887653                                  


Q ss_pred             cccCCCCCCCCcccCCCEEEEEEEEEcC---C-CcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEE
Q 011538          243 AMSGGSGPGRPVVETGTVLFAEVLGRTL---S-GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKF  304 (483)
Q Consensus       243 ~~~~~~~~~~~~~kVGd~V~v~Vi~~d~---~-G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV  304 (483)
                                ..|++|+.+.|.|.....   . -.++||+..+..-   .+|.+ .+.=++..|.|
T Consensus       194 ----------E~y~~Gdrika~i~~V~~~~~kGpqIilSRt~p~lv---~~Lfe-~EVPEI~dG~V  245 (449)
T PRK12329        194 ----------DNYRANATFKVFLKEVSEGPRRGPQLFVSRANAGLV---VYLFE-NEVPEIEEGVV  245 (449)
T ss_pred             ----------CcCCCCCEEEEEEEEeecCCCCCCEEEEEcCCHHHH---HHHHH-hhCcccccCeE
Confidence                      248899999999998532   2 3678998776532   22222 24555555543

>PRK10811 rne ribonuclease E; Reviewed

Probab=96.63  E-value=0.0045  Score=71.31  Aligned_cols=92  Identities=18%  Similarity=0.281  Sum_probs=64.4

Q ss_pred             CCCcEEEEEEEEEeC--ceEEEEECCCceEEEEeccCcCccccc---------CcccccCCCCEEEEEEEEEe-CCCeEE
Q 011538          374 REGTLLEGTVKKIYP--YGAQIRIGDSNRSGLLHISNMSRTRVT---------SVSDLLNEGERVKVLVVKSM-FPDKIS  441 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~--~GaFV~I~~~gi~GLlhiSels~~~i~---------~~~~~~kvGd~VkVkVi~vd-ek~rI~  441 (483)
                      .+|.||.|+|.+|.+  .++||+|+. +..||||.+++....+.         +..+.++.||.|-|.|.+-. ..+-..
T Consensus        37 ~vGnIYkGkVenIvPGInAAFVDIG~-gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~  115 (1068)
T PRK10811         37 KKANIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAA  115 (1068)
T ss_pred             CccceEEEEEecccCCcceeEEEecC-CcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCCCCCc
Confidence            489999999999987  589999998 89999999998643322         23456999999999999743 333333


Q ss_pred             EEEecCCCCcCcccccccccceee--EEEEeecc
Q 011538          442 LSIADLESEPGLFVSDKEVHIIFL--FILLFNKQ  473 (483)
Q Consensus       442 LSLK~~~~dPw~~l~~k~~V~~~~--~~~~~~~~  473 (483)
                      ||.+-       .|..+|-||+--  .++.||++
T Consensus       116 LTt~I-------SLpGRYLVLtP~~~~~IgISRK  142 (1068)
T PRK10811        116 LTTFI-------SLAGSYLVLMPNNPRAGGISRR  142 (1068)
T ss_pred             eeeeE-------EecceeEEEeCCCCCcceecCC
Confidence            33332       244566666555  25566654

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

Probab=96.61  E-value=0.0018  Score=70.69  Aligned_cols=71  Identities=18%  Similarity=0.351  Sum_probs=61.4

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      .+++.|.+++|+|.++..||+||++.. .+.||+|.++++..      ..+.+|+.+-|.+..+. +++.|.+....+.
T Consensus       118 ~Dve~g~~Y~g~v~~v~~~GvFv~Ln~-~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~  189 (715)
T COG1107         118 EDVEAGKYYKGIVSRVEKYGVFVELNS-HVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD  189 (715)
T ss_pred             hhcccceeeeccccchhhhcceeecCh-hhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence            479999999999999999999999998 69999999999852      34899999999999986 5578777666555

>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=96.04  E-value=0.023  Score=47.53  Aligned_cols=23  Identities=39%  Similarity=0.564  Sum_probs=17.9

Q ss_pred             CCCCcEEEEEEEEEeCCeEEEEe
Q 011538          170 PKPGDFVIGVVVSGNENKLDVNV  192 (483)
Q Consensus       170 ik~GdiV~G~Vv~V~~~gv~Vdi  192 (483)
                      +++|++|.|+|+++++..++++|
T Consensus         2 P~vGdiV~~rVtrv~~~~a~v~I   24 (82)
T PF10447_consen    2 PKVGDIVIARVTRVNPRQAKVEI   24 (82)
T ss_dssp             --TT-EEEEEEEEE-SSEEEEEE
T ss_pred             CCCCCEEEEEEEEEeccEEEEEE
Confidence            57899999999999999998877

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.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=95.82  E-value=0.025  Score=60.58  Aligned_cols=57  Identities=16%  Similarity=0.202  Sum_probs=46.2

Q ss_pred             hCCCeEEEEEEEEECC--eEEEEEC-CeEEEeecccccc-------------ccCChhhhhhhcCCEEEEEEEE
Q 011538          295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLS-------------RVNNFTELKEKVGRRMYVQITR  352 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~--G~fV~I~-Gi~gFVP~Sel~~-------------rv~~~~~l~~~VGq~V~vkVl~  352 (483)
                      ..|.++.|+|.++.++  |+||+|+ |-.||+|.+++..             +..++.+.. .+||.|.|.|++
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  9999996 5899999999831             122333433 689999999988

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.

>PRK11712 ribonuclease G; Provisional

Probab=95.67  E-value=0.027  Score=61.48  Aligned_cols=61  Identities=30%  Similarity=0.523  Sum_probs=49.5

Q ss_pred             CCCCcEEEEEEEEEeC--ceEEEEECCCceEEEEeccCcCcc------------cccCcccccCCCCEEEEEEEEE
Q 011538          373 LREGTLLEGTVKKIYP--YGAQIRIGDSNRSGLLHISNMSRT------------RVTSVSDLLNEGERVKVLVVKS  434 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~--~GaFV~I~~~gi~GLlhiSels~~------------~i~~~~~~~kvGd~VkVkVi~v  434 (483)
                      ..+|.++.|+|.+|.|  .+|||+|+. +..||+|.+++...            ....+.+.++.||.|-|.|++-
T Consensus        36 ~~vGnIY~G~V~~v~pg~~AAFVdIG~-~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke  110 (489)
T PRK11712         36 GIVGNIYKGRVSRVLPGMQAAFVDIGL-DKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD  110 (489)
T ss_pred             cccccEEEEEEeecCCCCceeEEeeCC-CccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence            4589999999999988  579999998 89999999997321            1123456699999999999874

>PRK05054 exoribonuclease II; Provisional

Probab=95.56  E-value=0.052  Score=61.30  Aligned_cols=67  Identities=21%  Similarity=0.346  Sum_probs=51.5

Q ss_pred             CCeEEEEEEEEECCeEEEEEC--CeEEEeecccc-cc--ccC---C------hhhhhhhcCCEEEEEEEEEECCCCceee
Q 011538          297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LS--RVN---N------FTELKEKVGRRMYVQITRINEDTNDLIL  362 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel-~~--rv~---~------~~~l~~~VGq~V~vkVl~ID~e~~rLiL  362 (483)
                      |+.+.|.|+++.++|+||++.  |+.||||.+.+ ..  .+.   +      .....+.+||+|+|+|.++|..+++|.+
T Consensus       562 ~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~  641 (644)
T PRK05054        562 DTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIA  641 (644)
T ss_pred             CeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEE
Confidence            459999999999999999994  79999999988 21  110   0      0011247899999999999988888765


Q ss_pred             c
Q 011538          363 S  363 (483)
Q Consensus       363 S  363 (483)
                      +
T Consensus       642 ~  642 (644)
T PRK05054        642 R  642 (644)
T ss_pred             E
Confidence            4

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

Probab=95.54  E-value=0.016  Score=57.90  Aligned_cols=71  Identities=21%  Similarity=0.372  Sum_probs=64.3

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEE---CCeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I---~Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      -+.+++|-+.|..+..-|++|.+   +.+.|+|-.|+|+ +|++++..+- +||..=.|.|+++|+++|-|-||.|
T Consensus        14 Pev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~kli-rVGr~E~vvVlrVDkekGYIDLSkr   88 (304)
T KOG2916|consen   14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLI-RVGRNEPVVVLRVDKEKGYIDLSKR   88 (304)
T ss_pred             CCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHH-hcCCcceEEEEEEcCCCCceechhc
Confidence            36899999999999999999988   7899999999994 6788887776 8999999999999999999999987

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

Probab=95.37  E-value=0.031  Score=65.28  Aligned_cols=72  Identities=21%  Similarity=0.236  Sum_probs=58.6

Q ss_pred             hhCCCeEEEEEEEEECC--eE-EEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538          294 KQLNEPIEVKFTEWNTG--GL-LTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~--G~-fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~  366 (483)
                      +..|.+|.++|+++..+  +| -|.+ +|++||||.+.+ +..+.+|.... .+|+.|.|+|+++|.++=.+-||.|.
T Consensus       983 ~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v-~vgq~v~~kvi~id~e~f~v~Ls~r~ 1059 (1299)
T KOG1856|consen  983 FYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRV-KVGQTVYCKVIKIDKERFSVELSCRT 1059 (1299)
T ss_pred             hccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhh-ccCceEEEEeeeeeHhhhhhhhhhhh
Confidence            56899999999999754  44 3455 599999999999 45677777766 79999999999999887777788763

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

Probab=94.96  E-value=0.12  Score=49.51  Aligned_cols=105  Identities=15%  Similarity=0.173  Sum_probs=68.1

Q ss_pred             CCCcccCCCEEEEEEEEE--cCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEECC----------
Q 011538          251 GRPVVETGTVLFAEVLGR--TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEG----------  318 (483)
Q Consensus       251 ~~~~~kVGd~V~v~Vi~~--d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~G----------  318 (483)
                      +...+..|..|.+.+.+.  -.+.+...|.+....      .-...+.|++|-|+|+++....+.|++-+          
T Consensus        23 G~gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~p~~~------~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~   96 (188)
T COG1096          23 GEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKK------TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELAT   96 (188)
T ss_pred             CCCeEeECCEEEEeecccEEEcccceEEEeccCCC------CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCC
Confidence            455677788888777662  123445555554432      22446899999999999999999999833          


Q ss_pred             -eEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          319 -LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       319 -i~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                       ..|-+|.|+. ....++.++.+ .+|+-|+++|++.-   ..+.||.+
T Consensus        97 ~~~~~ihvs~~~~~~~~~~~d~f-~~GDivrA~Vis~~---~~~~Lst~  141 (188)
T COG1096          97 SGAADIHVSQVRDGYVEKLSDAF-RIGDIVRARVISTG---DPIQLSTK  141 (188)
T ss_pred             CceeeEEEEeccccccccccccc-ccccEEEEEEEecC---CCeEEEec
Confidence             3466777777 44455555443 67777777777652   33555544

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

Probab=94.95  E-value=0.15  Score=56.32  Aligned_cols=150  Identities=14%  Similarity=0.187  Sum_probs=96.9

Q ss_pred             ccccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccc
Q 011538          165 VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAM  244 (483)
Q Consensus       165 ~~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~  244 (483)
                      -+++++..|.+-.|+|.++...|+||++...+.|+|+.+.+..                                     
T Consensus       115 c~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~-------------------------------------  157 (715)
T COG1107         115 CTMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGG-------------------------------------  157 (715)
T ss_pred             cchhhcccceeeeccccchhhhcceeecChhhhccccccccCC-------------------------------------
Confidence            3678899999999999999999999999999999888777642                                     


Q ss_pred             cCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHH------HH-----hhhHHHHHHhhCCCe--EEEEEEEEEC-
Q 011538          245 SGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLF------RK-----MAWHRVRQIKQLNEP--IEVKFTEWNT-  309 (483)
Q Consensus       245 ~~~~~~~~~~~kVGd~V~v~Vi~~-d~~G~iiLS~k~~~------~~-----~~w~~L~~~~k~Gei--V~GkV~~v~k-  309 (483)
                             .+.+.+|+++.+.|... ...|.+-+....+.      .+     .....|.+  ..|+.  |+|+|+.+.. 
T Consensus       158 -------~~~~~vgdeiiV~v~~vr~~~geidf~~~~~~~Y~~~~~~ke~~r~~i~~id~--~ig~tV~I~GeV~qikqT  228 (715)
T COG1107         158 -------DPDYAVGDEIIVQVSDVRPEKGEIDFEPVGLDRYREVQVEKELPRTLIDDLDE--MIGKTVRIEGEVTQIKQT  228 (715)
T ss_pred             -------CCCCCCCCeEEEEeeccCCCCCccceeecCCccchhhhhhhhcccccHHHHHh--hcCceEEEEEEEEEEEEc
Confidence                   12367888888888774 34465543322221      11     12233333  35554  7889998853 


Q ss_pred             Ce-EEEEECCeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEEEECCCCceeec
Q 011538          310 GG-LLTRIEGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (483)
Q Consensus       310 ~G-~fV~I~Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS  363 (483)
                      .| -+..+-.-+|++|..-+. .-++.--++  .+|+.|.+. =.++...+++.+-
T Consensus       229 ~GPTVFtltDetg~i~aAAFe~aGvRAyP~I--evGdiV~Vi-G~V~~r~g~lQiE  281 (715)
T COG1107         229 SGPTVFTLTDETGAIWAAAFEEAGVRAYPEI--EVGDIVEVI-GEVTRRDGRLQIE  281 (715)
T ss_pred             CCCEEEEEecCCCceehhhhccCCcccCCCC--CCCceEEEE-EEEeecCCcEEEe
Confidence            44 334444457888877762 111111123  489988875 5667777877554

>TIGR02062 RNase_B exoribonuclease II

Probab=94.78  E-value=0.12  Score=58.53  Aligned_cols=66  Identities=27%  Similarity=0.422  Sum_probs=50.5

Q ss_pred             CCeEEEEEEEEECCeEEEEE--CCeEEEeecccccc---cc-CCh--------hhhhhhcCCEEEEEEEEEECCCCceee
Q 011538          297 NEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAELLS---RV-NNF--------TELKEKVGRRMYVQITRINEDTNDLIL  362 (483)
Q Consensus       297 GeiV~GkV~~v~k~G~fV~I--~Gi~gFVP~Sel~~---rv-~~~--------~~l~~~VGq~V~vkVl~ID~e~~rLiL  362 (483)
                      |+...|.|+++.++|+||++  .|+.||||.+.+.+   .. -+.        ..-.+.+|++|+++|.++|..+++|.+
T Consensus       558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~  637 (639)
T TIGR02062       558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIA  637 (639)
T ss_pred             CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEee
Confidence            45899999999999999999  47999999998822   11 010        010247899999999999988887764

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.

>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]

Probab=94.58  E-value=0.058  Score=53.89  Aligned_cols=87  Identities=24%  Similarity=0.376  Sum_probs=64.4

Q ss_pred             ccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccC
Q 011538          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (483)
Q Consensus       167 ~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~  246 (483)
                      -|..++||+|.|+|+.|.....-||++.+.++.++++-+.-.                     +|..+.-.+.|+..++ 
T Consensus        80 rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLP---------------------Gg~~RRk~~~DEl~MR-  137 (301)
T KOG3013|consen   80 RYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLP---------------------GGIQRRKSEEDELQMR-  137 (301)
T ss_pred             hcCCccCCEEEEEeeeeecceeEEecccccceEEEeecccCC---------------------chhhhccchhhHHHHH-
Confidence            377899999999999999999999999999999988776311                     1222222223444454 


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (483)
Q Consensus       247 ~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~  281 (483)
                            ..++.||.|.++|-..-.+|.+.|-.|..
T Consensus       138 ------~fl~egDLi~AEVQ~v~~dGs~sLhTRS~  166 (301)
T KOG3013|consen  138 ------SFLKEGDLIVAEVQNVFHDGSLSLHTRSL  166 (301)
T ss_pred             ------HHhhccCeehHHHHHhccCCeEEEEecch
Confidence                  34899999999987766788888776654

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

Probab=93.51  E-value=0.58  Score=43.95  Aligned_cols=60  Identities=15%  Similarity=0.268  Sum_probs=43.0

Q ss_pred             CCCcEEEEEEEEEeCceEEEEECCCceEEEEec----cCcCcccccC-------cccccCCCCEEEEEEEEEe
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHI----SNMSRTRVTS-------VSDLLNEGERVKVLVVKSM  435 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhi----Sels~~~i~~-------~~~~~kvGd~VkVkVi~vd  435 (483)
                      =.|++++|+|+++...|+|+++++  ++.++..    .++....-++       -...+++|..|+++|+...
T Consensus        80 fKGEVvdgvV~~Vnk~G~F~~~GP--l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr  150 (170)
T KOG3298|consen   80 FKGEVVDGVVTKVNKMGVFARSGP--LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR  150 (170)
T ss_pred             cCCcEEEEEEEEEeeeeEEEeccc--eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence            369999999999999999999997  4555432    2332222222       1236899999999999874

>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=93.32  E-value=0.37  Score=41.98  Aligned_cols=32  Identities=19%  Similarity=0.327  Sum_probs=28.9

Q ss_pred             CCCcEEEEEEEEEeCCeEEEEeCCceeeEeec
Q 011538          171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLT  202 (483)
Q Consensus       171 k~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~  202 (483)
                      ..|.+|.|+|.++-++-+|+|+|.|..++++.
T Consensus        22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~r   53 (104)
T PF10246_consen   22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKR   53 (104)
T ss_pred             ccCCEEEEEEEEEecCceEEEeCCceeEEEec
Confidence            36999999999999999999999999998653

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 [].

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

Probab=93.14  E-value=0.42  Score=45.35  Aligned_cols=71  Identities=20%  Similarity=0.165  Sum_probs=49.6

Q ss_pred             CCCcEEEEEEEEEeCceEEEEEC--------CCceEEEEeccCcCcc--cccCcccccCCCCEEEEEEEEEeCCCeEEEE
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIG--------DSNRSGLLHISNMSRT--RVTSVSDLLNEGERVKVLVVKSMFPDKISLS  443 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~--------~~gi~GLlhiSels~~--~i~~~~~~~kvGd~VkVkVi~vdek~rI~LS  443 (483)
                      ..|+||.++|..|...-|-|+|.        . ...|+||..++...  .--++-+.|++||.|.|+|++..+.....|+
T Consensus        67 ~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~-~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LT  145 (193)
T KOG3409|consen   67 FVGAIVTARVSRINLRFAKVDILSVGDKPLKK-SFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLT  145 (193)
T ss_pred             ccCcEEEEEEEeeccceeeEEEEEEcCEEhhh-hhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEE
Confidence            46777777777776655555552        2 47899999988643  2235567799999999999996555566666


Q ss_pred             Ee
Q 011538          444 IA  445 (483)
Q Consensus       444 LK  445 (483)
                      ..
T Consensus       146 tA  147 (193)
T KOG3409|consen  146 TA  147 (193)
T ss_pred             Ee
Confidence            54

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=91.95  E-value=0.57  Score=53.63  Aligned_cols=70  Identities=16%  Similarity=0.261  Sum_probs=53.6

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC--CeEEEeecccccc-ccC-Ch---------hhhhhhcCCEEEEEEEEEECCCCce
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS-RVN-NF---------TELKEKVGRRMYVQITRINEDTNDL  360 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel~~-rv~-~~---------~~l~~~VGq~V~vkVl~ID~e~~rL  360 (483)
                      ...|+..+|.|+++.++|+||.+.  |++|++|.+.+.. ++. +.         ....+.+|+.|+++|.+++...+++
T Consensus       620 ~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i  699 (706)
T COG0557         620 KRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERKI  699 (706)
T ss_pred             HhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccce
Confidence            368999999999999999999995  5899999999942 211 00         0012368999999999998877776


Q ss_pred             eec
Q 011538          361 ILS  363 (483)
Q Consensus       361 iLS  363 (483)
                      .++
T Consensus       700 ~~~  702 (706)
T COG0557         700 DFE  702 (706)
T ss_pred             EEE
Confidence            654

>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=91.65  E-value=0.79  Score=41.20  Aligned_cols=60  Identities=18%  Similarity=0.222  Sum_probs=43.0

Q ss_pred             CCCeEEEEEEEEECCeEEEEECCe-EEEeeccccc--cccC-----------ChhhhhhhcCCEEEEEEEEEEC
Q 011538          296 LNEPIEVKFTEWNTGGLLTRIEGL-RAFLPKAELL--SRVN-----------NFTELKEKVGRRMYVQITRINE  355 (483)
Q Consensus       296 ~GeiV~GkV~~v~k~G~fV~I~Gi-~gFVP~Sel~--~rv~-----------~~~~l~~~VGq~V~vkVl~ID~  355 (483)
                      .|+++.|+|.+.++.|+.|.++-. +.|||.+.|.  ....           .-.++....|+.|+|||.++.-
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            699999999999999999999653 6899988882  1111           2233444689999999988853

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

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

Probab=91.02  E-value=0.3  Score=53.55  Aligned_cols=62  Identities=31%  Similarity=0.458  Sum_probs=51.9

Q ss_pred             CCCCCcEEEEEEEEEeCc--eEEEEECCCceEEEEeccCcCcccccCc-----ccccCCCCEEEEEEEEEe
Q 011538          372 NLREGTLLEGTVKKIYPY--GAQIRIGDSNRSGLLHISNMSRTRVTSV-----SDLLNEGERVKVLVVKSM  435 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~--GaFV~I~~~gi~GLlhiSels~~~i~~~-----~~~~kvGd~VkVkVi~vd  435 (483)
                      ...+|.++.|+|++|.|.  .+||+|+. +-.||+|.+++.+ ++..+     ...++.||.+-|.|++-.
T Consensus        34 ~~~~gniy~grv~~i~p~~~aafvdig~-~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~  102 (487)
T COG1530          34 EQIVGNIYKGRVTRVLPSLEAAFVDIGL-ERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEP  102 (487)
T ss_pred             EeeecCceEEEecccCccchhheeeccC-CccceEEecccch-hhhhcccccceeeecCCceEEEEEEeec
Confidence            345899999999999884  68999998 7999999999988 44333     458999999999998753

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

Probab=90.81  E-value=1.1  Score=42.68  Aligned_cols=76  Identities=24%  Similarity=0.293  Sum_probs=52.2

Q ss_pred             CCCCcEEEEEEEEEeCCeEEEEe---CC-----ceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecccc
Q 011538          170 PKPGDFVIGVVVSGNENKLDVNV---GA-----DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA  241 (483)
Q Consensus       170 ik~GdiV~G~Vv~V~~~gv~Vdi---G~-----k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~  241 (483)
                      +..|+||.++|.+++...+-|+|   |.     ...|+|+..++.+.   |         +|.        +.+      
T Consensus        66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~t---E---------kdr--------v~v------  119 (193)
T KOG3409|consen   66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRAT---E---------KDR--------VKV------  119 (193)
T ss_pred             CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhcccc---c---------cch--------hhh------
Confidence            56799999999999998877665   43     35687777776432   0         111        111      


Q ss_pred             ccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538          242 IAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (483)
Q Consensus       242 ~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~  281 (483)
                                -.-|++||.|.|.|++.....+..||..+.
T Consensus       120 ----------~ksFrPgDiVlAkVis~~~~~~y~LTtAen  149 (193)
T KOG3409|consen  120 ----------YKSFRPGDIVLAKVISLGDGSNYLLTTAEN  149 (193)
T ss_pred             ----------hhccCCCcEEEEEEeecCCCCcEEEEEecc
Confidence                      134889999999999855556677876543

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

Probab=90.60  E-value=1  Score=42.35  Aligned_cols=34  Identities=21%  Similarity=0.176  Sum_probs=29.5

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeecccc
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL  328 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel  328 (483)
                      -.|++++|+|+++++.|+|+++|.++.|+-...+
T Consensus        80 fKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~  113 (170)
T KOG3298|consen   80 FKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLK  113 (170)
T ss_pred             cCCcEEEEEEEEEeeeeEEEeccceEeeeecccC
Confidence            3799999999999999999999999988764443

>PRK11712 ribonuclease G; Provisional

Probab=89.99  E-value=0.8  Score=50.25  Aligned_cols=58  Identities=19%  Similarity=0.336  Sum_probs=44.4

Q ss_pred             hCCCeEEEEEEEEECC--eEEEEEC-CeEEEeeccccccc-------------cCChhhhhhhcCCEEEEEEEEE
Q 011538          295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLSR-------------VNNFTELKEKVGRRMYVQITRI  353 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~--G~fV~I~-Gi~gFVP~Sel~~r-------------v~~~~~l~~~VGq~V~vkVl~I  353 (483)
                      ..|.++.|+|.++.++  ++||+|| +-.||+|.+++...             ..+..++. ..||.|-|.|.+-
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            4899999999999996  8999997 68999999987210             11122333 6799999998874

>PRK10811 rne ribonuclease E; Reviewed

Probab=89.93  E-value=0.6  Score=54.57  Aligned_cols=61  Identities=18%  Similarity=0.255  Sum_probs=45.5

Q ss_pred             hCCCeEEEEEEEEECC--eEEEEEC-CeEEEeecccccc-ccC---------ChhhhhhhcCCEEEEEEEEEECC
Q 011538          295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLS-RVN---------NFTELKEKVGRRMYVQITRINED  356 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~--G~fV~I~-Gi~gFVP~Sel~~-rv~---------~~~~l~~~VGq~V~vkVl~ID~e  356 (483)
                      ..|.|+.|+|.++.++  ++||+|| |..||||.++... .+.         +..... ..||.|-|.|.+-...
T Consensus        37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~L-k~GqeILVQV~KEa~g  110 (1068)
T PRK10811         37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVL-REGQEVIVQIDKEERG  110 (1068)
T ss_pred             CccceEEEEEecccCCcceeEEEecCCcceEEEhhhcccccccccccccccccccccc-CCCCEEEEEEeecccC
Confidence            3799999999999985  9999997 6899999998832 111         112212 5799999999885433

>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=89.05  E-value=1.7  Score=37.95  Aligned_cols=53  Identities=15%  Similarity=0.234  Sum_probs=45.9

Q ss_pred             CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS  434 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v  434 (483)
                      ..|.+|.|+|..|...-+||++++ ...+.|+.....       .+.|..|.+|.+++.+.
T Consensus        22 ~~gk~V~G~I~hvv~ddLYIDfG~-KFhcVc~rp~~~-------~~~y~~G~rV~lrLkdl   74 (104)
T PF10246_consen   22 PEGKIVIGKIFHVVDDDLYIDFGG-KFHCVCKRPAVN-------GEKYVRGSRVRLRLKDL   74 (104)
T ss_pred             ccCCEEEEEEEEEecCceEEEeCC-ceeEEEeccccc-------ccccccCCEEEEEECCH
Confidence            579999999999999999999998 799999987754       35689999999998754

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 [].

>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=88.06  E-value=3.2  Score=37.30  Aligned_cols=60  Identities=17%  Similarity=0.231  Sum_probs=43.8

Q ss_pred             CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc-------------cccCcccccCCCCEEEEEEEEEe
Q 011538          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-------------RVTSVSDLLNEGERVKVLVVKSM  435 (483)
Q Consensus       375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~-------------~i~~~~~~~kvGd~VkVkVi~vd  435 (483)
                      +|+++.|+|++-++.|+.|.++= --+-+||.+.|...             +-..-.-.+..|+.|++||.++.
T Consensus         3 ~gEvl~g~I~~~~~~Gi~vslgF-FddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~   75 (122)
T PF08292_consen    3 VGEVLTGKIKSSTAEGIRVSLGF-FDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEI   75 (122)
T ss_dssp             TT-EEEEEEEEEETTEEEEEECC-EEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred             CCCEEEEEEEecCCCcEEEEecc-cccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence            69999999999999999999963 46778888887621             11333445799999999999875

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

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=87.02  E-value=4.2  Score=34.53  Aligned_cols=64  Identities=17%  Similarity=0.160  Sum_probs=50.1

Q ss_pred             EEEEEEEEEeCceEE-EEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 011538          378 LLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD  446 (483)
Q Consensus       378 iv~G~V~~I~~~GaF-V~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~  446 (483)
                      .++|+|+.+.+.+.| |.+.+ |..-+.|++---..    -.-.+.+||.|+|.+-..| .++||..-.|.
T Consensus         8 e~~G~V~e~Lp~~~frV~Len-G~~vla~isGKmR~----~rIrIl~GD~V~VE~spYDltkGRIiyR~~~   73 (87)
T PRK12442          8 ELDGIVDEVLPDSRFRVTLEN-GVEVGAYASGRMRK----HRIRILAGDRVTLELSPYDLTKGRINFRHKD   73 (87)
T ss_pred             EEEEEEEEECCCCEEEEEeCC-CCEEEEEeccceee----eeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence            478999999999987 68887 77888888753211    1223789999999998777 88999998885

>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]

Probab=85.42  E-value=4.8  Score=39.53  Aligned_cols=63  Identities=27%  Similarity=0.513  Sum_probs=46.8

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      |-+.+||.|-|.|+....+...||||....+.||.--+.                                       +.
T Consensus        61 YiP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe---------------------------------------~A  101 (230)
T KOG1004|consen   61 YIPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFE---------------------------------------GA  101 (230)
T ss_pred             ecCCCCCEEEEEEEeccCceEEEecCCCCeeeeeecccc---------------------------------------Cc
Confidence            667889999999999999999999998666755432221                                       11


Q ss_pred             CCCCCCcccCCCEEEEEEEEEc
Q 011538          248 SGPGRPVVETGTVLFAEVLGRT  269 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d  269 (483)
                      ..+.++.+++||.|-|+|...+
T Consensus       102 tkrNrPnl~vGdliyakv~~a~  123 (230)
T KOG1004|consen  102 TKRNRPNLQVGDLIYAKVVDAN  123 (230)
T ss_pred             cccCCCccccccEEEEEEEecC
Confidence            1223577999999999998644

>TIGR00008 infA translation initiation factor IF-1

Probab=84.68  E-value=5.4  Score=32.36  Aligned_cols=59  Identities=24%  Similarity=0.266  Sum_probs=44.3

Q ss_pred             EEEEEEEEEeCceEE-EEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEE
Q 011538          378 LLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKIS  441 (483)
Q Consensus       378 iv~G~V~~I~~~GaF-V~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~  441 (483)
                      .+.|+|+...+.+.| |.+.+ |..-+.|++---.    .-.-.+.+||.|.|.+-..+ ++++|.
T Consensus         6 e~~G~V~e~L~~~~f~V~l~n-g~~vla~i~GKmr----~~rI~I~~GD~V~Ve~spyd~tkgrIi   66 (68)
T TIGR00008         6 EMEGKVTESLPNAMFRVELEN-GHEVLAHISGKIR----MHYIRILPGDKVKVELSPYDLTRGRIT   66 (68)
T ss_pred             EEEEEEEEECCCCEEEEEECC-CCEEEEEecCcch----hccEEECCCCEEEEEECcccCCcEeEE
Confidence            478999999999987 68887 7888888875321    11234889999999887666 666764

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).

>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []

Probab=80.42  E-value=19  Score=28.07  Aligned_cols=55  Identities=33%  Similarity=0.389  Sum_probs=38.4

Q ss_pred             EEEEEEEEeC---ceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCe
Q 011538          379 LEGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDK  439 (483)
Q Consensus       379 v~G~V~~I~~---~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~r  439 (483)
                      ..|+|+...+   || ||.-.+.+-+-|+|.+++....    -..+..|+.|...+.. .+++-
T Consensus         1 ~~G~V~~~~~~kgyG-FI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~-~~~g~   58 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYG-FITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE-GKKGP   58 (66)
T ss_dssp             EEEEEEEEETTTTEE-EEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE-CTTSE
T ss_pred             CeEEEEEEECCCCce-EEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE-CCCCC
Confidence            4799999976   44 5555553569999999998553    2568999999999986 44443

During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	483
2cqo_A	119	Solution Structure Of The S1 Rna Binding Domain Of		1e-04
2eqs_A	103	Solution Structure Of The S1 Rna Binding Domain Of		2e-04
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		2e-04
4aid_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		2e-04
4aim_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		2e-04
4am3_A	717	Crystal Structure Of C. Crescentus Pnpase Bound To		3e-04
1sro_A	76	S1 Rna Binding Domain, Nmr, 20 Structures Length =		3e-04
1yz6_A	274	Crystal Structure Of Intact Alpha Subunit Of Aif2 F		8e-04
3aev_A	275	Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex		8e-04

>pdb|2CQO|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human Hypothetical Protein Flj11067 Length = 119

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 44/70 (62%), Gaps = 1/70 (1%)
Query: 377 TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKV-LVVKSM 435
           T+ +G V  +  YGA I+I    + GL+H ++MS  RV   S++++ G++V V L+ + M
Sbjct: 24  TIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREM 83
Query: 436 FPDKISLSIA 445
             D+I +S++
Sbjct: 84  KNDRIKVSLS 93

>pdb|2EQS|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human Atp-Dependent Rna Helicase Dhx8 Length = 103

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 49/80 (61%), Gaps = 4/80 (5%)
Query: 376 GTLLEGTVKKIYPYGAQIRI-GDSNR-SGLLHISNMSR-TRVTSVSDLLNEGERVKVLVV 432
           G +  G V  I  +G  +++ G   R  GL+HIS + R  RV +V+D++++G+RVKV V+
Sbjct: 13  GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVL 72
Query: 433 KSMFPDKISLSIADLESEPG 452
            S    K SLS+ D++ E G
Sbjct: 73  -SFTGTKTSLSMKDVDQETG 91

>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase Length = 723

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 370 TLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKV 429
           T  +  G +  G V +I  +GA + IG   + GL+HIS ++  RV  V+D L  G+ V V
Sbjct: 622 TAEIEVGRVYTGKVTRIVDFGAFVAIG-GGKEGLVHISQIADKRVEKVTDYLQMGQEVPV 680
Query: 430 LVVKSMFPDKISLSI 444
            V++     +I LSI
Sbjct: 681 KVLEVDRQGRIRLSI 695

>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E Recognition Peptide Length = 726

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435
           G + +G V K+  +GA +    + + GL+H+S +S  RV   SD+L EG+ VKV ++   
Sbjct: 638 GKIYDGKVVKVVDFGAFVNFFGA-KDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD 696
Query: 436 FPDKISLSIADLESEPGLFVSDKE 459
              K  LS+  ++ E G  +S KE
Sbjct: 697 DRGKTKLSMKVVDQETGEDLSKKE 720

>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E Recognition Peptide Length = 726

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435
           G + +G V K+  +GA +    + + GL+H+S +S  RV   SD+L EG+ VKV ++   
Sbjct: 638 GKIYDGKVVKVVDFGAFVNFFGA-KDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD 696
Query: 436 FPDKISLSIADLESEPGLFVSDKE 459
              K  LS+  ++ E G  +S KE
Sbjct: 697 DRGKTKLSMKVVDQETGEDLSKKE 720

>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna Length = 717

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435
           G + +G V K+  +GA +    + + GL+H+S +S  RV   SD+L EG+ VKV ++   
Sbjct: 629 GKIYDGKVVKVVDFGAFVNFFGA-KDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD 687
Query: 436 FPDKISLSIADLESEPGLFVSDKE 459
              K  LS+  ++ E G  +S KE
Sbjct: 688 DRGKTKLSMKVVDQETGEDLSKKE 711

>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures Length = 76

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435
           G +  G V +I  +GA + IG   + GL+HIS ++  RV  V+D L  G+ V V V++  
Sbjct: 6   GRVYTGKVTRIVDFGAFVAIG-GGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVD 64
Query: 436 FPDKISLSIAD 446
              +I LSI +
Sbjct: 65  RQGRIRLSIKE 75

>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From Pyrococcus Abyssi Length = 274

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 375 EGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433
           EG  +  TVK+I+ YGA + + +   +   +HIS ++ T V ++ D L EG++V   V++
Sbjct: 10  EGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIR 69

>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From Pyrococcus Horikoshii Ot3 Length = 275

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 375 EGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433
           EG  +  TVK+I+ YGA + + +   +   +HIS ++ T V ++ D L EG++V   V++
Sbjct: 11  EGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIR 70

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	483
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	1e-17
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	2e-15
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	1e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	9e-13
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	2e-12
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	3e-12
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	4e-12
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	8e-12
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	4e-11
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	2e-10
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	3e-10
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	5e-10
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	2e-09
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	1e-08
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	6e-07
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	6e-06
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	3e-05
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	6e-05
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	1e-04

>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 = 77.8 bits (192), Expect = 1e-17
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 3/80 (3%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM 435
            T+ +G V  +  YGA I+I    + GL+H ++MS  RV   S++++ G++V V ++   
Sbjct: 23  YTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGRE 82

Query: 436 FPD---KISLSIADLESEPG 452
             +   K+SLS+  +    G
Sbjct: 83  MKNDRIKVSLSMKVVNQGTG 102

>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 = 71.2 bits (175), Expect = 2e-15
 Identities = 30/80 (37%), Positives = 46/80 (57%), Gaps = 4/80 (5%)

Query: 376 GTLLEGTVKKIYPYGA--QIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVV 432
           G +  G V  I  +G   Q+        GL+HIS + R  RV +V+D++++G+RVKV V+
Sbjct: 13  GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVL 72

Query: 433 KSMFPDKISLSIADLESEPG 452
            S    K SLS+ D++ E G
Sbjct: 73  -SFTGTKTSLSMKDVDQETG 91

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

 Score = 69.7 bits (171), Expect = 1e-14
 Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 2/81 (2%)

Query: 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLV 431
               G++  G V  +  YGA + + +    GL+HIS ++   V  +++ L+ G+ V+V V
Sbjct: 4   KFEVGSVYTGKVTGLQAYGAFVALDE-ETQGLVHISEVTHGFVKDINEHLSVGDEVQVKV 62

Query: 432 VK-SMFPDKISLSIADLESEP 451
           +       KISLSI   ++ P
Sbjct: 63  LAVDEEKGKISLSIRATQAAP 83

>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 = 72.2 bits (176), Expect = 2e-13
 Identities = 69/484 (14%), Positives = 140/484 (28%), Gaps = 151/484 (31%)

Query: 125 FLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGN 184
           F   F      ++V++    +    E   +D  +                 +   ++S  
Sbjct: 25  FEDAFVDNFDCKDVQDMPKSILSKEE---IDHIIMSKDAVSGTL------RLFWTLLSKQ 75

Query: 185 ENKLDVNVGADL------LGTMLTKE------VLPLYDKEMDFLLCDLKKDAEEFMVRGK 232
           E  +   V   L      L + +  E      +  +Y ++ D L  D +  A+  + R +
Sbjct: 76  EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ 135

Query: 233 MGI--------VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRK 284
             +        ++    + + G  G G+      T +  +V              ++  K
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGK------TWVALDVC------LSYKVQCKMDFK 183

Query: 285 MAWHRVRQ-------IKQLNE---PIEVKFTEWNTGGLLTRI------EGLRAFL----- 323
           + W  ++        ++ L +    I+  +T  +      ++        LR  L     
Sbjct: 184 IFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPY 243

Query: 324 PKAEL-LSRVNNFTELKE-KVGRRMYVQITRINEDTNDLI---------------LSERE 366
               L L  V N        +  ++ +  TR  + T+ L                L+  E
Sbjct: 244 ENCLLVLLNVQNAKAWNAFNLSCKILL-TTRFKQVTDFLSAATTTHISLDHHSMTLTPDE 302

Query: 367 A------WATLNLREGTL-LEGTVKKIYPY-----GAQIRIGDSNRSGLLHISNMSRTRV 414
                  +  L+ R   L  E  V    P         IR G +      H++    T +
Sbjct: 303 VKSLLLKY--LDCRPQDLPRE--VLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI 358

Query: 415 TSVS-DLLNEGERVKVLVVKSMFPD--KIS---LSI---ADLESEPGLFVS--------- 456
              S ++L   E  K+    S+FP    I    LS+     ++S+  + V+         
Sbjct: 359 IESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE 418

Query: 457 -----------------------DKEVHIIFL-------------FILLFNKQYSVWFLV 480
                                  +  +H   +              I  +  QY    + 
Sbjct: 419 KQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIG 478

Query: 481 -HLR 483
            HL+
Sbjct: 479 HHLK 482

>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 = 42.9 bits (100), Expect = 2e-04
 Identities = 61/392 (15%), Positives = 129/392 (32%), Gaps = 120/392 (30%)

Query: 38  QQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSA---QFPENVENEGLEGNEELELLN 94
           Q ++ +++F  S + L +T       K V D LS+A       +  +  L  +E   LL 
Sbjct: 254 QNAKAWNAFNLSCKILLTT-----RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL- 307

Query: 95  KPNLVPISNGVASEVDKKSEK-PDEEEALAPF-LKFFKPRDSAEEVEEEGSEVGVSR--- 149
                         +D + +  P E     P  L        AE + +     G++    
Sbjct: 308 -----------LKYLDCRPQDLPREVLTTNPRRLSII-----AESIRD-----GLATWDN 346

Query: 150 -ESIDVDDKVGEDKVSVE---------YYEPKPGDFVIGVVVSGNENKL--DVNVGADLL 197
            + ++ D      + S+           ++       +               ++   LL
Sbjct: 347 WKHVNCDKLTTIIESSLNVLEPAEYRKMFD----RLSV----------FPPSAHIPTILL 392

Query: 198 GT----MLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI-----VKDDDAIAMSGGS 248
                 ++  +V+ + +K   + L  ++K  +E  +     I     VK ++  A+    
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSL--VEKQPKESTIS-IPSIYLELKVKLENEYALH--- 446

Query: 249 GPGRPVVETGTVL----------------FAEVLGRTLSGRPLLSTRRLFRKM----AWH 288
              R +V+   +                 F   +G  L          LFR +     + 
Sbjct: 447 ---RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRF- 502

Query: 289 RVRQIKQLNEPIEVKFTEWNTGG----LLTRIEGLRAFL----PKAE-LLSRVNNFTE-L 338
                  L + I    T WN  G     L +++  + ++    PK E L++ + +F   +
Sbjct: 503 -------LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKI 555

Query: 339 KEKVGRRMY---VQITRINEDTNDLILSEREA 367
           +E +    Y   ++I  + ED      + ++ 
Sbjct: 556 EENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 63.7 bits (156), Expect = 9e-13
 Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 4/82 (4%)

Query: 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLV 431
             ++G ++ G V  +   GA + + D    G L  S  SR RV   + +L+ G+ V+   
Sbjct: 28  LNKKGAIVTGKVTAVDAKGATVELAD-GVEGYLRASEASRDRVEDATLVLSVGDEVEAKF 86

Query: 432 VKSMFPD--KISLSIADLESEP 451
              +      ISLS+   +   
Sbjct: 87  T-GVDRKNRAISLSVRAKDEAD 107

>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 = 64.4 bits (157), Expect = 2e-12
 Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 4/81 (4%)

Query: 374 REGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432
               ++   V+ I   GA + + + +N  G++ +S +SR R+ S++ L+  G    V+V+
Sbjct: 14  EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVI 73

Query: 433 KSMFPDK--ISLSIADLESEP 451
           + +  +K  I LS   +  E 
Sbjct: 74  R-VDKEKGYIDLSKRRVSPEE 93

>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 = 64.0 bits (156), Expect = 3e-12
 Identities = 20/81 (24%), Positives = 42/81 (51%), Gaps = 4/81 (4%)

Query: 374 REGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432
               ++   V++I   GA +++ +  N  G++ +S +SR R+ S+  L+  G+    +V+
Sbjct: 14  EIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVL 73

Query: 433 KSMFPDK--ISLSIADLESEP 451
           + +  +K  I LS   + SE 
Sbjct: 74  R-VDKEKGYIDLSKRRVSSED 93

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 67.5 bits (166), Expect = 4e-12
 Identities = 29/85 (34%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434
            G + +G V K+  +GA +      + GL+H+S +S  RV   SD+L EG+ VKV ++  
Sbjct: 637 VGKIYDGKVVKVVDFGAFVNFF-GAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGF 695

Query: 435 MFPDKISLSIADLESEPGLFVSDKE 459
               K  LS+  ++ E G  +S KE
Sbjct: 696 DDRGKTKLSMKVVDQETGEDLSKKE 720

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

 Score = 66.7 bits (164), Expect = 8e-12
 Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS 434
            G +  G V +I  +GA + IG   + GL+HIS ++  RV  V+D L  G+ V V V++ 
Sbjct: 627 VGRVYTGKVTRIVDFGAFVAIG-GGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEV 685

Query: 435 MFPDKISLSIADLESEPG 452
               +I LSI +   +  
Sbjct: 686 DRQGRIRLSIKEATEQSQ 703

>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 = 63.1 bits (153), Expect = 4e-11
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 4/80 (5%)

Query: 375 EGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433
              ++   V+ I   GA + + + +N  G++H+S +SR R+ S++ L+  G    V V++
Sbjct: 13  VEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIR 72

Query: 434 SMFPDK--ISLSIADLESEP 451
            +  +K  I LS   +  E 
Sbjct: 73  -VDKEKGYIDLSKRRVSPEE 91

>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 = 60.8 bits (147), Expect = 2e-10
 Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 375 EGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433
           EG +L  TVK+++ YG+ + + +       L  S +S   V ++ D+L E  +V V V++
Sbjct: 11  EGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIR 70

>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 = 61.4 bits (150), Expect = 3e-10
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 5/81 (6%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT----RVTSVSDLLNEGERVKVLV 431
           G  + G+V K   +GA + +    + GLLHIS + +     RV +V D+L  G++V+V +
Sbjct: 668 GERILGSVVKTTTFGAFVSLL-PGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEI 726

Query: 432 VKSMFPDKISLSIADLESEPG 452
            +     K+SL       E  
Sbjct: 727 AEIDSRGKLSLIPVIEGEEAA 747

>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 = 59.3 bits (143), Expect = 5e-10
 Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 375 EGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433
           EG  +  TVK+I+ YGA + + +   +   +HIS ++ T V ++ D L EG++V   V++
Sbjct: 11  EGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIR 70

Query: 434 -SMFPDKISLSIADLESEP 451
                  I LS+  +  + 
Sbjct: 71  VDPRKGHIDLSLRRVTQQQ 89

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 8/80 (10%)

Query: 371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGE--RVK 428
           +++  G   +G V +I  YGA I + +    GLL   +M   R+ ++    N G+   V+
Sbjct: 1   MDVEPGKFYKGVVTRIEKYGAFINLNE-QVRGLLRPRDMISLRLENL----NVGDEIIVQ 55

Query: 429 VLVVKSMFPDKISLSIADLE 448
            + V+     +I      LE
Sbjct: 56  AIDVRPE-KREIDFKYIPLE 74

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115

 Score = 52.3 bits (126), Expect = 1e-08
 Identities = 27/89 (30%), Positives = 45/89 (50%), Gaps = 7/89 (7%)

Query: 368 WATLNLR--EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEG 424
           W  +  R  EGT L G V  +  YG  + I +    GL+H+S M  T +    S ++N G
Sbjct: 21  WVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEE-GVEGLVHVSEMDWTNKNIHPSKVVNVG 79

Query: 425 ERVKVLVVKSMFPDK--ISLSIADLESEP 451
           + V+V +V  +  ++  ISL +   ++ P
Sbjct: 80  DVVEV-MVLDIDEERRRISLGLKQCKANP 107

>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 = 51.1 bits (123), Expect = 6e-07
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432
           L+ G +LEG V  +  +GA + IG     GL+HIS +S   V    +++  G+ VKV V+
Sbjct: 652 LKPGMVLEGVVTNVTNFGAFVDIGVHQ-DGLVHISALSEKFVKDPYEVVKAGDIVKVKVM 710

Query: 433 KSMFPDK-ISLSI 444
           +   P   + LS+
Sbjct: 711 EVDIPRNRVGLSM 723

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

 Score = 48.0 bits (114), Expect = 6e-06
 Identities = 8/92 (8%), Positives = 32/92 (34%), Gaps = 7/92 (7%)

Query: 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-SVSDLLNEGERVKVLV 431
             +G+++   V++ +          S    +++    +  ++    +++   G+      
Sbjct: 903 FFKGSIIPVRVERFWHNDIICTTN-SEVECVVNAQRHAGAQLRRPANEIYEIGKTYPA-K 960

Query: 432 VKSMFPDK--ISLSI--ADLESEPGLFVSDKE 459
           V  +        +S+   D++ +       K+
Sbjct: 961 VIYIDYANITAEVSLLDHDVKQQYVPISYSKD 992

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

 Score = 45.6 bits (108), Expect = 3e-05
 Identities = 6/74 (8%), Positives = 25/74 (33%), Gaps = 5/74 (6%)

Query: 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-SVSDLLNEGERVKVLV 431
             +G+++   V++ +          S    +++    +  ++    +++   G+      
Sbjct: 900 FFKGSIIPVRVERFWHNDIICTTN-SEVECVVNAQRHAGAQLRRPANEIYEIGKTYPA-K 957

Query: 432 VKSMFPDK--ISLS 443
           V  +        +S
Sbjct: 958 VIYIDYANITAEVS 971

>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 = 43.8 bits (103), Expect = 6e-05
 Identities = 18/133 (13%), Positives = 41/133 (30%), Gaps = 21/133 (15%)

Query: 300 IEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTND 359
           I     + N      + +G    L K           E +  VG  +        +    
Sbjct: 10  IVGLIIDENDRFYFVQKDGQTYALAK----------EEGQHTVGDTVKGFAYTDMKQ--K 57

Query: 360 LILSEREAWATLNLREGTLLEGTVKKIYP-YGAQIRIGDSNRSGLLHISNMSRTRVTSVS 418
           L L+  E  AT          G V ++    G  +  G  ++  ++ +  +   +     
Sbjct: 58  LRLTTLEVTATQ----DQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKELWPK 113

Query: 419 DLLNEGERVKVLV 431
               +G+++ + +
Sbjct: 114 ----KGDQLYIRL 122

>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 = 43.0 bits (101), Expect = 1e-04
 Identities = 21/128 (16%), Positives = 43/128 (33%), Gaps = 14/128 (10%)

Query: 337 ELKEKVGRRMYVQITRINED-----TNDLILSEREAWATLNLREGTLLEGTVKKIYPYGA 391
           EL  K G ++Y+++    +D            +R A    N  +       V ++   G 
Sbjct: 109 ELWPKKGDQLYIRLEVDKKDRIWGLLAYQEDFQRLARPAYNNMQNQNWPAIVYRLKLSGT 168

Query: 392 QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPD-KISLSIADLESE 450
            + + ++N  G +H S                G+ +   V+     D  ++LS+     E
Sbjct: 169 FVYLPENNMLGFIHPSERYAE--------PRLGQVLDARVIGFREVDRTLNLSLKPRSFE 220

Query: 451 PGLFVSDK 458
                +  
Sbjct: 221 MLENDAQM 228

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	483
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	100.0
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.84
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.71
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.7
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.67
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.65
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.64
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.62
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.6
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.56
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.54
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.54
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.52
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.52
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.45
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.43
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.38
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.29
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.25
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.25
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.22
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.2
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.15
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.14
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	99.14
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.09
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.09
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.08
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	99.06
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.05
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.04
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.04
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	99.01
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	99.01
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	98.99
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	98.96
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.92
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.92
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.89
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.85
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.84
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.83
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.75
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.71
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.69
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.68
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.68
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.66
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.61
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.56
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.5
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.47
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	98.43
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.4
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.39
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.37
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.35
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.33
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.32
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	98.24
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.23
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.23
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	98.21
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.2
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.18
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.16
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	98.14
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.11
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	98.06
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	98.04
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.03
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	98.01
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	97.99
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.9
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.89
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.84
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.72
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.56
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.38
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	97.35
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.3
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	97.15
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	97.11
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	97.06
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	96.93
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	96.93
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	96.71
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	96.39
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	91.72
2r7d_A	469	Ribonuclease II family protein; structural genomic	89.76
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	88.33
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	88.01
1jjg_A	102	M156R; beta barrel, S1 motif, OB fold, MYXV156R, N	87.72
4b9w_A	201	TDRD1, tudor domain-containing protein 1; replicat	86.78

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

Probab=100.00  E-value=2.2e-31  Score=266.71  Aligned_cols=216  Identities=14%  Similarity=0.089  Sum_probs=184.1

Q ss_pred             CCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCCCCC
Q 011538          171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGP  250 (483)
Q Consensus       171 k~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~~~~  250 (483)
                      .+|++++|+|+++++.|+||++| +.+|+||.+|+.                                            
T Consensus         5 ~~G~~v~g~V~~~~~~G~fv~~~-g~egllp~se~~--------------------------------------------   39 (285)
T 3go5_A            5 NLASFIVGLIIDENDRFYFVQKD-GQTYALAKEEGQ--------------------------------------------   39 (285)
T ss_dssp             TTTEEEEEEEEEECSSEEEEEET-TEEEEEEGGGCC--------------------------------------------
T ss_pred             cCCCEEEEEEEEEECCEEEEEcC-CeEEEEEHHHCc--------------------------------------------
Confidence            47999999999999999999998 899999998872                                            


Q ss_pred             CCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEE-CCeEEEEECC--eEEEeeccc
Q 011538          251 GRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN-TGGLLTRIEG--LRAFLPKAE  327 (483)
Q Consensus       251 ~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~-k~G~fV~I~G--i~gFVP~Se  327 (483)
                        .  ++||+|+|+|+ .|.++++++|++.+     |      ++.|++++|+|++++ ++|+||++++  .+||||.|+
T Consensus        40 --~--~vGdevev~v~-~d~~~r~iat~~~p-----~------~~~G~~~~g~V~~v~~~~GaFVdiG~~~~d~lvp~se  103 (285)
T 3go5_A           40 --H--TVGDTVKGFAY-TDMKQKLRLTTLEV-----T------ATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDI  103 (285)
T ss_dssp             --C--CTTSEEEEEEE-ECTTSCEEEECSCC-----C------SCSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGG
T ss_pred             --c--ccCCEEEEEEE-ECCCCCEEEecccc-----c------ccCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHH
Confidence              1  58999999999 57889999998754     2      479999999999999 7999999974  899999999


Q ss_pred             c-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh-----Hhhh--cCCCCCcEEEEEEEEEeCceEEE-EECCC
Q 011538          328 L-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE-----AWAT--LNLREGTLLEGTVKKIYPYGAQI-RIGDS  398 (483)
Q Consensus       328 l-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~-----~~e~--~~l~vG~iv~G~V~~I~~~GaFV-~I~~~  398 (483)
                      + |.+.     ....+|+++.++ +.+|+ ++||.+|+|+     +|..  ..+++|++|+|+|++++++|+|| .+.+ 
T Consensus       104 l~~~~~-----~~~~~Gd~v~v~-l~iD~-~~Ri~ls~k~~~~~~~~~~~~~~~~~G~~V~g~V~~i~~~G~fV~~i~~-  175 (285)
T 3go5_A          104 LPELKE-----LWPKKGDQLYIR-LEVDK-KDRIWGLLAYQEDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYLPEN-  175 (285)
T ss_dssp             SCSSGG-----GSCCTTCEEEEE-EEECT-TSCEEEEECCHHHHHHHCCCCCSCCTTCEEEEEEEEEETTEEEEEETTT-
T ss_pred             CCcccc-----cccCCCCEEEEE-EEECC-CCcEEEEehhhhhcchhhhhhhhCCCCCEEEEEEEEEeCCcEEEEEeCC-
Confidence            9 5332     123799999776 69998 7899999863     4543  47999999999999999999999 9987 


Q ss_pred             ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeC-CCeEEEEEecCCCCcCcccccccccceee
Q 011538          399 NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMF-PDKISLSIADLESEPGLFVSDKEVHIIFL  465 (483)
Q Consensus       399 gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vde-k~rI~LSLK~~~~dPw~~l~~k~~V~~~~  465 (483)
                      ++.||||.||++        +.+++||+|+|+|+++++ ++||+||+|++..++|+..+  +.|+++|
T Consensus       176 g~~Glih~SEl~--------~~l~~Gd~v~~~V~~id~~d~kI~LSlk~~~~~~~~~~a--~~il~~L  233 (285)
T 3go5_A          176 NMLGFIHPSERY--------AEPRLGQVLDARVIGFREVDRTLNLSLKPRSFEMLENDA--QMILTYL  233 (285)
T ss_dssp             TEEEEECGGGCS--------SCCCTTCEEEEEEEEEETTTTEEEEECSCCCCCCCCHHH--HHHHHHH
T ss_pred             CeEEEEEHHHcc--------ccCCCCCEEEEEEEEEECCCCeEEEEeChhhhhccchHH--HHHHHHH
Confidence            799999999997        469999999999999985 89999999999998886543  4444443

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

Probab=99.84  E-value=4.4e-20  Score=184.84  Aligned_cols=164  Identities=13%  Similarity=0.060  Sum_probs=139.9

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhhhcCCC
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLR  374 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e~~~l~  374 (483)
                      ..|++++|+|++++++|+||+++|.+||||.+++..          .+|++|+|.|+ .| ..+|+++|++.++    ++
T Consensus         5 ~~G~~v~g~V~~~~~~G~fv~~~g~egllp~se~~~----------~vGdevev~v~-~d-~~~r~iat~~~p~----~~   68 (285)
T 3go5_A            5 NLASFIVGLIIDENDRFYFVQKDGQTYALAKEEGQH----------TVGDTVKGFAY-TD-MKQKLRLTTLEVT----AT   68 (285)
T ss_dssp             TTTEEEEEEEEEECSSEEEEEETTEEEEEEGGGCCC----------CTTSEEEEEEE-EC-TTSCEEEECSCCC----SC
T ss_pred             cCCCEEEEEEEEEECCEEEEEcCCeEEEEEHHHCcc----------ccCCEEEEEEE-EC-CCCCEEEeccccc----cc
Confidence            479999999999999999999999999999999842          48999999997 45 4668888987664    78


Q ss_pred             CCcEEEEEEEEEe-CceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC-CCCcC
Q 011538          375 EGTLLEGTVKKIY-PYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL-ESEPG  452 (483)
Q Consensus       375 vG~iv~G~V~~I~-~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~-~~dPw  452 (483)
                      +|+++.|+|++++ ++||||+++..+++||||.|+++|.+.    ..+++||.|.|+ +.+|.++||.||+|+. ..+||
T Consensus        69 ~G~~~~g~V~~v~~~~GaFVdiG~~~~d~lvp~sel~~~~~----~~~~~Gd~v~v~-l~iD~~~Ri~ls~k~~~~~~~~  143 (285)
T 3go5_A           69 QDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKE----LWPKKGDQLYIR-LEVDKKDRIWGLLAYQEDFQRL  143 (285)
T ss_dssp             SSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGGSCSSGG----GSCCTTCEEEEE-EEECTTSCEEEEECCHHHHHHH
T ss_pred             CCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHHCCcccc----cccCCCCEEEEE-EEECCCCcEEEEehhhhhcchh
Confidence            9999999999999 799999997414899999999998654    347999999766 5788788999999987 57899


Q ss_pred             cccccccccceeeEEEEeecccceEEE
Q 011538          453 LFVSDKEVHIIFLFILLFNKQYSVWFL  479 (483)
Q Consensus       453 ~~l~~k~~V~~~~~~~~~~~~~~~~~~  479 (483)
                      .....++++++.+.-.+.+....-.|.
T Consensus       144 ~~~~~~~~~G~~V~g~V~~i~~~G~fV  170 (285)
T 3go5_A          144 ARPAYNNMQNQNWPAIVYRLKLSGTFV  170 (285)
T ss_dssp             CCCCCSCCTTCEEEEEEEEEETTEEEE
T ss_pred             hhhhhhCCCCCEEEEEEEEEeCCcEEE
Confidence            999999999999977777765555553

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

Probab=99.71  E-value=4e-17  Score=142.37  Aligned_cols=88  Identities=28%  Similarity=0.438  Sum_probs=82.3

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc-cccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~-~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      ..+++|+++.|+|++|+++|+||+|++ +++||||+++++|+ +..++.+.|++||.|+|+|++++ +++||.||+|++.
T Consensus        26 ~~~~~G~~~~G~V~~v~~~G~FV~l~~-~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~rI~lslk~~~  104 (115)
T 2khi_A           26 KRYPEGTKLTGRVTNLTDYGCFVEIEE-GVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRRISLGLKQCK  104 (115)
T ss_dssp             CSSCSSCEEEEEEEEEETTEEEEECST-TCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEETTTTEEEECCCCCC
T ss_pred             hcCCCCCEEEEEEEEEECCEEEEEECC-CCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEECCCCEEEEEEEecC
Confidence            478999999999999999999999987 79999999999984 78889999999999999999998 5899999999999


Q ss_pred             CCcCccccccc
Q 011538          449 SEPGLFVSDKE  459 (483)
Q Consensus       449 ~dPw~~l~~k~  459 (483)
                      +|||+.+.++|
T Consensus       105 ~~p~~~~~~~~  115 (115)
T 2khi_A          105 ANPWQQFAETH  115 (115)
T ss_dssp             SSCCCCCCCCC
T ss_pred             cCHHHHHHhhC
Confidence            99999998765

>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=99.70  E-value=9.2e-18  Score=157.84  Aligned_cols=92  Identities=23%  Similarity=0.287  Sum_probs=75.4

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEE--CCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCC
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRI--GDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I--~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~  449 (483)
                      +++|+++.|+|++|++||+||+|  .+ +++||||+|+|+|+++.++++.+++||.|+|+|+++| +++||.||+|++.+
T Consensus        13 p~~G~iv~G~V~~I~~fGaFV~L~e~~-g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~~~~   91 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAEMGAYVSLLEYN-NIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSP   91 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTT-TEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTTCCH
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccCC-CcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeecCc
Confidence            48999999999999999999999  45 7999999999999999999999999999999999998 78999999999999


Q ss_pred             CcCcccccccccceee
Q 011538          450 EPGLFVSDKEVHIIFL  465 (483)
Q Consensus       450 dPw~~l~~k~~V~~~~  465 (483)
                      +||..+.++|++++.+
T Consensus        92 ~p~~~~~~~~~~g~~v  107 (182)
T 1kl9_A           92 EEAIKCEDKFTKSKTV  107 (182)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHhccCCCEE
Confidence            9999999999988775

>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=99.67  E-value=3.6e-17  Score=152.94  Aligned_cols=91  Identities=23%  Similarity=0.288  Sum_probs=78.3

Q ss_pred             CCCcEEEEEEEEEeCceEEEEEC--CCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCC
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIG--DSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE  450 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~--~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~d  450 (483)
                      ++|+++.|+|++|++||+||+|.  + +++||||+|+|+|+++.++++.+++||.|+|+|+++| +++||.||+|++.++
T Consensus        14 ~~G~iv~G~V~~i~~fGaFV~L~e~~-gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~~~~~   92 (175)
T 2a19_A           14 EIDDIVMVNVQQIAEMGAYVKLLEYD-NIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSSE   92 (175)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTTT-TCEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTTCCHH
T ss_pred             CCCCEEEEEEEEEecceEEEEEcCCC-CcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEecCcC
Confidence            48999999999999999999994  5 7999999999999999999999999999999999998 789999999999999


Q ss_pred             cCcccccccccceee
Q 011538          451 PGLFVSDKEVHIIFL  465 (483)
Q Consensus       451 Pw~~l~~k~~V~~~~  465 (483)
                      ||..+.+++++++.+
T Consensus        93 ~~~~~~~~~~~g~~v  107 (175)
T 2a19_A           93 DIIKCEEKYQKSKTV  107 (175)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             hHHHHHHhccCCCcc
Confidence            999999999988765

>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=99.65  E-value=2.5e-16  Score=134.76  Aligned_cols=87  Identities=31%  Similarity=0.484  Sum_probs=79.2

Q ss_pred             hcCCCCCcEEEEEEEEEeCceEEEEECCC--ceEEEEeccCc-CcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEec
Q 011538          370 TLNLREGTLLEGTVKKIYPYGAQIRIGDS--NRSGLLHISNM-SRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIAD  446 (483)
Q Consensus       370 ~~~l~vG~iv~G~V~~I~~~GaFV~I~~~--gi~GLlhiSel-s~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~  446 (483)
                      ...+++|+++.|+|++|++||+||+|++.  +++||||+|++ ++.++.++.+.|++||.|+|+|++++. +||.||+|+
T Consensus         7 ~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~-~~i~LSlk~   85 (103)
T 2eqs_A            7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG-TKTSLSMKD   85 (103)
T ss_dssp             CSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET-TEEEEESTT
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC-CeeEEEEee
Confidence            44689999999999999999999999852  68999999999 677888999999999999999999986 699999999


Q ss_pred             CCCCcCccccc
Q 011538          447 LESEPGLFVSD  457 (483)
Q Consensus       447 ~~~dPw~~l~~  457 (483)
                      +.++||+.+..
T Consensus        86 ~~~~~~~~~~~   96 (103)
T 2eqs_A           86 VDQETGEDLNP   96 (103)
T ss_dssp             BCTTTCCBCCS
T ss_pred             cccCCchhcCc
Confidence            99999998764

>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=99.64  E-value=2.1e-16  Score=138.86  Aligned_cols=87  Identities=28%  Similarity=0.361  Sum_probs=79.4

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CC--CeEEEEEecC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP--DKISLSIADL  447 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek--~rI~LSLK~~  447 (483)
                      ..+++|+++.|+|++|++||+||+|.+.+++||||+++++|.++.++.+.|++||.|+|+|++++ ++  ++|.||+|++
T Consensus        18 ~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~~~~i~LSlk~~   97 (119)
T 2cqo_A           18 NLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVV   97 (119)
T ss_dssp             CSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECSSCEEEEEESTTB
T ss_pred             cccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEeccccCceEEEEEeec
Confidence            36889999999999999999999996534699999999999999999999999999999999998 33  6999999999


Q ss_pred             CCCcCccccc
Q 011538          448 ESEPGLFVSD  457 (483)
Q Consensus       448 ~~dPw~~l~~  457 (483)
                      .++||+.+..
T Consensus        98 ~~~~~~~~~~  107 (119)
T 2cqo_A           98 NQGTGKDLDP  107 (119)
T ss_dssp             CSSSCCBSCT
T ss_pred             ccCCccccCc
Confidence            9999998865

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

Probab=99.62  E-value=8.3e-16  Score=136.95  Aligned_cols=82  Identities=29%  Similarity=0.470  Sum_probs=78.1

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE  450 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~d  450 (483)
                      .+++|+++.|+|++|++||+||+|.+ +++||||++++++.++.++.+.|++||.|+|+|++++ ++++|.||+|++.++
T Consensus         4 ~~~vG~iv~G~V~~i~~~G~FV~l~~-~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk~~~~~   82 (130)
T 2k4k_A            4 KFEVGSVYTGKVTGLQAYGAFVALDE-ETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIRATQAA   82 (130)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEET-TEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESHHHHHS
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEECC-CcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEeecccC
Confidence            68899999999999999999999987 7999999999999999999999999999999999998 589999999999999


Q ss_pred             cCcc
Q 011538          451 PGLF  454 (483)
Q Consensus       451 Pw~~  454 (483)
                      ||..
T Consensus        83 p~~~   86 (130)
T 2k4k_A           83 PEKK   86 (130)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            9863

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

Probab=99.60  E-value=1.5e-15  Score=126.74  Aligned_cols=77  Identities=23%  Similarity=0.235  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEecc-CcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHIS-NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiS-els~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      ..++|+++.|+|+ |++||+||+|.+. +++||+|+| +++|+++.++++.+ +||+|+|+|+++| +++||.||+|++.
T Consensus         8 ~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lslk~~~   85 (88)
T 1luz_A            8 LPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKRMC   85 (88)
T ss_dssp             CCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEEEC
T ss_pred             CCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEEeecC
Confidence            4689999999999 9999999999742 699999999 99999999999999 9999999999998 6899999999987


Q ss_pred             CC
Q 011538          449 SE  450 (483)
Q Consensus       449 ~d  450 (483)
                      +|
T Consensus        86 ~~   87 (88)
T 1luz_A           86 RH   87 (88)
T ss_dssp             SC
T ss_pred             CC
Confidence            75

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

Probab=99.56  E-value=1.7e-14  Score=117.68  Aligned_cols=74  Identities=27%  Similarity=0.451  Sum_probs=67.1

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE  450 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~d  450 (483)
                      ++++|+++.|+|++++++|+||+|++ +++||+|+|+++|.++    +.|++||.|+|+|++++ +++||.||+|++.+.
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~~-~~~Gllh~sel~~~~~----~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~~~~~   76 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLNE-QVRGLLRPRDMISLRL----ENLNVGDEIIVQAIDVRPEKREIDFKYIPLEHH   76 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEET-TEEEEECGGGCSSCCG----GGCCTTCEEEEEEEEEETTTTEEEEEECSCC--
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECC-CCEEEEEHHHCCcccc----eeeCCCCEEEEEEEEEECCCCEEEEEEeecccc
Confidence            47899999999999999999999998 7999999999998775    78999999999999998 569999999988764

>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=99.54  E-value=3.2e-15  Score=150.95  Aligned_cols=93  Identities=24%  Similarity=0.288  Sum_probs=87.4

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEEC--CCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIG--DSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~--~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      .+++|+++.|+|++|++||+||+|+  + +++||||+|+++|+++.++.+.|++||.|.|+|+++| ++++|.||+|++.
T Consensus        10 ~~~vG~iv~G~V~~I~~fGaFV~L~ey~-gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~~   88 (308)
T 1q8k_A           10 FPEVEDVVMVNVRSIQEMGAYVSLLEYN-NIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRVS   88 (308)
T ss_dssp             CCSSCCEEEEEEEEEETTEEEEESCTTT-SCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSSCC
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEECCCC-CeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEecc
Confidence            4579999999999999999999997  4 7999999999999999999999999999999999998 6899999999999


Q ss_pred             CCcCcccccccccceee
Q 011538          449 SEPGLFVSDKEVHIIFL  465 (483)
Q Consensus       449 ~dPw~~l~~k~~V~~~~  465 (483)
                      ++||..+.+++++++.+
T Consensus        89 ~~p~~~~~~~~~~G~~v  105 (308)
T 1q8k_A           89 PEEAIKCEDKFTKSKTV  105 (308)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             cChHHHHHHHccCCCee
Confidence            99999999999888765

>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=99.54  E-value=4.2e-17  Score=153.38  Aligned_cols=118  Identities=12%  Similarity=0.227  Sum_probs=96.2

Q ss_pred             hCCCeEEEEEEEEECCeEEEEE---CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh----
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----  366 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I---~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~----  366 (483)
                      +.|+++.|+|+++.++|+||++   +|++||||.|+| +.++.++.+.. .+||.|.|+|+++|+++++|.||+|+    
T Consensus        14 ~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~-~vGd~V~VkVl~vD~~~~rI~LSlk~~~~~   92 (182)
T 1kl9_A           14 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLI-RIGRNECVVVIRVDKEKGYIDLSKRRVSPE   92 (182)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC-------------CTTCEEEEEEEEEETTTTEEEEESTTCCHH
T ss_pred             CCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhc-CCCCEEEEEEEEEECCCCEEEEEEeecCcC
Confidence            6899999999999999999999   689999999999 77888888775 89999999999999999999999996    


Q ss_pred             Hhhh--cCCCCCcEEEEEEEEEeC-ceEEEEECCCceEEEEeccCcCcc-cccC
Q 011538          367 AWAT--LNLREGTLLEGTVKKIYP-YGAQIRIGDSNRSGLLHISNMSRT-RVTS  416 (483)
Q Consensus       367 ~~e~--~~l~vG~iv~G~V~~I~~-~GaFV~I~~~gi~GLlhiSels~~-~i~~  416 (483)
                      +|..  ..+..|+.+.|+|+++++ ||  |.|.+ |++||+|+++++|. ++.+
T Consensus        93 p~~~~~~~~~~g~~v~g~v~~i~~~~g--v~l~~-giegl~h~s~~~~~~~~~~  143 (182)
T 1kl9_A           93 EAIKCEDKFTKSKTVYSILRHVAEVLE--YTKDE-QLESLFQRTAWVFDDKYKR  143 (182)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTT--CCSHH-HHHHHHHHTHHHHHHHHTC
T ss_pred             hHHHHHHhccCCCEEEEEEEEchhhcC--CcccC-ChhheEEeeecchhhhcCC
Confidence            3542  478899999999999998 99  78877 89999999998876 3455

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

Probab=99.52  E-value=9.7e-15  Score=145.39  Aligned_cols=93  Identities=25%  Similarity=0.365  Sum_probs=86.0

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECC-CceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCC
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE  450 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~-~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~d  450 (483)
                      .++|+++.|+|++|++||+||+|++ .|++||||+|+++|+++.++.+.+++||.|.|+|+++| ++++|.||+|++.++
T Consensus         9 p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~~~~   88 (275)
T 3aev_A            9 PEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQQ   88 (275)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESTTCCHH
T ss_pred             CCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEEeecCcc
Confidence            4689999999999999999999973 27999999999999999999999999999999999998 689999999999999


Q ss_pred             cCcccccccccceee
Q 011538          451 PGLFVSDKEVHIIFL  465 (483)
Q Consensus       451 Pw~~l~~k~~V~~~~  465 (483)
                      ||....++++.++.+
T Consensus        89 ~~~~~~~~~~~g~~v  103 (275)
T 3aev_A           89 QRKAKLQEFKRAQKA  103 (275)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             hhHHHHHhccCCCeE
Confidence            999888888877654

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

Probab=99.52  E-value=2e-14  Score=123.87  Aligned_cols=83  Identities=24%  Similarity=0.352  Sum_probs=75.5

Q ss_pred             Hhhh--cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 011538          367 AWAT--LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (483)
Q Consensus       367 ~~e~--~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LS  443 (483)
                      +|+.  ..+++|+++.|+|++|+++|+||+|++ +++||||++++++.++.++.+.|++||.|+|+|++++ ++++|.||
T Consensus        21 p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~~-~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~~~~ki~LS   99 (109)
T 2khj_A           21 MFNNWVALNKKGAIVTGKVTAVDAKGATVELAD-GVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDRKNRAISLS   99 (109)
T ss_dssp             CHHHHTTTCCSSSEEEEEEEEECSSCEEEECST-TCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEETTTTEEEEE
T ss_pred             HHHHHhhcCCCCCEEEEEEEEEECCeEEEEECC-CCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEECCCCEEEEE
Confidence            4543  479999999999999999999999998 7999999999999999999999999999999999998 55799999


Q ss_pred             EecCCCC
Q 011538          444 IADLESE  450 (483)
Q Consensus       444 LK~~~~d  450 (483)
                      +|++.++
T Consensus       100 ~k~~~~~  106 (109)
T 2khj_A          100 VRAKDEA  106 (109)
T ss_dssp             TTSSSSC
T ss_pred             EeecChh
Confidence            9997653

>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=99.45  E-value=1.3e-14  Score=143.97  Aligned_cols=93  Identities=22%  Similarity=0.290  Sum_probs=86.1

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEEC--CCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIG--DSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADL  447 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~--~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~  447 (483)
                      ..+++|+++.|+|++|++||+||+|+  + +++||||+|+++|+++.++++.+++||.|.|+|++++ ++++|.||+|++
T Consensus         7 ~~~~vG~iv~G~V~~I~~~GaFV~l~e~~-~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~~   85 (266)
T 3cw2_C            7 KLPSEGEILIATVKQVFDYGSYVSLDEYG-GLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKKV   85 (266)
T ss_dssp             SSCCTTCEEEEEEEECCSSSBEEEETTTT-SEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEESTTS
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEEcCCC-CeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEEec
Confidence            35789999999999999999999997  5 7999999999999999999999999999999999998 589999999999


Q ss_pred             CCCcCccccccccccee
Q 011538          448 ESEPGLFVSDKEVHIIF  464 (483)
Q Consensus       448 ~~dPw~~l~~k~~V~~~  464 (483)
                      .++||..+.++++.++.
T Consensus        86 ~~~~~~~~~~~~~~~~~  102 (266)
T 3cw2_C           86 TDDERRKKNLQWKKIQR  102 (266)
T ss_dssp             CTTHHHHHHHHHHHHHH
T ss_pred             chhhHHHHHHhccccCc
Confidence            99999998888877653

>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=99.43  E-value=2.3e-15  Score=167.73  Aligned_cols=132  Identities=20%  Similarity=0.228  Sum_probs=50.3

Q ss_pred             EEEEE--EECCeEEEEECCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhhhcCCCCCcE
Q 011538          302 VKFTE--WNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTL  378 (483)
Q Consensus       302 GkV~~--v~k~G~fV~I~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e~~~l~vG~i  378 (483)
                      |++++  +.+.|++|+|+. +|.++.+.. +.......+       .+..           +  .  .+   ..+++|++
T Consensus       617 Gk~Ik~I~~~~G~~IdI~~-dG~v~Is~~~~~~~~~a~~-------~i~~-----------i--~--~p---~~~~vG~i  670 (757)
T 1e3p_A          617 RQMINQIQEDTGAEITIED-DGTIYIGAADGPAAEAARA-------TING-----------I--A--NP---TSPEVGER  670 (757)
T ss_dssp             ----CTTCCCCCSCC---------CCCBSSHHHHCC--------------------------------------------
T ss_pred             ceeeehhhHhhCCEEEecC-CceEEEecCCHHHHHHHHH-------HHHH-----------h--c--ch---hhcccccE
Confidence            55555  356799999975 888888877 222211100       0100           0  0  01   35789999


Q ss_pred             EEEEEEEEeCceEEEEECCCceEEEEeccCc----CcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCCcCcc
Q 011538          379 LEGTVKKIYPYGAQIRIGDSNRSGLLHISNM----SRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLF  454 (483)
Q Consensus       379 v~G~V~~I~~~GaFV~I~~~gi~GLlhiSel----s~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~dPw~~  454 (483)
                      +.|+|++|++||+||+|.+ |++||||+|++    +|+++.++++.|++||+|+|+|+++|.++||.||+|++.++||..
T Consensus       671 ~~G~V~~i~~fGaFV~l~~-g~eGLvHiSel~~~~s~~rv~~~~~~~~vGd~V~VkVi~vd~~grI~LS~k~~~~~pw~~  749 (757)
T 1e3p_A          671 ILGSVVKTTTFGAFVSLLP-GKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGKLSLIPVIEGEEAASD  749 (757)
T ss_dssp             --CBEEECC-CSCEECCC----CCCCC-------------------CCSSCBCCCCCCCCCSSCC---------------
T ss_pred             EEEEEEEccccEEEEEEcC-CcEEEEEhHHhccccCCCcccCcccccCCCCEEEEEEEEECCCCCEEEEEecCCCCchhh
Confidence            9999999999999999987 79999999999    999999999999999999999999988899999999999999998


Q ss_pred             cccccc
Q 011538          455 VSDKEV  460 (483)
Q Consensus       455 l~~k~~  460 (483)
                      ...+|+
T Consensus       750 ~~~~~~  755 (757)
T 1e3p_A          750 EKKDDA  755 (757)
T ss_dssp             ------
T ss_pred             hhhccc
Confidence            887764

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

Probab=99.38  E-value=3.5e-14  Score=157.25  Aligned_cols=90  Identities=32%  Similarity=0.441  Sum_probs=0.0

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESE  450 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~d  450 (483)
                      ..+++|++|.|+|++|++||+||+|.+ +++||||+|+++|+++.++.+.|++||.|+|+|+++|.++||.||+|++.++
T Consensus       633 ~~~~vG~v~~G~V~~I~~fGaFVel~~-g~eGLvHiSels~~rv~~~~d~~kvGD~V~VkVi~iD~~grI~LS~K~~~~~  711 (726)
T 4aid_A          633 DEAEVGKIYDGKVVKVVDFGAFVNFFG-AKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMKVVDQE  711 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhcCCcEEEEEEEEEeccEEEEEECC-CcEEEEEHHHcCcccccCccccCCCCCEEEEEEEEECCCCcEEEEEeecccC
Confidence            478999999999999999999999988 7999999999999999999999999999999999998889999999999999


Q ss_pred             cCccccccccc
Q 011538          451 PGLFVSDKEVH  461 (483)
Q Consensus       451 Pw~~l~~k~~V  461 (483)
                      ||+.+.+|.++
T Consensus       712 ~G~~~~~k~~~  722 (726)
T 4aid_A          712 TGEDLSKKEAA  722 (726)
T ss_dssp             -----------
T ss_pred             cchhhhhhhhh
Confidence            99999888765

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

Probab=99.29  E-value=2.4e-13  Score=150.92  Aligned_cols=91  Identities=29%  Similarity=0.462  Sum_probs=0.0

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESE  450 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~d  450 (483)
                      .++++|++|.|+|++|++||+||+|.+ |++||||+|+++|+|+.++++.|++||.|+|+|+++|.++||.||+|++.++
T Consensus       623 ~~~~vG~i~~G~V~~i~~fGaFVel~~-g~eGLvHiSel~~~~v~~~~~~~~vGd~V~VkVi~vd~~grI~LS~k~~~~~  701 (723)
T 3cdi_A          623 AEIEVGRVYTGKVTRIVDFGAFVAIGG-GKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEATEQ  701 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhcCcEEEEEEEEEecceEEEEeCC-CceEEEEHHHcCCccccCcccccCCCCEEEEEEEEECCCCcEEEEEEeccCC
Confidence            368999999999999999999999987 7999999999999999999999999999999999998889999999999999


Q ss_pred             cCcccccccccc
Q 011538          451 PGLFVSDKEVHI  462 (483)
Q Consensus       451 Pw~~l~~k~~V~  462 (483)
                      ||..++.....+
T Consensus       702 ~g~~~~p~~~~~  713 (723)
T 3cdi_A          702 SQPAAAPEAPAA  713 (723)
T ss_dssp             ------------
T ss_pred             CCcccCccccch
Confidence            999887665544

>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=99.25  E-value=4.2e-13  Score=125.36  Aligned_cols=96  Identities=13%  Similarity=0.284  Sum_probs=79.7

Q ss_pred             hCCCeEEEEEEEEECCeEEEEE---CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh----
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----  366 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I---~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~----  366 (483)
                      +.|+++.|+|+++.++|+||++   +|++||||.|++ +.++.++.+.. .+||.|.|+|+++|+++++|.||+|+    
T Consensus        14 ~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~-~vGd~V~vkVl~vd~~~~~I~LSlk~~~~~   92 (175)
T 2a19_A           14 EIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLI-RVGKNDVAVVLRVDKEKGYIDLSKRRVSSE   92 (175)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--------CCCCCC-CTTSEEEEEEEEEETTTTEEEEESTTCCHH
T ss_pred             CCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcC-CCCCEEEEEEEEEECCCCeEEEEEEecCcC
Confidence            4899999999999999999999   689999999999 77787877765 89999999999999999999999996    


Q ss_pred             Hhhh--cCCCCCcEEEEEEEEEe-CceE
Q 011538          367 AWAT--LNLREGTLLEGTVKKIY-PYGA  391 (483)
Q Consensus       367 ~~e~--~~l~vG~iv~G~V~~I~-~~Ga  391 (483)
                      +|..  ..++.|+.+.|+|++++ ++|+
T Consensus        93 ~~~~~~~~~~~g~~v~g~V~~i~~~~G~  120 (175)
T 2a19_A           93 DIIKCEEKYQKSKTVHSILRYCAEKFQI  120 (175)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHhccCCCcceEEEEEchhhcCC
Confidence            4542  46889999999999998 7887

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

Probab=99.25  E-value=8e-12  Score=107.57  Aligned_cols=89  Identities=17%  Similarity=0.214  Sum_probs=73.4

Q ss_pred             EehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEE
Q 011538          277 STRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRIN  354 (483)
Q Consensus       277 S~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID  354 (483)
                      |+|++. ..+|+.+...++.|+++.|+|+++.++|+||+++ |+.||||.+++ +.++.++.+.. .+||.|.|+|+++|
T Consensus        13 ~iKq~~-~~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~~-~vGd~V~v~V~~vd   90 (109)
T 2khj_A           13 GLVPRG-SHMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVL-SVGDEVEAKFTGVD   90 (109)
T ss_dssp             ---------CHHHHTTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSSSGGGSC-CTTCEEEEEEEEEE
T ss_pred             chhhcc-cCHHHHHhhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccccChhhcc-CCCCEEEEEEEEEE
Confidence            445544 4599998888999999999999999999999996 89999999999 66666666654 89999999999999


Q ss_pred             CCCCceeechhhH
Q 011538          355 EDTNDLILSEREA  367 (483)
Q Consensus       355 ~e~~rLiLS~K~~  367 (483)
                      ++++++.||+|..
T Consensus        91 ~~~~ki~LS~k~~  103 (109)
T 2khj_A           91 RKNRAISLSVRAK  103 (109)
T ss_dssp             TTTTEEEEETTSS
T ss_pred             CCCCEEEEEEeec
Confidence            9888999999864

>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=99.22  E-value=1.1e-11  Score=108.26  Aligned_cols=80  Identities=25%  Similarity=0.302  Sum_probs=66.9

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCc-CcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNM-SRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSel-s~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      .++++|+++.|+|++|++||+||+|+..+..|++|.+++ +|.++.++.+.|++||.|+|+|++++ ++++|.||+|+..
T Consensus        17 ~~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~Lslk~~~   96 (119)
T 1wi5_A           17 EALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSE   96 (119)
T ss_dssp             TTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCCC
T ss_pred             hcCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCCCCEEEEEEchhh
Confidence            478999999999999999999999983256777666664 35556688999999999999999998 6789999999765


Q ss_pred             CC
Q 011538          449 SE  450 (483)
Q Consensus       449 ~d  450 (483)
                      -.
T Consensus        97 l~   98 (119)
T 1wi5_A           97 VS   98 (119)
T ss_dssp             SC
T ss_pred             cc
Confidence            43

>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=99.20  E-value=2.2e-11  Score=114.13  Aligned_cols=84  Identities=23%  Similarity=0.365  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc-----------CcccccCCCCEEEEEEEEEe-CC--
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FP--  437 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~-----------~~~~~~kvGd~VkVkVi~vd-ek--  437 (483)
                      ..++|+++.|+|++++++|+||++++  .+||+|+|+++++++.           ++.+.|++||.|+|+|++++ ++  
T Consensus        78 ~~~~Gev~~G~V~~v~~~G~fV~l~~--~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~  155 (187)
T 1go3_E           78 IPEMYELIEGEVVDVVEFGSFVRLGP--LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAER  155 (187)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECSS--SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC--
T ss_pred             ccCCCCEEEEEEEEEeCcEEEEEEcC--ccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccCC
Confidence            46799999999999999999999974  8999999999988775           78899999999999999998 33  


Q ss_pred             ---CeEEEEEecCCCCcCccccc
Q 011538          438 ---DKISLSIADLESEPGLFVSD  457 (483)
Q Consensus       438 ---~rI~LSLK~~~~dPw~~l~~  457 (483)
                         ++|.||+|+...-|+..+..
T Consensus       156 p~~~~I~lS~k~~~LG~~~w~~~  178 (187)
T 1go3_E          156 KRGSKIALTMRQPYLGKLEWIEE  178 (187)
T ss_dssp             ---CEEEEECCSTTCEEHHHHHH
T ss_pred             CCccEEEEEEcCCCCCcHHHHhh
Confidence               49999999976656554544

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

Probab=99.15  E-value=5.8e-11  Score=137.86  Aligned_cols=77  Identities=8%  Similarity=0.119  Sum_probs=72.7

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccc-ccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR-VTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~-i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      ..+++|+++.|+|++|++||+||+|+. |++||||+|+|+|++ +.++.+.|++||.|+|+|+++| +++||.||||...
T Consensus       898 ~~l~~G~iv~G~V~~V~~fGaFV~L~~-gveGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~d  976 (1219)
T 3psi_A          898 KTFFKGSIIPVRVERFWHNDIICTTNS-EVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDHD  976 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECSSCEEEECTT-SCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEECCHHH
T ss_pred             hhCCCCCEEEEEEEEEecceEEEEeCC-CceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEecHHH
Confidence            478999999999999999999999987 899999999999998 8999999999999999999998 8899999999654

>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=99.14  E-value=2e-12  Score=130.58  Aligned_cols=99  Identities=13%  Similarity=0.256  Sum_probs=88.4

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC---CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh----
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----  366 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~---Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~----  366 (483)
                      +.|+++.|+|+++.++|+||+++   |+.||||.|++ +.++.++.+.. ++||.|.|+|+++|++++++.||+|.    
T Consensus        12 ~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~-kvGd~V~VkVl~vD~~~~rI~LSlK~~~~~   90 (308)
T 1q8k_A           12 EVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLI-RIGRNECVKVIRVDKEKGYIDLSKRRVSPE   90 (308)
T ss_dssp             SSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTC-SSSCEEEEEEEEEETTTTEEEEECSSCCHH
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccccCHHHhc-CCCCEEEEEEEEEeCCCCEEEEEEEecccC
Confidence            58999999999999999999994   79999999999 77788887765 89999999999999999999999985    


Q ss_pred             Hhhh--cCCCCCcEEEEEEEEEeC-ceEEEE
Q 011538          367 AWAT--LNLREGTLLEGTVKKIYP-YGAQIR  394 (483)
Q Consensus       367 ~~e~--~~l~vG~iv~G~V~~I~~-~GaFV~  394 (483)
                      +|..  ..+++|+++.|+|+++.+ ||+|++
T Consensus        91 p~~~~~~~~~~G~~v~G~V~~v~~~~G~fi~  121 (308)
T 1q8k_A           91 EAIKCEDKFTKSKTVYSILRHVAEVLEYTKD  121 (308)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCCSS
T ss_pred             hHHHHHHHccCCCeeEEEEEEcccccCCccC
Confidence            4543  368899999999999998 699864

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

Probab=99.14  E-value=9e-11  Score=109.44  Aligned_cols=84  Identities=19%  Similarity=0.363  Sum_probs=69.3

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc-----------cCcccccCCCCEEEEEEEEEe-C---
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-F---  436 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i-----------~~~~~~~kvGd~VkVkVi~vd-e---  436 (483)
                      +..+|++++|+|++++++|+||++++  .+||+|+++++++++           ++..+.+++||.|+|||++++ +   
T Consensus        78 ~p~~Gev~~G~V~~v~~~G~fv~l~~--~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~~~  155 (180)
T 4ayb_E           78 VPVVQEVVEGEVLQVDNYGVFVNLGP--MDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTG  155 (180)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECSS--SEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC----
T ss_pred             eccCCCEEEEEEeeeccceEEEEECC--ccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCCCCc
Confidence            46799999999999999999999974  799999999999877           577889999999999999997 2   


Q ss_pred             -CCeEEEEEecCCCCcCccccc
Q 011538          437 -PDKISLSIADLESEPGLFVSD  457 (483)
Q Consensus       437 -k~rI~LSLK~~~~dPw~~l~~  457 (483)
                       ..||.||||+...-|++.+++
T Consensus       156 ~~~rI~ls~k~~gLG~~~W~~~  177 (180)
T 4ayb_E          156 RLPRIALTMRQPYLGKLEWITQ  177 (180)
T ss_dssp             ---CEEEECCSTTCEEHHHHTT
T ss_pred             ccCcEEEEcCCCCCCCChhHhh
Confidence             359999999855444333443

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

Probab=99.09  E-value=1.2e-10  Score=97.00  Aligned_cols=70  Identities=13%  Similarity=0.225  Sum_probs=63.1

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC---CeEEEeecc-cc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKA-EL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~---Gi~gFVP~S-el-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      +.|++++|+|+ +.++|+||+++   |++||+|.| ++ ++++.++++..  +||+|+++|+++|++++++.||+|+.
T Consensus        10 ~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~--~Gd~V~VkV~~vd~~~~kI~lslk~~   84 (88)
T 1luz_A           10 NAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL--VGKTVKVKVIRVDYTKGYIDVNYKRM   84 (88)
T ss_dssp             CTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH--TTCEEEEEEEEEETTTTEEEEEEEEE
T ss_pred             CCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHEe--CCCEEEEEEEEEECCCCEEEEEEeec
Confidence            68999999999 99999999994   799999999 99 66776777764  99999999999999999999999864

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

Probab=99.09  E-value=7.8e-11  Score=102.44  Aligned_cols=89  Identities=16%  Similarity=0.224  Sum_probs=69.8

Q ss_pred             EehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-c-cccCChhhhhhhcCCEEEEEEEEE
Q 011538          277 STRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-L-SRVNNFTELKEKVGRRMYVQITRI  353 (483)
Q Consensus       277 S~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~-~rv~~~~~l~~~VGq~V~vkVl~I  353 (483)
                      |+|... ...|..+...++.|+++.|+|+++.++|+||+++ |+.||||.+++ + .+..++.+.. .+||.|+|+|+++
T Consensus        12 ~~k~~~-~~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~-~vGd~V~vkV~~v   89 (115)
T 2khi_A           12 SGLVPR-GSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVV-NVGDVVEVMVLDI   89 (115)
T ss_dssp             ----------CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTTC-CTTCEEEEEEEEE
T ss_pred             chhhcc-cCCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccEE-CCCCEEEEEEEEE
Confidence            344433 4578777667899999999999999999999995 79999999999 4 2555555544 8999999999999


Q ss_pred             ECCCCceeechhhH
Q 011538          354 NEDTNDLILSEREA  367 (483)
Q Consensus       354 D~e~~rLiLS~K~~  367 (483)
                      |.++++|.||+|..
T Consensus        90 d~~~~rI~lslk~~  103 (115)
T 2khi_A           90 DEERRRISLGLKQC  103 (115)
T ss_dssp             ETTTTEEEECCCCC
T ss_pred             ECCCCEEEEEEEec
Confidence            99899999999863

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

Probab=99.08  E-value=5.6e-10  Score=99.21  Aligned_cols=75  Identities=20%  Similarity=0.259  Sum_probs=67.6

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhh
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA  369 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e  369 (483)
                      ++.|+++.|+|+++.++|+||++ +|+.||||.+++ +.++.++.+.. .+||.|.|+|+++|.++++|.||++....
T Consensus         5 ~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~~~~~~~~-~vGd~V~vkV~~vd~~~~kI~LSlk~~~~   81 (130)
T 2k4k_A            5 FEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHL-SVGDEVQVKVLAVDEEKGKISLSIRATQA   81 (130)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCCSCGGGTC-CTTCEEEEEEEEEETTTTEEEEESHHHHH
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccccCccccC-CCCCEEEEEEEEEeCCCCEEEEEEeeccc
Confidence            57899999999999999999999 689999999999 67777777654 89999999999999989999999998654

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

Probab=99.06  E-value=5.7e-11  Score=132.87  Aligned_cols=76  Identities=32%  Similarity=0.530  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      ++++|+++.|+|++|++||+||+|+. +++||||+|+|+|.++.++.+.|++||.|+|+|+++| ++++|.||+|...
T Consensus       651 ~l~vG~iv~G~V~~V~~fGaFV~l~~-~~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~LSlk~~~  727 (785)
T 3bzc_A          651 DLKPGMVLEGVVTNVTNFGAFVDIGV-HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMSD  727 (785)
T ss_dssp             TCCTTCBCCCEEEEEETTEEEEECSS-SSEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEECCSSCC
T ss_pred             hcCCCCEEEEEEEEEecCCeEEEeCC-CcEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEEEecCC
Confidence            68899999999999999999999987 7999999999999999999999999999999999998 7899999999654

>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2

Probab=99.05  E-value=2.8e-10  Score=109.07  Aligned_cols=77  Identities=17%  Similarity=0.127  Sum_probs=68.9

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECC-------CceEEEEeccCcCccccc--CcccccCCCCEEEEEEEEEeC-CCeEE
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGD-------SNRSGLLHISNMSRTRVT--SVSDLLNEGERVKVLVVKSMF-PDKIS  441 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~-------~gi~GLlhiSels~~~i~--~~~~~~kvGd~VkVkVi~vde-k~rI~  441 (483)
                      .+++|++|.|+|++|+++|+||+|.+       .+.+|+||++|+++.+..  ++.+.|++||.|.|+|+++++ ++++.
T Consensus        78 ~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i~  157 (209)
T 2nn6_I           78 LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYL  157 (209)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEE
T ss_pred             CCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeEE
Confidence            57899999999999999999999852       157999999999999888  999999999999999999975 45899


Q ss_pred             EEEecCC
Q 011538          442 LSIADLE  448 (483)
Q Consensus       442 LSLK~~~  448 (483)
                      ||+|+..
T Consensus       158 LS~k~~~  164 (209)
T 2nn6_I          158 LTTAENE  164 (209)
T ss_dssp             EECCSSS
T ss_pred             EEEecCC
Confidence            9999754

>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=99.04  E-value=1.1e-10  Score=102.39  Aligned_cols=81  Identities=15%  Similarity=0.239  Sum_probs=69.3

Q ss_pred             hhHHHHHHhhCCCeEEEEEEEEECCeEEEEECC--eEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCC--Cce
Q 011538          286 AWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEG--LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDT--NDL  360 (483)
Q Consensus       286 ~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~G--i~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~--~rL  360 (483)
                      .|+.+....+.|+++.|+|+++.++|+||+++|  +.||||.+++ +.++.++.+.. .+||.|.|+|+++|..+  ++|
T Consensus        12 ~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~-~~Gd~V~VkV~~vd~~~~~~~i   90 (119)
T 2cqo_A           12 RPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIV-DVGDKVWVKLIGREMKNDRIKV   90 (119)
T ss_dssp             CCCCSCCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHC-CTTCEEEEEEEEEEECSSCEEE
T ss_pred             chhhhhcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhhcC-CCCCEEEEEEEEEeccccCceE
Confidence            455555567899999999999999999999976  4999999999 67777777764 89999999999999754  699


Q ss_pred             eechhhH
Q 011538          361 ILSEREA  367 (483)
Q Consensus       361 iLS~K~~  367 (483)
                      .||+|..
T Consensus        91 ~LSlk~~   97 (119)
T 2cqo_A           91 SLSMKVV   97 (119)
T ss_dssp             EEESTTB
T ss_pred             EEEEeec
Confidence            9999974

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

Probab=99.04  E-value=6.1e-10  Score=90.54  Aligned_cols=69  Identities=13%  Similarity=0.175  Sum_probs=60.7

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      ++.|+++.|+|+++.++|+||+++ ++.||+|.|++ +.++   +.  ..+||.|+|+|+++|++++++.||+++.
T Consensus         3 ~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel~~~~~---~~--~~~Gd~V~v~V~~vd~~~~~i~lsl~~~   73 (80)
T 2k52_A            3 VEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRL---EN--LNVGDEIIVQAIDVRPEKREIDFKYIPL   73 (80)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSCCG---GG--CCTTCEEEEEEEEEETTTTEEEEEECSC
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCcccc---ee--eCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence            468999999999999999999996 89999999999 4443   22  2799999999999999889999999865

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

Probab=99.01  E-value=3.2e-11  Score=138.07  Aligned_cols=78  Identities=8%  Similarity=0.113  Sum_probs=0.0

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccc-ccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR-VTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~-i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      ..+++|+++.|+|++|++||+||+|+. |++||||+|+|++.+ +.++.+.|++||.|+|+|+++| +++||.||||+..
T Consensus       901 ~~l~~G~iv~G~V~~V~~fGaFV~L~~-gveGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~d  979 (1030)
T 3psf_A          901 KTFFKGSIIPVRVERFWHNDIICTTNS-EVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDHD  979 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHhcCCCEEEEEEEEEccCeEEEEeCC-CcEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEechHH
Confidence            478999999999999999999999987 899999999999998 8999999999999999999998 8899999999765


Q ss_pred             C
Q 011538          449 S  449 (483)
Q Consensus       449 ~  449 (483)
                      -
T Consensus       980 l  980 (1030)
T 3psf_A          980 V  980 (1030)
T ss_dssp             -
T ss_pred             h
Confidence            3

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

Probab=99.01  E-value=5.4e-10  Score=104.53  Aligned_cols=72  Identities=25%  Similarity=0.359  Sum_probs=65.9

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCC---------ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDS---------NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL  442 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~---------gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~L  442 (483)
                      ..+ |++|.|+|++|+++|+||+|...         +.+|+||+|++++.++.++.+.|++||.|.|+|++    +++.|
T Consensus        55 ~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~----~~i~L  129 (179)
T 3m7n_A           55 IVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG----DNLRL  129 (179)
T ss_dssp             CCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE----TTTEE
T ss_pred             cCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC----CeEEE
Confidence            357 99999999999999999999752         58999999999999999999999999999999996    89999


Q ss_pred             EEecCC
Q 011538          443 SIADLE  448 (483)
Q Consensus       443 SLK~~~  448 (483)
                      |+|+..
T Consensus       130 S~k~~~  135 (179)
T 3m7n_A          130 STKEEE  135 (179)
T ss_dssp             ECCSTT
T ss_pred             EEecCC
Confidence            999743

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

Probab=98.99  E-value=5.1e-11  Score=118.60  Aligned_cols=100  Identities=16%  Similarity=0.268  Sum_probs=87.4

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC---CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh---
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE---  366 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~---Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~---  366 (483)
                      .+.|+++.|+|+++.++|+||+++   |+.||||.|++ +.++.++.+.. .+||.|.|+|+++|++++++.||+|.   
T Consensus         9 p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~-kvGd~V~vkVi~vD~~~~~I~LSlk~~~~   87 (275)
T 3aev_A            9 PEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYL-KEGQKVVAKVIRVDPRKGHIDLSLRRVTQ   87 (275)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTC-CTTCEEEEEEEEEETTTTEEEEESTTCCH
T ss_pred             CCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhcc-CCCCEEEEEEEEEECCCCEEEEEEeecCc
Confidence            358999999999999999999995   89999999999 67788887765 89999999999999999999999986   


Q ss_pred             -Hhhh--cCCCCCcEEEEEEEEEe-CceEEEE
Q 011538          367 -AWAT--LNLREGTLLEGTVKKIY-PYGAQIR  394 (483)
Q Consensus       367 -~~e~--~~l~vG~iv~G~V~~I~-~~GaFV~  394 (483)
                       +|..  ..++.|+.+.|+|..+. ++|++++
T Consensus        88 ~~~~~~~~~~~~g~~v~g~v~~v~~~~G~~~e  119 (275)
T 3aev_A           88 QQRKAKLQEFKRAQKAENLLRLAAEKLGKDFE  119 (275)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTCCHH
T ss_pred             chhHHHHHhccCCCeEEEEEEEchhhcCCCHH
Confidence             3432  36788999999999998 8888665

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.96  E-value=2e-09  Score=91.73  Aligned_cols=71  Identities=20%  Similarity=0.277  Sum_probs=62.7

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC----CeEEEeecccc-c-cccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE----GLRAFLPKAEL-L-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~----Gi~gFVP~Sel-~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      .+.|+++.|+|+++.++|+||+++    ++.||||.|++ + .++.++.+.. .+||.|+|+|+++|+  ++|.||+|..
T Consensus        10 ~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~-~~Gd~V~VkV~~vd~--~~i~LSlk~~   86 (103)
T 2eqs_A           10 PTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVV-SKGQRVKVKVLSFTG--TKTSLSMKDV   86 (103)
T ss_dssp             CCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHC-CTTCEEEEEEEEEET--TEEEEESTTB
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEe-CCCCEEEEEEEEEEC--CeeEEEEeec
Confidence            578999999999999999999997    79999999999 4 4566776654 899999999999996  5999999974

>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=98.92  E-value=2.3e-09  Score=103.18  Aligned_cols=83  Identities=16%  Similarity=0.170  Sum_probs=65.2

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCc----------ccccCCCCEEEEEEEEEe-CC---
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSV----------SDLLNEGERVKVLVVKSM-FP---  437 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~----------~~~~kvGd~VkVkVi~vd-ek---  437 (483)
                      ..++|++++|+|++|+++|+||+++.  .+||+|+|+|++.+.-++          .+.+++||.|+|+|++++ ++   
T Consensus        80 ~p~vGev~~G~V~~vt~fG~FVelg~--~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~~i  157 (215)
T 2b8k_G           80 KPFKGEVVDGTVVSCSQHGFEVQVGP--MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSI  157 (215)
T ss_dssp             CCCTTEEEEEEEEEEETTEEEEECTT--SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETTEE
T ss_pred             ccCCCCEEEEEEEEEecceEEEEecC--cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcCCCcc
Confidence            35799999999999999999999975  799999999986533222          267999999999999998 44   


Q ss_pred             CeEEEEEecCCCCcCccccc
Q 011538          438 DKISLSIADLESEPGLFVSD  457 (483)
Q Consensus       438 ~rI~LSLK~~~~dPw~~l~~  457 (483)
                      .+|. |||+...-||+....
T Consensus       158 ~~Ig-Smk~~~LG~~~~~~~  176 (215)
T 2b8k_G          158 HAIG-SIKEDYLGAISHEKR  176 (215)
T ss_dssp             EEEE-ECCSTTCEEC-----
T ss_pred             EEEE-EcCCCCCCCcchhhH
Confidence            3777 999887777764443

>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=98.92  E-value=1.1e-09  Score=106.66  Aligned_cols=75  Identities=16%  Similarity=0.186  Sum_probs=67.8

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc----cccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT----RVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~----~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~  447 (483)
                      .+++|++|.|+|+++.++|+||+|+. ..+|+||+++++..    +..++++.|++||.|.|+|+++++.+++.||+|+.
T Consensus        63 ~p~~GDiV~G~V~~v~~~~~~V~I~~-~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k~~  141 (235)
T 2z0s_A           63 VPQAGDVVIGLIQSVGIMNWFVDINS-PYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGE  141 (235)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECSS-SSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSS
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECCCCcEEEEEecc
Confidence            57899999999999999999999987 68999999999863    45778889999999999999998777999999864

>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=98.89  E-value=1.8e-09  Score=106.17  Aligned_cols=75  Identities=17%  Similarity=0.162  Sum_probs=69.3

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc---cCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV---TSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i---~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~  447 (483)
                      ..++|++|.|+|+++.++|+||+|++ ..+|+||++++++.+.   .++++.|++||.|.|+|+++++.+++.||+|+.
T Consensus        71 ~p~~GDiV~G~V~~v~~~ga~VdI~~-~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r~~  148 (251)
T 2je6_I           71 YPKINDIVIGLVEDVEIYGWVVDIKA-PYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGK  148 (251)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSS-SSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCST
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEcCC-CeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECCCCcEEEEEccc
Confidence            46899999999999999999999987 6899999999998877   888999999999999999998778999999864

>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=98.85  E-value=7.1e-09  Score=95.97  Aligned_cols=72  Identities=18%  Similarity=0.288  Sum_probs=56.9

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc----cCc------ccccCCCCEEEEEEEEEe-CCC--
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----TSV------SDLLNEGERVKVLVVKSM-FPD--  438 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i----~~~------~~~~kvGd~VkVkVi~vd-ek~--  438 (483)
                      ...+|++++|+|+++++||+||+++.  .+||+|+|+|++.+.    .++      ++.+++||.|+|||++++ +++  
T Consensus        80 ~~~~Gev~~G~V~~v~~fG~FV~l~~--~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~~  157 (171)
T 1y14_B           80 KPFKGEVVDGTVVSCSQHGFEVQVGP--MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSI  157 (171)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETT--EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTEE
T ss_pred             cCCCCCEEEEEEEEEecCEEEEEecC--eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEEcCCCCc
Confidence            35699999999999999999999985  899999999975422    111      267999999999999998 443  


Q ss_pred             -eEEEEEec
Q 011538          439 -KISLSIAD  446 (483)
Q Consensus       439 -rI~LSLK~  446 (483)
                       ++. ||++
T Consensus       158 ~~ig-sm~~  165 (171)
T 1y14_B          158 HAIG-SIKE  165 (171)
T ss_dssp             EEEE-ECCS
T ss_pred             EEEE-EcCC
Confidence             444 5553

>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=98.84  E-value=7.5e-09  Score=100.39  Aligned_cols=75  Identities=16%  Similarity=0.238  Sum_probs=68.8

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc-cccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~-~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~  447 (483)
                      ..++||+|.|+|+++.++|+||+|+. ...|+||+++++.. +..++++.|++||.|.|+|+++++++++.||+|+.
T Consensus        54 ~p~~GDiV~G~V~~v~~~~a~V~I~~-~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~~  129 (229)
T 2ba0_A           54 TPSVGDVVIGIIREVAANGWAVDIYS-PYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDR  129 (229)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSS-SSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCSS
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECCCCcEEEEEccc
Confidence            46899999999999999999999987 58999999999964 67889999999999999999998778999999874

>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=8e-09  Score=95.58  Aligned_cols=71  Identities=14%  Similarity=0.259  Sum_probs=57.3

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc----c--------CcccccCCCCEEEEEEEEEe-CCC-
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----T--------SVSDLLNEGERVKVLVVKSM-FPD-  438 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i----~--------~~~~~~kvGd~VkVkVi~vd-ek~-  438 (483)
                      ..+|++++|+|++++++|+||+++.  .+||+|+|+|++.+.    .        +....+++||.|+|||+++| +++ 
T Consensus        79 ~~~Gev~~G~V~~v~~fG~fV~l~~--~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~  156 (172)
T 2c35_B           79 PFKGEVVDAVVTQVNKVGLFTEIGP--MSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKND  156 (172)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETT--EEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTE
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEECC--EEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCCCC
Confidence            3589999999999999999999974  679999999975422    2        12557999999999999998 444 


Q ss_pred             --eEEEEEec
Q 011538          439 --KISLSIAD  446 (483)
Q Consensus       439 --rI~LSLK~  446 (483)
                        ++. |||+
T Consensus       157 ~~~ig-sm~~  165 (172)
T 2c35_B          157 IFAIG-SLMD  165 (172)
T ss_dssp             EEEEE-ECCS
T ss_pred             cEEEE-EecC
Confidence              555 7765

>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=98.75  E-value=6.3e-09  Score=106.37  Aligned_cols=109  Identities=17%  Similarity=0.179  Sum_probs=80.4

Q ss_pred             CcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhH----HHHHHhh--CCCeEEEEEEEEECCeEEEEECCeEEEeecc
Q 011538          253 PVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWH----RVRQIKQ--LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKA  326 (483)
Q Consensus       253 ~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~----~L~~~~k--~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~S  326 (483)
                      +.+++||.+.+.|...+.++....+.|+....+..+    .+.+.++  .|++|+|+|.++.++|++|++|+++|+||.+
T Consensus        85 ~~~~vGd~ie~~I~~~dfgR~aa~~aKqvi~qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~v~VDlGk~EgiLp~s  164 (344)
T 1hh2_P           85 PLAEVGSIVKKELNVKNFGRIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIGKLETRLPKK  164 (344)
T ss_dssp             TTCCTTCEEEEECCCCCSSSCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEETTEEEEEEGG
T ss_pred             ccccCCCEEEEEEccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCcEEEEeCCeEEEEeHH
Confidence            347899999999876554444445556554322111    1223333  8999999999999999999999999999999


Q ss_pred             ccccccCChhhhhhhcCCEEEEEEEEEECCC--CceeechhhH
Q 011538          327 ELLSRVNNFTELKEKVGRRMYVQITRINEDT--NDLILSEREA  367 (483)
Q Consensus       327 el~~rv~~~~~l~~~VGq~V~vkVl~ID~e~--~rLiLS~K~~  367 (483)
                      ++..     .+. +.+|++|+|+|+++++.+  .++.|||+.+
T Consensus       165 E~ip-----~E~-~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p  201 (344)
T 1hh2_P          165 EWIP-----GEE-IKAGDLVKVYIIDVVKTTKGPKILVSRRVP  201 (344)
T ss_dssp             GSCT-----TCC-CCTTCEEEEEEEEEEEETTEEEEEEESSSH
T ss_pred             HcCC-----CcC-CCCCCEEEEEEEEEEcCCCCcEEEEEeecc
Confidence            9941     122 269999999999999654  3899999854

>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=98.71  E-value=3.1e-08  Score=101.24  Aligned_cols=104  Identities=16%  Similarity=0.144  Sum_probs=78.3

Q ss_pred             hcCCEEEEEEEEEECCCCceeechhhHh-h----------hcC--CCCCcEEEEEEEEEeCceEEEEECCCceEEEEecc
Q 011538          341 KVGRRMYVQITRINEDTNDLILSEREAW-A----------TLN--LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHIS  407 (483)
Q Consensus       341 ~VGq~V~vkVl~ID~e~~rLiLS~K~~~-e----------~~~--l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiS  407 (483)
                      .+|+.+.+.|...|.. ++...+.|+.+ +          ...  .++|+++.|+|.+++++|+||+++  +.+|+||.+
T Consensus        88 ~vGd~ie~~I~~~dfg-R~aa~~aKqvi~qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~v~VDlG--k~EgiLp~s  164 (344)
T 1hh2_P           88 EVGSIVKKELNVKNFG-RIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIG--KLETRLPKK  164 (344)
T ss_dssp             CTTCEEEEECCCCCSS-SCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEET--TEEEEEEGG
T ss_pred             cCCCEEEEEEccccCc-cHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCcEEEEeC--CeEEEEeHH
Confidence            6999999999877643 34455545432 1          023  348999999999999999999997  589999999


Q ss_pred             CcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCCCcCc
Q 011538          408 NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGL  453 (483)
Q Consensus       408 els~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~dPw~  453 (483)
                      |++      |.+.|++||+|+|.|++++ +++...+++....++...
T Consensus       165 E~i------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p~~lk  205 (344)
T 1hh2_P          165 EWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVI  205 (344)
T ss_dssp             GSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESSSHHHHH
T ss_pred             HcC------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEeeccHHHH
Confidence            996      5688999999999999997 455444444444444433

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

Probab=98.69  E-value=2.4e-08  Score=85.03  Aligned_cols=82  Identities=20%  Similarity=0.245  Sum_probs=64.0

Q ss_pred             hCCCeEEEEEEEEE---CCeEEEEE--CCeEEEeeccccc-cccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHh
Q 011538          295 QLNEPIEVKFTEWN---TGGLLTRI--EGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAW  368 (483)
Q Consensus       295 k~GeiV~GkV~~v~---k~G~fV~I--~Gi~gFVP~Sel~-~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~  368 (483)
                      +.++.++|+|+..+   .+| |+..  +|.++|+|.+.+. ..+                                    
T Consensus        12 ~~~~~~~G~Vk~fn~~kGfG-FI~~~~gg~dvfvH~s~l~~~~~------------------------------------   54 (101)
T 2bh8_A           12 LQSGKMTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAGSSGAA------------------------------------   54 (101)
T ss_dssp             ----CEEEEEEEEEGGGTEE-EEEESSSSCEEEEECCCSCSSSC------------------------------------
T ss_pred             cccccceeEEEEEECCCCCE-EEEeCCCCcEEEEEEEEEecCCc------------------------------------
Confidence            46778999999995   358 5554  4599999999983 211                                    


Q ss_pred             hhcCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc
Q 011538          369 ATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV  414 (483)
Q Consensus       369 e~~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i  414 (483)
                      ....+++|++|+++|.++++||+||+|.+ +++||||+|+++|.++
T Consensus        55 ~~~~l~~Ge~V~g~V~~i~~fG~fv~l~~-~~eGlvhis~i~~~~~   99 (101)
T 2bh8_A           55 VRGNPQQGDRVEGKIKSITDFGIFIGLDG-GIDGLVHLSDISWAQA   99 (101)
T ss_dssp             CCCCCCTTCEEEEEEEECCSEEEEECTTS-CEEEEEEEEEEEECCC
T ss_pred             cccCCCCCCEEEEEEEEeCCcEEEEEcCC-CceEEEEHHHCccCcC
Confidence            01257899999999999999999999987 7999999999999865

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

Probab=98.68  E-value=1.2e-08  Score=101.13  Aligned_cols=72  Identities=22%  Similarity=0.334  Sum_probs=66.1

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEE---CCeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I---~Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~  366 (483)
                      .+.|+++.|+|+++.++|+||++   +|+.||||.|++ +.++.++.+.. .+||.|.|+|+++|++++++.||+|.
T Consensus         9 ~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~~~~~~~-~vGd~V~VkVi~vd~~~g~I~LSlk~   84 (266)
T 3cw2_C            9 PSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVL-KENRKVIVKVIRVDRRKGTVDVSLKK   84 (266)
T ss_dssp             CCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCCCHHHHS-CTTCEEEEEECCCCSSSCCCBEESTT
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccccCHHHhC-cCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            47899999999999999999999   579999999999 77888887765 89999999999999889999999984

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

Probab=98.68  E-value=9.4e-09  Score=95.40  Aligned_cols=71  Identities=13%  Similarity=0.198  Sum_probs=58.0

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc----------CcccccCCCCEEEEEEEEEe-CCC--
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT----------SVSDLLNEGERVKVLVVKSM-FPD--  438 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~----------~~~~~~kvGd~VkVkVi~vd-ek~--  438 (483)
                      ...+|++++|+|++++++|+||+++.  .+||+|+|+|++.+.-          +..+.+++||.|+|||++++ +.+  
T Consensus        81 ~p~~Gev~~G~V~~v~~fG~FV~l~~--~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~~~~~~  158 (172)
T 3h0g_G           81 RPFRGEVVDAIVTTVNKMGFFANIGP--LNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDATEI  158 (172)
T ss_dssp             CCCTTCEEECCCCEEETTEEECCBTT--BCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEESSSCE
T ss_pred             ccCCCCEEEEEEEEEEcceEEEEeCC--eEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEECCCCCc
Confidence            35689999999999999999999974  6799999999765432          33578999999999999998 443  


Q ss_pred             -eEEEEEe
Q 011538          439 -KISLSIA  445 (483)
Q Consensus       439 -rI~LSLK  445 (483)
                       +|. |||
T Consensus       159 ~~Ig-tm~  165 (172)
T 3h0g_G          159 FAIA-TMK  165 (172)
T ss_dssp             EEEE-ECC
T ss_pred             eEEE-EcC
Confidence             455 555

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=98.66  E-value=1.4e-08  Score=88.47  Aligned_cols=74  Identities=22%  Similarity=0.253  Sum_probs=60.9

Q ss_pred             HhhCCCeEEEEEEEEECCeEEEEEC--CeEEEeecccc--ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          293 IKQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL--LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       293 ~~k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel--~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      .++.|++++|+|+++.++|+||+++  ++.||+|.+++  +.++.++.+.. .+||.|+|+|+++|++++++.||+++.
T Consensus        18 ~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~~~~~~~~~~~~-~~Gd~V~vkV~~vd~~~~~i~Lslk~~   95 (119)
T 1wi5_A           18 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKL-KVGQYLNCIVEKVKGNGGVVSLSVGHS   95 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCC-CTTCEEEEEEEECCTTSCEEEEECCCC
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccccccccCccCEe-CCCCEEEEEEEEEeCCCCEEEEEEchh
Confidence            3579999999999999999999997  68888888876  22222333433 799999999999999889999999864

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

Probab=98.61  E-value=5.1e-08  Score=91.19  Aligned_cols=73  Identities=16%  Similarity=0.242  Sum_probs=60.9

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccC-----------ChhhhhhhcCCEEEEEEEEEECCCC---
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVN-----------NFTELKEKVGRRMYVQITRINEDTN---  358 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~-----------~~~~l~~~VGq~V~vkVl~ID~e~~---  358 (483)
                      ...|+++.|+|+++.++|+||++++++||+|.|++ +.++.           +..+. ..+|+.|+|+|+++|...+   
T Consensus        79 ~~~Gev~~G~V~~v~~~G~fV~l~~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~-~~~Gd~V~vkV~~vd~~~~~p~  157 (187)
T 1go3_E           79 PEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKV-LEIGDYVRARIVAISLKAERKR  157 (187)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC--CEEETTTCCE-ECTTCEEEEEEEEEECCC----
T ss_pred             cCCCCEEEEEEEEEeCcEEEEEEcCccEEEEhHHhCCCcceECCccceEEecCCCeE-EcCCCEEEEEEEEEEcccCCCC
Confidence            46899999999999999999999889999999999 44432           33333 3799999999999998654   


Q ss_pred             --ceeechhhH
Q 011538          359 --DLILSEREA  367 (483)
Q Consensus       359 --rLiLS~K~~  367 (483)
                        ++.||++.+
T Consensus       158 ~~~I~lS~k~~  168 (187)
T 1go3_E          158 GSKIALTMRQP  168 (187)
T ss_dssp             -CEEEEECCST
T ss_pred             ccEEEEEEcCC
Confidence              999999863

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

Probab=98.56  E-value=8.5e-09  Score=114.41  Aligned_cols=100  Identities=11%  Similarity=0.050  Sum_probs=3.5

Q ss_pred             EcCCCcEEEEeh-HHH---HHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhh
Q 011538          268 RTLSGRPLLSTR-RLF---RKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEK  341 (483)
Q Consensus       268 ~d~~G~iiLS~k-~~~---~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~  341 (483)
                      ++.+|++.++.. +..   ....|+.+...++.|++++|+|+++.++|+||++ +|++||||.|++ +.++.++.+.. +
T Consensus       605 i~ddG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~~rv~~~~d~~-k  683 (726)
T 4aid_A          605 INDDGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVL-K  683 (726)
T ss_dssp             ---------CCSCHHHHHHHHHC---------------------------------------------------------
T ss_pred             EECCceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCcccccCccccC-C
Confidence            345677755443 221   2245677777789999999999999999999999 579999999999 77888888775 8


Q ss_pred             cCCEEEEEEEEEECCCCceeechhhHhh
Q 011538          342 VGRRMYVQITRINEDTNDLILSEREAWA  369 (483)
Q Consensus       342 VGq~V~vkVl~ID~e~~rLiLS~K~~~e  369 (483)
                      +||.|+|+|+++|+ +++|.||+|....
T Consensus       684 vGD~V~VkVi~iD~-~grI~LS~K~~~~  710 (726)
T 4aid_A          684 EGQMVKVKLLGFDD-RGKTKLSMKVVDQ  710 (726)
T ss_dssp             ----------------------------
T ss_pred             CCCEEEEEEEEECC-CCcEEEEEeeccc
Confidence            99999999999997 7899999997643

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

Probab=98.50  E-value=1.4e-08  Score=112.99  Aligned_cols=99  Identities=15%  Similarity=0.156  Sum_probs=0.0

Q ss_pred             EcCCCcEEEEehHHHH----HhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccCChhhhhhh
Q 011538          268 RTLSGRPLLSTRRLFR----KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEK  341 (483)
Q Consensus       268 ~d~~G~iiLS~k~~~~----~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~~~~~l~~~  341 (483)
                      .+.+|.+.++......    ...++.+....+.|++++|+|+++.++|+||++ +|++||||.|++ +.++.++.+.. +
T Consensus       595 I~~dg~v~I~~~~~~~~~~a~~~i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~~~~v~~~~~~~-~  673 (723)
T 3cdi_A          595 IEDDGTVKIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYL-Q  673 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ecCCccEEEecCCHHHHHHHHHHHHHHhhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCccccCccccc-C
Confidence            3456777766543322    234555556678999999999999999999999 479999999999 77888877765 8


Q ss_pred             cCCEEEEEEEEEECCCCceeechhhHh
Q 011538          342 VGRRMYVQITRINEDTNDLILSEREAW  368 (483)
Q Consensus       342 VGq~V~vkVl~ID~e~~rLiLS~K~~~  368 (483)
                      +||.|+|+|+++|+ +++|.||+|...
T Consensus       674 vGd~V~VkVi~vd~-~grI~LS~k~~~  699 (723)
T 3cdi_A          674 MGQEVPVKVLEVDR-QGRIRLSIKEAT  699 (723)
T ss_dssp             ---------------------------
T ss_pred             CCCEEEEEEEEECC-CCcEEEEEEecc
Confidence            99999999999998 899999999753

>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=98.47  E-value=2.2e-07  Score=86.39  Aligned_cols=73  Identities=8%  Similarity=0.213  Sum_probs=59.2

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEECCeEEEeecccc-cccc-----------CChhhhhhhcCCEEEEEEEEEECC----C
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRV-----------NNFTELKEKVGRRMYVQITRINED----T  357 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv-----------~~~~~l~~~VGq~V~vkVl~ID~e----~  357 (483)
                      ...|++++|+|++++++|+||++++++|++|.+++ ++++           ++.... ..+|+.|++||+++|.+    .
T Consensus        79 p~~Gev~~G~V~~v~~~G~fv~l~~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~-~~~Gd~VrvkV~~v~~~~~~~~  157 (180)
T 4ayb_E           79 PVVQEVVEGEVLQVDNYGVFVNLGPMDGLVHISQITDDTLKYDNVRGIIFGEKSKKV-IQKGDKVRARVISVASTVTGRL  157 (180)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECSSSCCEEETTTCCC-CCTTCEEEEEEEEECC------
T ss_pred             ccCCCEEEEEEeeeccceEEEEECCccceEEeeecCCCccccchhcceEEEeccCeE-ECCCCEEEEEEEEEeCCCCccc
Confidence            46899999999999999999999999999999999 4443           222333 37999999999999864    3


Q ss_pred             CceeechhhH
Q 011538          358 NDLILSEREA  367 (483)
Q Consensus       358 ~rLiLS~K~~  367 (483)
                      .+|.+|+|++
T Consensus       158 ~rI~ls~k~~  167 (180)
T 4ayb_E          158 PRIALTMRQP  167 (180)
T ss_dssp             -CEEEECCST
T ss_pred             CcEEEEcCCC
Confidence            4899999974

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

Probab=98.43  E-value=2.1e-07  Score=108.41  Aligned_cols=74  Identities=8%  Similarity=0.076  Sum_probs=66.5

Q ss_pred             HHhhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccc-cCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538          292 QIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSR-VNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (483)
Q Consensus       292 ~~~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~r-v~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~  366 (483)
                      +.++.|+++.|+|+++.++|+||+++ |+.|+||.|++ +.+ +.++.+.. .+||.|+|+|++||.++++|.||+|.
T Consensus       898 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~p~~v~-kvGd~V~vkVl~VD~~~~rI~LSlk~  974 (1219)
T 3psi_A          898 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIY-EIGKTYPAKVIYIDYANITAEVSLLD  974 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTTSCSCSTTTS-CTTCEEEEEEEEEEGGGTEEEEECCH
T ss_pred             hhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCcccCCHHHcC-CCCCEEEEEEEEEECCCCEEEEEecH
Confidence            34689999999999999999999996 89999999999 555 57777765 89999999999999999999999885

>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=7.3e-07  Score=86.65  Aligned_cols=78  Identities=21%  Similarity=0.322  Sum_probs=63.2

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      +.+++||+|.|+|+++.++++||++|.+.+|+||++|+...+ .+           +               +       
T Consensus        62 y~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~~-~~-----------~---------------~-------  107 (235)
T 2z0s_A           62 YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRP-FN-----------P---------------A-------  107 (235)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSC-CC-----------T---------------T-------
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCc-cc-----------c---------------c-------
Confidence            678999999999999999999999999999999999986321 00           0               0       


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEeh
Q 011538          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTR  279 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k  279 (483)
                      ..+....+++||.|.|+|+..+.++++.||++
T Consensus       108 ~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k  139 (235)
T 2z0s_A          108 VDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQ  139 (235)
T ss_dssp             TTCCTTSSCTTCEEEEEEEEECTTSCEEEECC
T ss_pred             hhhHhhcCCCCCEEEEEEEEECCCCcEEEEEe
Confidence            01124568999999999999887889999986

>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=98.39  E-value=4.1e-07  Score=87.03  Aligned_cols=73  Identities=11%  Similarity=0.210  Sum_probs=63.4

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC---------CeEEEeecccc-ccccC--ChhhhhhhcCCEEEEEEEEEECCCCcee
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE---------GLRAFLPKAEL-LSRVN--NFTELKEKVGRRMYVQITRINEDTNDLI  361 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~---------Gi~gFVP~Sel-~~rv~--~~~~l~~~VGq~V~vkVl~ID~e~~rLi  361 (483)
                      .+.|++|.|+|+++.++|+||+|+         +++|+||.+++ +.+..  ++.+.+ .+||.|.|+|++++..++++.
T Consensus        79 p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l-~~GD~V~akVisi~~~~~~i~  157 (209)
T 2nn6_I           79 PDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSF-RPGDIVLAKVISLGDAQSNYL  157 (209)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTC-CSSSEEEEEEEEEETTTTEEE
T ss_pred             CCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhc-CCCCEEEEEEEEEeCCCCeEE
Confidence            579999999999999999999995         56899999999 55555  666664 899999999999997777899


Q ss_pred             echhhH
Q 011538          362 LSEREA  367 (483)
Q Consensus       362 LS~K~~  367 (483)
                      ||.|..
T Consensus       158 LS~k~~  163 (209)
T 2nn6_I          158 LTTAEN  163 (209)
T ss_dssp             EECCSS
T ss_pred             EEEecC
Confidence            999865

>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=98.37  E-value=1.3e-06  Score=84.62  Aligned_cols=76  Identities=21%  Similarity=0.299  Sum_probs=63.1

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      |.+++||+|.|+|+++.+++++|+++....|+||++|+....+          .                          
T Consensus        53 y~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~~~----------~--------------------------   96 (229)
T 2ba0_A           53 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKP----------N--------------------------   96 (229)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCT----------T--------------------------
T ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHcccccc----------c--------------------------
Confidence            5689999999999999999999999999999999999862100          0                          


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 011538          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~  280 (483)
                       .+..+.+++||.|.|+|+..+.++.+.||++.
T Consensus        97 -~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~  128 (229)
T 2ba0_A           97 -KKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKD  128 (229)
T ss_dssp             -SCGGGTCCTTCEEEEEEEEECTTCCEEEECCS
T ss_pred             -cchhcccCCCCEEEEEEEEECCCCcEEEEEcc
Confidence             01134589999999999998888999999864

>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=98.35  E-value=9.6e-07  Score=86.71  Aligned_cols=79  Identities=23%  Similarity=0.262  Sum_probs=64.2

Q ss_pred             ccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccC
Q 011538          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (483)
Q Consensus       167 ~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~  246 (483)
                      .|.+++||+|.|+|+++.++++||++|...+|+||++|+...+            .++               +      
T Consensus        69 ~y~p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei~~~~------------~~~---------------~------  115 (251)
T 2je6_I           69 FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRS------------INV---------------G------  115 (251)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSC------------CCT---------------T------
T ss_pred             ccCCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCc------------ccc---------------c------
Confidence            4678999999999999999999999999999999999985321            000               0      


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 011538          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (483)
Q Consensus       247 ~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~  280 (483)
                        .+....+++||.|.|+|+..+.++++.||++.
T Consensus       116 --~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r~  147 (251)
T 2je6_I          116 --EDLRRYLDVGDYVIARIENFDRSIDPVLSVKG  147 (251)
T ss_dssp             --CCCSSSCCTTCEEEEEEEEEETTEEEEEECCS
T ss_pred             --cchhhcCCCCCEEEEEEEEECCCCcEEEEEcc
Confidence              11235689999999999998878899999864

>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=98.33  E-value=2.2e-07  Score=104.12  Aligned_cols=72  Identities=19%  Similarity=0.129  Sum_probs=65.9

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~  366 (483)
                      ++.|++++|+|+++.++|+||+++ +++||||.|+| +.++.++.+.. .+||.|+|+|+++|.++++|.||+|.
T Consensus       652 l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v~d~~~~~-~vGd~V~VkVi~VD~~~~rI~LSlk~  725 (785)
T 3bzc_A          652 LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVV-KAGDIVKVKVMEVDIPRNRVGLSMRM  725 (785)
T ss_dssp             CCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCCSCHHHHC-CTTCCCCCBEEEEETTTTEEEECCSS
T ss_pred             cCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCccccCChhhee-CCCCEEEEEEEEEECCCCEEEEEEec
Confidence            579999999999999999999996 68999999999 66777887765 89999999999999999999999984

>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=98.32  E-value=1.2e-06  Score=96.52  Aligned_cols=74  Identities=11%  Similarity=0.144  Sum_probs=62.7

Q ss_pred             CCCCCc--EEEEEEEEEeCceEEEEECCCceEEEEeccCcCc--ccc--c--------CcccccCCCCEEEEEEEEEe-C
Q 011538          372 NLREGT--LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR--TRV--T--------SVSDLLNEGERVKVLVVKSM-F  436 (483)
Q Consensus       372 ~l~vG~--iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~--~~i--~--------~~~~~~kvGd~VkVkVi~vd-e  436 (483)
                      .-++|+  +++|+|++|+++|+||+|.+.|++||||+|++++  +++  .        +....|++||+|+|+|+++| +
T Consensus       555 ~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~vd~~  634 (644)
T 2id0_A          555 KDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRME  634 (644)
T ss_dssp             GGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETT
T ss_pred             hhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEEEEEeCC
Confidence            457899  9999999999999999996558999999999973  321  1        44577999999999999998 7


Q ss_pred             CCeEEEEEe
Q 011538          437 PDKISLSIA  445 (483)
Q Consensus       437 k~rI~LSLK  445 (483)
                      +++|.+++-
T Consensus       635 ~~~I~~~l~  643 (644)
T 2id0_A          635 TRSIIARPV  643 (644)
T ss_dssp             TTEEEEEEC
T ss_pred             CCEEEEEEc
Confidence            899999874

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

Probab=98.24  E-value=1.3e-07  Score=108.59  Aligned_cols=75  Identities=8%  Similarity=0.071  Sum_probs=0.0

Q ss_pred             HHhhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccc-cCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          292 QIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSR-VNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       292 ~~~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~r-v~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      +.++.|+++.|+|+++.++|+||+++ |+.|+||.|++ +.+ +.++.+.. .+||.|+|+|++||.++++|.||+|..
T Consensus       901 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~~~~v~-kvGd~V~vkVl~VD~~~~rI~LSlk~~  978 (1030)
T 3psf_A          901 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIY-EIGKTYPAKVIYIDYANITAEVSLLDH  978 (1030)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             HHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCCcccCCHHHcC-CCCCEEEEEEEEEECCCCEEEEEechH
Confidence            34589999999999999999999996 89999999999 555 57777765 899999999999999999999999864

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

Probab=98.23  E-value=1.9e-06  Score=81.90  Aligned_cols=61  Identities=11%  Similarity=0.135  Sum_probs=53.8

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc-------------------cCcccccCCCCEEEEEEEE
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-------------------TSVSDLLNEGERVKVLVVK  433 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i-------------------~~~~~~~kvGd~VkVkVi~  433 (483)
                      -.+|+++.|+|++++++|+||+++  .++|++|.+++.++++                   ++....+++||.|++||++
T Consensus        79 p~~GEv~~G~Vs~vt~~GifV~lg--~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV~~  156 (203)
T 3ayh_B           79 PFRGEVMLGKIKSCSEEGIRVTIS--FFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQIES  156 (203)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS--SCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEEEE
T ss_pred             cCCCCEEEEEEEEEeccEEEEEEe--CceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEEEE
Confidence            468999999999999999999995  4899999999987654                   4556679999999999999


Q ss_pred             Ee
Q 011538          434 SM  435 (483)
Q Consensus       434 vd  435 (483)
                      ++
T Consensus       157 v~  158 (203)
T 3ayh_B          157 ED  158 (203)
T ss_dssp             EE
T ss_pred             EE
Confidence            87

>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=98.23  E-value=1.8e-06  Score=79.76  Aligned_cols=72  Identities=21%  Similarity=0.217  Sum_probs=54.5

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccccc-----cCC-------hhhhhhhcCCEEEEEEEEEECCCC--ce
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR-----VNN-------FTELKEKVGRRMYVQITRINEDTN--DL  360 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~~r-----v~~-------~~~l~~~VGq~V~vkVl~ID~e~~--rL  360 (483)
                      ..|++++|+|++++++|+||+++..+||+|.|+|.+.     ..+       .......+|+.|+|+|+++|.+.+  ..
T Consensus        80 ~~Gev~~G~V~~v~~fG~fV~l~~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~~~~  159 (172)
T 2c35_B           80 FKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFA  159 (172)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEEEE
T ss_pred             CCCCEEEEEEEEEeCCEEEEEECCEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCCCCcEE
Confidence            5899999999999999999999889999999998422     111       001123799999999999997654  12


Q ss_pred             eechhh
Q 011538          361 ILSERE  366 (483)
Q Consensus       361 iLS~K~  366 (483)
                      +.|+++
T Consensus       160 igsm~~  165 (172)
T 2c35_B          160 IGSLMD  165 (172)
T ss_dssp             EEECCS
T ss_pred             EEEecC
Confidence            336654

>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=98.21  E-value=4.5e-08  Score=109.36  Aligned_cols=97  Identities=18%  Similarity=0.192  Sum_probs=41.9

Q ss_pred             cCCCcEEEEehHHHHH-h---hhHHHH--HHhhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-----ccccCChh
Q 011538          269 TLSGRPLLSTRRLFRK-M---AWHRVR--QIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-----LSRVNNFT  336 (483)
Q Consensus       269 d~~G~iiLS~k~~~~~-~---~w~~L~--~~~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-----~~rv~~~~  336 (483)
                      +.+|.+.+|....... .   ..+.+.  ...+.|++++|+|+++.++|+||++ +|++||||.|++     +.+++++.
T Consensus       634 ~~dG~v~Is~~~~~~~~~a~~~i~~i~~p~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s~~rv~~~~  713 (757)
T 1e3p_A          634 EDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVE  713 (757)
T ss_dssp             ------CCCBSSHHHHCC---------------------CBEEECC-CSCEECCC---CCCCC-----------------
T ss_pred             cCCceEEEecCCHHHHHHHHHHHHHhcchhhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccCCCcccCcc
Confidence            3467787776543221 1   223343  4568999999999999999999999 579999999999     46777777


Q ss_pred             hhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          337 ELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       337 ~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      +.. ++||+|+|+|+++|+ +++|.||+|..
T Consensus       714 ~~~-~vGd~V~VkVi~vd~-~grI~LS~k~~  742 (757)
T 1e3p_A          714 DVL-GVGQKVQVEIAEIDS-RGKLSLIPVIE  742 (757)
T ss_dssp             --C-CSSCBCCCCCCCCCS-SCC--------
T ss_pred             ccc-CCCCEEEEEEEEECC-CCCEEEEEecC
Confidence            765 899999999999998 89999999964

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

Probab=98.20  E-value=2.9e-06  Score=79.19  Aligned_cols=67  Identities=12%  Similarity=0.108  Sum_probs=58.9

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC-----------CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCcee
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE-----------GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLI  361 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~-----------Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLi  361 (483)
                      .+ |++|.|+|+++.++|+||+|+           +++|+||.|++ +.+..++.+.+ .+||.|.++|++     +++.
T Consensus        56 p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~-~~GD~V~akVi~-----~~i~  128 (179)
T 3m7n_A           56 VK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAV-GYLDILKARVIG-----DNLR  128 (179)
T ss_dssp             CT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTC-CTTCEEEEEEEE-----TTTE
T ss_pred             CC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcC-CCCCEEEEEEEC-----CeEE
Confidence            37 999999999999999999994           68999999999 66667777765 899999999997     7899


Q ss_pred             echhhH
Q 011538          362 LSEREA  367 (483)
Q Consensus       362 LS~K~~  367 (483)
                      ||.|..
T Consensus       129 LS~k~~  134 (179)
T 3m7n_A          129 LSTKEE  134 (179)
T ss_dssp             EECCST
T ss_pred             EEEecC
Confidence            998864

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

Probab=98.18  E-value=3.4e-06  Score=90.43  Aligned_cols=73  Identities=23%  Similarity=0.421  Sum_probs=61.1

Q ss_pred             CCCCCcEEEEEEEEEeCc--eEEEEECCCceEEEEeccCcCcccc---------cCcccccCCCCEEEEEEEEEe-CCCe
Q 011538          372 NLREGTLLEGTVKKIYPY--GAQIRIGDSNRSGLLHISNMSRTRV---------TSVSDLLNEGERVKVLVVKSM-FPDK  439 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~--GaFV~I~~~gi~GLlhiSels~~~i---------~~~~~~~kvGd~VkVkVi~vd-ek~r  439 (483)
                      ...+|.+|.|+|++|.++  ||||+|+. |..||||.++++|.++         .++.+.+++||.|.|+|++.. ..+.
T Consensus        42 ~~~vGnIY~GkV~rv~p~~~aAFVdiG~-gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g~KG  120 (517)
T 2bx2_L           42 EQKKANIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKG  120 (517)
T ss_dssp             CCCTTCEEEEEEEEEETTTTEEEEESSS-SSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCTTCC
T ss_pred             cCCCCCEEEEEEEEeccCCceEEEEeCC-CcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeeccccCC
Confidence            467899999999999999  99999998 8999999999998764         346688999999999999875 4444


Q ss_pred             EEEEEe
Q 011538          440 ISLSIA  445 (483)
Q Consensus       440 I~LSLK  445 (483)
                      ..||..
T Consensus       121 a~lTt~  126 (517)
T 2bx2_L          121 AALTTF  126 (517)
T ss_dssp             CEEESS
T ss_pred             ceEEee
Confidence            455543

>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=98.16  E-value=2.9e-06  Score=78.34  Aligned_cols=63  Identities=13%  Similarity=0.199  Sum_probs=50.7

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccccc--c---CCh------hhhhhhcCCEEEEEEEEEECCCC
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR--V---NNF------TELKEKVGRRMYVQITRINEDTN  358 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~~r--v---~~~------~~l~~~VGq~V~vkVl~ID~e~~  358 (483)
                      ..|++++|+|++++++|+||+++..+||+|.|+|...  .   .++      ++. ..+|+.|+|+|+++|.+.+
T Consensus        82 ~~Gev~~G~V~~v~~fG~FV~l~~~dglvhis~l~~~~~~d~~~~~~~~~~~~~~-~~~Gd~V~vkV~~vd~~~~  155 (171)
T 1y14_B           82 FKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDV-ITIKSRIRVKIEGCISQVS  155 (171)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTCEECC-----CEECSSCE-ECTTCEEEEEEEEEEEETT
T ss_pred             CCCCEEEEEEEEEecCEEEEEecCeEEEEEHHHCCCCceECcccCceEEeccceE-ECCCCEEEEEEEEEEcCCC
Confidence            5899999999999999999999779999999999422  1   110      123 3789999999999997654

>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=98.14  E-value=7e-06  Score=80.31  Aligned_cols=77  Identities=22%  Similarity=0.211  Sum_probs=63.3

Q ss_pred             CCCCCcEEEEEEEE----EeCCeEEEEeCC---ceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecccc
Q 011538          169 EPKPGDFVIGVVVS----GNENKLDVNVGA---DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA  241 (483)
Q Consensus       169 ~ik~GdiV~G~Vv~----V~~~gv~VdiG~---k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~  241 (483)
                      .-+.|++|+|+|.+    ++++.++||+|.   +.+|+||.+|+.|.                                 
T Consensus         4 ~~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqip~---------------------------------   50 (251)
T 2asb_A            4 STREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPG---------------------------------   50 (251)
T ss_dssp             CCCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSCTT---------------------------------
T ss_pred             hhcCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcCCC---------------------------------
Confidence            34579999999999    899999999997   69999999998653                                 


Q ss_pred             ccccCCCCCCCCcccCCCEEEEEEEEEc---CCCcEEEEehHHHHHhhhHH
Q 011538          242 IAMSGGSGPGRPVVETGTVLFAEVLGRT---LSGRPLLSTRRLFRKMAWHR  289 (483)
Q Consensus       242 ~~~~~~~~~~~~~~kVGd~V~v~Vi~~d---~~G~iiLS~k~~~~~~~w~~  289 (483)
                                 ..|++||.|.|.|++..   ..++++||+..+...+.|-+
T Consensus        51 -----------E~~~~GDrIkayV~~V~~~~~gpqIiLSRt~p~lvk~Lfe   90 (251)
T 2asb_A           51 -----------ESYEHGNRLRCYVVGVTRGAREPLITLSRTHPNLVRKLFS   90 (251)
T ss_dssp             -----------CCCCTTCEEEEEEEEEECCSSSCEEEEESSCHHHHHHHHH
T ss_pred             -----------ccCCCCCEEEEEEEEEEcCCCCCEEEEEeccHHHHHHHHH
Confidence                       24789999999999853   34789999998876555543

>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=98.11  E-value=3.2e-06  Score=81.21  Aligned_cols=70  Identities=14%  Similarity=0.185  Sum_probs=54.8

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccccc-cCCh----------hhhhhhcCCEEEEEEEEEECCCC---ce
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR-VNNF----------TELKEKVGRRMYVQITRINEDTN---DL  360 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~~r-v~~~----------~~l~~~VGq~V~vkVl~ID~e~~---rL  360 (483)
                      +.|++++|+|+++.++|+||+++..+||||.|+|.+. ..++          ++. ..+|+.|+|+|+++|.+.+   ++
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 FKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDV-ITIKSRIRVKIEGCISQVSSIHAI  160 (215)
T ss_dssp             CTTEEEEEEEEEEETTEEEEECTTSEEEEEGGGSCSSCCCBSSCSSCEEECSSCE-EETTCEEEEEEEEEEEETTEEEEE
T ss_pred             CCCCEEEEEEEEEecceEEEEecCcEEEEEHHHCCccceeccccccceeeccccE-ECCCCEEEEEEEEEEcCCCccEEE
Confidence            6899999999999999999999779999999999432 1111          123 3799999999999997654   33


Q ss_pred             eechhh
Q 011538          361 ILSERE  366 (483)
Q Consensus       361 iLS~K~  366 (483)
                      . |+++
T Consensus       161 g-Smk~  165 (215)
T 2b8k_G          161 G-SIKE  165 (215)
T ss_dssp             E-ECCS
T ss_pred             E-EcCC
Confidence            3 6654

>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=98.06  E-value=4e-06  Score=84.61  Aligned_cols=74  Identities=16%  Similarity=0.235  Sum_probs=62.3

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc----cc------cCcccccCCCCEEEEEEEEEeCCCeEE
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT----RV------TSVSDLLNEGERVKVLVVKSMFPDKIS  441 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~----~i------~~~~~~~kvGd~VkVkVi~vdek~rI~  441 (483)
                      ..++|++|.|+|+++.++|+||+|+. ...|++|.++++..    |.      .++++.|++||.|.|||+++++..++.
T Consensus        92 ~P~vGDvViG~Vt~V~~~~a~VdI~s-~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~~~~i~  170 (308)
T 2nn6_H           92 IGEVGDIVVGRITEVQQKRWKVETNS-RLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVS  170 (308)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECSS-SSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTEEE
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEECC-CcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCCCCCEE
Confidence            46899999999999999999999986 47899999998752    22      234578999999999999998788999


Q ss_pred             EEEec
Q 011538          442 LSIAD  446 (483)
Q Consensus       442 LSLK~  446 (483)
                      ||+|+
T Consensus       171 LStr~  175 (308)
T 2nn6_H          171 LHTRS  175 (308)
T ss_dssp             EECCS
T ss_pred             EEecC
Confidence            99985

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

Probab=98.04  E-value=6.6e-06  Score=79.18  Aligned_cols=62  Identities=11%  Similarity=0.145  Sum_probs=53.2

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc--------------cCcccccCCCCEEEEEEEEEe
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV--------------TSVSDLLNEGERVKVLVVKSM  435 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i--------------~~~~~~~kvGd~VkVkVi~vd  435 (483)
                      -.+|++++|+|++++++|+||++.+ .++|++|++++..+++              ++....|++||.|++||++++
T Consensus        79 p~vGEv~~G~Is~Vt~fGifVeL~g-~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~  154 (218)
T 2ckz_B           79 PFLGEIVTGWISKCTAEGIKVSLLG-IFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREV  154 (218)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECTT-SCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEccCcEEEEccC-ccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEE
Confidence            4689999999999999999999965 4899999999976653              344667999999999999997

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

Probab=98.03  E-value=1.4e-06  Score=80.61  Aligned_cols=72  Identities=17%  Similarity=0.196  Sum_probs=55.7

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccccc-cCChh---------hhhhhcCCEEEEEEEEEECCCC---cee
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR-VNNFT---------ELKEKVGRRMYVQITRINEDTN---DLI  361 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~~r-v~~~~---------~l~~~VGq~V~vkVl~ID~e~~---rLi  361 (483)
                      ..|++++|+|++++++|+||+++.++||+|.|+|.+. .-+..         +....+|+.|+++|+++|.+.+   ++.
T Consensus        83 ~~Gev~~G~V~~v~~fG~FV~l~~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~~~~~~~~Ig  162 (172)
T 3h0g_G           83 FRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDATEIFAIA  162 (172)
T ss_dssp             CTTCEEECCCCEEETTEEECCBTTBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEESSSCEEEEE
T ss_pred             CCCCEEEEEEEEEEcceEEEEeCCeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEECCCCCceEEE
Confidence            6899999999999999999999989999999999422 11110         1123799999999999998764   333


Q ss_pred             echhhH
Q 011538          362 LSEREA  367 (483)
Q Consensus       362 LS~K~~  367 (483)
                       |+|++
T Consensus       163 -tm~~~  167 (172)
T 3h0g_G          163 -TMKED  167 (172)
T ss_dssp             -ECCST
T ss_pred             -EcCCC
Confidence             66554

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

Probab=98.01  E-value=5.5e-06  Score=95.06  Aligned_cols=70  Identities=19%  Similarity=0.219  Sum_probs=60.4

Q ss_pred             CcEEEEEEEEEeCceEEEEECCCceEEEEeccCcC--cccc-----------cC----cccccCCCCEEEEEEEEEeC--
Q 011538          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS--RTRV-----------TS----VSDLLNEGERVKVLVVKSMF--  436 (483)
Q Consensus       376 G~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels--~~~i-----------~~----~~~~~kvGd~VkVkVi~vde--  436 (483)
                      |+++.|+|++|+++|+||.|.+.|++|+||+++|+  .+++           .+    ....|++||+|+|+|+.++.  
T Consensus       887 ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~VkV~~vd~~~  966 (977)
T 2wp8_J          887 ESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPI  966 (977)
T ss_dssp             TCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEEECCCCCSS
T ss_pred             ceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCCEEEEEEEEEcCcc
Confidence            99999999999999999999876899999999997  4431           22    35789999999999999874  


Q ss_pred             --CCeEEEEEe
Q 011538          437 --PDKISLSIA  445 (483)
Q Consensus       437 --k~rI~LSLK  445 (483)
                        ++||.||||
T Consensus       967 ~~~~kI~Lslk  977 (977)
T 2wp8_J          967 TSKRKAELLLK  977 (977)
T ss_dssp             SCCCCCCEEEC
T ss_pred             cCCCceEEEeC
Confidence              379999997

>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=97.99  E-value=6.1e-06  Score=92.53  Aligned_cols=69  Identities=19%  Similarity=0.230  Sum_probs=53.7

Q ss_pred             cEEEEEEEEEeCceEEEEECCCceEEEEeccCcC--cccc-----------cC----cccccCCCCEEEEEEEEEe-C--
Q 011538          377 TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS--RTRV-----------TS----VSDLLNEGERVKVLVVKSM-F--  436 (483)
Q Consensus       377 ~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels--~~~i-----------~~----~~~~~kvGd~VkVkVi~vd-e--  436 (483)
                      +++.|+|++|+++|+||.|...|++|+||+++++  .+++           .+    ....|++||+|+|+|+.++ +  
T Consensus       671 ~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV~~vd~~~~  750 (760)
T 2vnu_D          671 STETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPIT  750 (760)
T ss_dssp             SEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC-------
T ss_pred             eEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCCEEEEEEEEEECccc
Confidence            7999999999999999999876899999999996  4331           22    2578999999999999997 4  


Q ss_pred             -CCeEEEEEe
Q 011538          437 -PDKISLSIA  445 (483)
Q Consensus       437 -k~rI~LSLK  445 (483)
                       ++||.||||
T Consensus       751 ~~~kI~lslk  760 (760)
T 2vnu_D          751 SKRKAELLLK  760 (760)
T ss_dssp             -CCEEEC---
T ss_pred             cCCcEEEEeC
Confidence             589999987

>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=97.90  E-value=2.9e-05  Score=72.25  Aligned_cols=74  Identities=11%  Similarity=0.052  Sum_probs=63.5

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEec
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIAD  446 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~  446 (483)
                      ..++||+|.|+|+.+...+++|+|+.....|+||.+++. ...++.+..|++||.|.|||.+++...++.||+.+
T Consensus         4 ~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~-g~~k~~r~~l~~GDlV~ArV~~~~~~~~~~Ltc~~   77 (175)
T 2ja9_A            4 IPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFP-NASKKNRPTLQVGDLVYARVCTAEKELEAEIECFD   77 (175)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSST-TCCSSSCCCCCTTCEEEEEEEECCTTSCCEEESSC
T ss_pred             cCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCC-chhhhhhccCCCCCEEEEEEEEecCCCceEEEecc
Confidence            357899999999999999999999861279999999886 34567888999999999999998877889999443

>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=97.89  E-value=3.2e-05  Score=79.53  Aligned_cols=70  Identities=24%  Similarity=0.254  Sum_probs=59.0

Q ss_pred             CCCCcEEEEEEEE----EeCCeEEEEeCC---ceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccc
Q 011538          170 PKPGDFVIGVVVS----GNENKLDVNVGA---DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAI  242 (483)
Q Consensus       170 ik~GdiV~G~Vv~----V~~~gv~VdiG~---k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~  242 (483)
                      -+.|++|+|+|.+    ++++++|||+|.   +.+|+||.+|++|.                                  
T Consensus       128 ~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~EqiP~----------------------------------  173 (366)
T 1k0r_A          128 TREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPG----------------------------------  173 (366)
T ss_dssp             CCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSCTT----------------------------------
T ss_pred             hcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcCCC----------------------------------
Confidence            4599999999999    999999999997   69999999998753                                  


Q ss_pred             cccCCCCCCCCcccCCCEEEEEEEEEcC---CCcEEEEehHHHH
Q 011538          243 AMSGGSGPGRPVVETGTVLFAEVLGRTL---SGRPLLSTRRLFR  283 (483)
Q Consensus       243 ~~~~~~~~~~~~~kVGd~V~v~Vi~~d~---~G~iiLS~k~~~~  283 (483)
                                ..|++||.|.|.|++.+.   ...+.||+..+..
T Consensus       174 ----------E~~~~GDrVkvyV~~V~~~~kgpqI~LSRT~p~l  207 (366)
T 1k0r_A          174 ----------ESYEHGNRLRCYVVGVTRGAREPLITLSRTHPNL  207 (366)
T ss_dssp             ----------CCCCTTCEEEEEEEEEECCSSSCEEEEESSCHHH
T ss_pred             ----------ccCCCCCEEEEEEEEEecCCCccEEEEEeCChHH
Confidence                      247899999999999543   4578999887753

>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=97.84  E-value=1.5e-05  Score=81.99  Aligned_cols=78  Identities=15%  Similarity=0.242  Sum_probs=62.9

Q ss_pred             CCCCCcEEEEEEEE----EeCceEEEEECC--CceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538          372 NLREGTLLEGTVKK----IYPYGAQIRIGD--SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (483)
Q Consensus       372 ~l~vG~iv~G~V~~----I~~~GaFV~I~~--~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL  444 (483)
                      .-++|+++.|+|.+    +.+.++||+++.  .+++|+||.+|+.      |.+.|++||+|+|.|++++ +.+...+.|
T Consensus       127 ~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi------P~E~~~~GDrVkvyV~~V~~~~kgpqI~L  200 (366)
T 1k0r_A          127 STREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITL  200 (366)
T ss_dssp             CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEE
T ss_pred             HhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC------CCccCCCCCEEEEEEEEEecCCCccEEEE
Confidence            45599999999999    999999999974  1389999999986      4689999999999999997 445566666


Q ss_pred             ecCCCCcCccc
Q 011538          445 ADLESEPGLFV  455 (483)
Q Consensus       445 K~~~~dPw~~l  455 (483)
                      ..+.++....|
T Consensus       201 SRT~p~lv~~L  211 (366)
T 1k0r_A          201 SRTHPNLVRKL  211 (366)
T ss_dssp             ESSCHHHHHHH
T ss_pred             EeCChHHHHHH
Confidence            66666554433

>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=97.72  E-value=0.00015  Score=67.49  Aligned_cols=72  Identities=19%  Similarity=0.294  Sum_probs=59.9

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCC-ceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~-k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~  246 (483)
                      |.+++||+|.|+|+.+..++++||||. ...|+||.+.+....                                     
T Consensus         3 Y~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~g~~-------------------------------------   45 (175)
T 2ja9_A            3 YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNAS-------------------------------------   45 (175)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCC-------------------------------------
T ss_pred             ccCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCCchh-------------------------------------
Confidence            678899999999999999999999998 799999988763210                                     


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEe
Q 011538          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLST  278 (483)
Q Consensus       247 ~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~  278 (483)
                        .+.++.+++||.|.|+|...+.++.+.||.
T Consensus        46 --k~~r~~l~~GDlV~ArV~~~~~~~~~~Ltc   75 (175)
T 2ja9_A           46 --KKNRPTLQVGDLVYARVCTAEKELEAEIEC   75 (175)
T ss_dssp             --SSSCCCCCTTCEEEEEEEECCTTSCCEEES
T ss_pred             --hhhhccCCCCCEEEEEEEEecCCCceEEEe
Confidence              112466999999999999887788899983

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

Probab=97.56  E-value=0.00016  Score=70.81  Aligned_cols=68  Identities=22%  Similarity=0.344  Sum_probs=57.5

Q ss_pred             CCCCcEEEEEEEE----EeCceEEEEECCC--ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeC-C--CeEEEE
Q 011538          373 LREGTLLEGTVKK----IYPYGAQIRIGDS--NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMF-P--DKISLS  443 (483)
Q Consensus       373 l~vG~iv~G~V~~----I~~~GaFV~I~~~--gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vde-k--~rI~LS  443 (483)
                      -++|++|.|+|.+    +.+..++|+++..  +.+|+||.+|+.      |.+.|++||+|+|.|++++. .  .+|.||
T Consensus         5 ~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqi------p~E~~~~GDrIkayV~~V~~~~~gpqIiLS   78 (251)
T 2asb_A            5 TREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITLS   78 (251)
T ss_dssp             CCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEEE
T ss_pred             hcCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcC------CCccCCCCCEEEEEEEEEEcCCCCCEEEEE
Confidence            3689999999999    8888999999730  389999999986      56899999999999999963 2  588888


Q ss_pred             Eec
Q 011538          444 IAD  446 (483)
Q Consensus       444 LK~  446 (483)
                      ...
T Consensus        79 Rt~   81 (251)
T 2asb_A           79 RTH   81 (251)
T ss_dssp             SSC
T ss_pred             ecc
Confidence            664

>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=97.38  E-value=0.00014  Score=73.23  Aligned_cols=85  Identities=25%  Similarity=0.339  Sum_probs=61.0

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      |.+++||+|.|+|+++.+++++|+|+....|+++++++....                     |.+......|...+   
T Consensus        91 Y~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~g---------------------g~iR~~~~~D~~~m---  146 (308)
T 2nn6_H           91 YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPG---------------------GELRRRSAEDELAM---  146 (308)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC----------------------------------CHHH---
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhcccc---------------------ceeecccchhhhhh---
Confidence            578999999999999999999999998788999988874210                     00000000000001   


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 011538          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~  280 (483)
                          .+.|++||.|.|+|+..+.++.+.||.+.
T Consensus       147 ----~~~l~vGDlV~ArVisv~~~~~i~LStr~  175 (308)
T 2nn6_H          147 ----RGFLQEGDLISAEVQAVFSDGAVSLHTRS  175 (308)
T ss_dssp             ----HHHSCSSCEECCEEEEEETTTEEEEECCS
T ss_pred             ----hccCCCCCEEEEEEEEcCCCCCEEEEecC
Confidence                24589999999999998778899999875

>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=97.35  E-value=0.0006  Score=75.12  Aligned_cols=70  Identities=20%  Similarity=0.303  Sum_probs=56.5

Q ss_pred             hhCCC--eEEEEEEEEECCeEEEEE--CCeEEEeeccccc---cccC----------ChhhhhhhcCCEEEEEEEEEECC
Q 011538          294 KQLNE--PIEVKFTEWNTGGLLTRI--EGLRAFLPKAELL---SRVN----------NFTELKEKVGRRMYVQITRINED  356 (483)
Q Consensus       294 ~k~Ge--iV~GkV~~v~k~G~fV~I--~Gi~gFVP~Sel~---~rv~----------~~~~l~~~VGq~V~vkVl~ID~e  356 (483)
                      .+.|+  .++|+|+++.++|+||.+  .|++||||.+++.   +++.          +... ...+||.|+|+|.++|..
T Consensus       556 ~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~-~~~lGD~V~VkV~~vd~~  634 (644)
T 2id0_A          556 DKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGET-VYKVTDVIDVTIAEVRME  634 (644)
T ss_dssp             GGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEE-EEETTCEEEEEEEEEETT
T ss_pred             hccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCceeEEcccccEEEecCCC-EeCCCCEEEEEEEEEeCC
Confidence            46899  999999999999999999  4899999999983   2210          1111 237999999999999999


Q ss_pred             CCceeech
Q 011538          357 TNDLILSE  364 (483)
Q Consensus       357 ~~rLiLS~  364 (483)
                      +++|.++.
T Consensus       635 ~~~I~~~l  642 (644)
T 2id0_A          635 TRSIIARP  642 (644)
T ss_dssp             TTEEEEEE
T ss_pred             CCEEEEEE
Confidence            89988874

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

Probab=97.30  E-value=0.00046  Score=58.42  Aligned_cols=39  Identities=13%  Similarity=0.298  Sum_probs=34.3

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-cccc
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRV  332 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv  332 (483)
                      ++.|+.++++|+.+.++|+||++ ++++||||.|++ |.++
T Consensus        59 l~~Ge~V~g~V~~i~~fG~fv~l~~~~eGlvhis~i~~~~~   99 (101)
T 2bh8_A           59 PQQGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISWAQA   99 (101)
T ss_dssp             CCTTCEEEEEEEECCSEEEEECTTSCEEEEEEEEEEEECCC
T ss_pred             CCCCCEEEEEEEEeCCcEEEEEcCCCceEEEEHHHCccCcC
Confidence            36889999999999999999999 589999999999 6553

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

Probab=97.15  E-value=0.00056  Score=64.86  Aligned_cols=62  Identities=13%  Similarity=0.090  Sum_probs=48.2

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeecccc-cccc-------------------CChhhhhhhcCCEEEEEEEEEE
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRV-------------------NNFTELKEKVGRRMYVQITRIN  354 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv-------------------~~~~~l~~~VGq~V~vkVl~ID  354 (483)
                      ..|++++|+|++++++|+||.++.++|++|.+++ +++.                   ++. .....+|+.|++||.+++
T Consensus        80 ~~GEv~~G~Vs~vt~~GifV~lg~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~-~~~~~~Gd~VrvrV~~v~  158 (203)
T 3ayh_B           80 FRGEVMLGKIKSCSEEGIRVTISFFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGT-ELYFDIDEEIRFQIESED  158 (203)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCE-EEECCTTCEEEEEEEEEE
T ss_pred             CCCCEEEEEEEEEeccEEEEEEeCceEEEEcHHhCCCCceECccCceEEeecccccccccC-CcEEcCCCEEEEEEEEEE
Confidence            5899999999999999999999878999999998 3322                   111 122368888888888887


Q ss_pred             CCC
Q 011538          355 EDT  357 (483)
Q Consensus       355 ~e~  357 (483)
                      ...
T Consensus       159 ~~~  161 (203)
T 3ayh_B          159 FVD  161 (203)
T ss_dssp             ECC
T ss_pred             ccc
Confidence            543

>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=97.11  E-value=0.00081  Score=72.14  Aligned_cols=70  Identities=17%  Similarity=0.227  Sum_probs=55.2

Q ss_pred             hCCCeEEEEEEEEECC--eEEEEEC-CeEEEeecccc-cccc---------CChhhhhhhcCCEEEEEEEEEECCCCcee
Q 011538          295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAEL-LSRV---------NNFTELKEKVGRRMYVQITRINEDTNDLI  361 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~--G~fV~I~-Gi~gFVP~Sel-~~rv---------~~~~~l~~~VGq~V~vkVl~ID~e~~rLi  361 (483)
                      ..|.++.|+|+++.++  |+||+++ |-.||+|.+++ +.++         .++.+.. ++||+|.|.|++....++-..
T Consensus        44 ~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~l-k~Gq~VlVQV~Ke~~g~KGa~  122 (517)
T 2bx2_L           44 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVL-REGQEVIVQIDKEERGNKGAA  122 (517)
T ss_dssp             CTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC-------CCCGGGTC-CTTCEEEEEEEECCCTTCCCE
T ss_pred             CCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcChhhhccccccccccchhhhc-cCCCEEEEEEEeeccccCCce
Confidence            5899999999999999  9999997 78899999999 4442         2344443 689999999999776555555


Q ss_pred             echh
Q 011538          362 LSER  365 (483)
Q Consensus       362 LS~K  365 (483)
                      ||..
T Consensus       123 lTt~  126 (517)
T 2bx2_L          123 LTTF  126 (517)
T ss_dssp             EESS
T ss_pred             EEee
Confidence            5544

>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=97.06  E-value=0.001  Score=66.43  Aligned_cols=71  Identities=10%  Similarity=-0.000  Sum_probs=62.8

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI  444 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSL  444 (483)
                      -.++||+|-|+|+++....+.|+|.. -..|+||.+++. ...++.+..|++||.|.|+|++++....+.||+
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-GATKRNRPNVQVGDLIYGQFVVANKDMEPEMVC  194 (289)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECSS-SSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCTTSCCEEEC
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEECC-CceeEEehhhcC-cchhhhhhhcCCCCEEEEEEEEcCCCCceEEEe
Confidence            36899999999999999999999987 588999999875 345678889999999999999987777899998

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

Probab=96.93  E-value=0.0028  Score=63.34  Aligned_cols=72  Identities=22%  Similarity=0.374  Sum_probs=59.5

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      |-+++||+|.|+|+++..+.+.|||+....|+||.+++....                                      
T Consensus       123 YiP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~Gat--------------------------------------  164 (289)
T 2nn6_G          123 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGAT--------------------------------------  164 (289)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCS--------------------------------------
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcCcch--------------------------------------
Confidence            678999999999999999999999998888998887753110                                      


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEe
Q 011538          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLST  278 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~  278 (483)
                       .+..+.|++||.|.|+|+..+.++.+.||.
T Consensus       165 -k~~r~~f~~GDlV~ArV~s~~~~~~~eLsc  194 (289)
T 2nn6_G          165 -KRNRPNVQVGDLIYGQFVVANKDMEPEMVC  194 (289)
T ss_dssp             -SCSSSSSCTTCEEEEEEEECCTTSCCEEEC
T ss_pred             -hhhhhhcCCCCEEEEEEEEcCCCCceEEEe
Confidence             012456999999999999877788888987

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

Probab=96.93  E-value=0.0011  Score=63.73  Aligned_cols=65  Identities=12%  Similarity=0.078  Sum_probs=50.1

Q ss_pred             hCCCeEEEEEEEEECCeEEEEE-CCeEEEeecccc-ccccC-------------ChhhhhhhcCCEEEEEEEEEECCCCc
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVN-------------NFTELKEKVGRRMYVQITRINEDTND  359 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel-~~rv~-------------~~~~l~~~VGq~V~vkVl~ID~e~~r  359 (483)
                      ..|++++|+|++++++|+||.+ +.++|+++.+++ .+...             .-......+|+.|++||.++|...+.
T Consensus        80 ~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~~~~~  159 (218)
T 2ckz_B           80 FLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVDVK  159 (218)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEECCCC
T ss_pred             CCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEcccCC
Confidence            5899999999999999999999 557999999998 33220             00112247899999999999876543

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

Probab=96.71  E-value=0.003  Score=70.78  Aligned_cols=70  Identities=10%  Similarity=0.074  Sum_probs=48.9

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC--CeEEEeeccccc---ccc-----------CCh----hhhhhhcCCEEEEEEEEEE
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL---SRV-----------NNF----TELKEKVGRRMYVQITRIN  354 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel~---~rv-----------~~~----~~l~~~VGq~V~vkVl~ID  354 (483)
                      ...+.++|+|+++.++|+||.+.  |++|+||.+++.   +++           .+.    .. ..++|++|+|+|+.+|
T Consensus       668 ~~~~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~-~~~lGD~V~VkV~~vd  746 (760)
T 2vnu_D          668 NNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPR-DVYVFDKVEVQVRSVM  746 (760)
T ss_dssp             TCCSEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCE-EEETTCEEEEEEC---
T ss_pred             cCceEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCc-EEecCCEEEEEEEEEE
Confidence            34489999999999999999994  799999999983   211           111    12 2379999999999999


Q ss_pred             CC---CCceeechh
Q 011538          355 ED---TNDLILSER  365 (483)
Q Consensus       355 ~e---~~rLiLS~K  365 (483)
                      .+   +++|.+|+|
T Consensus       747 ~~~~~~~kI~lslk  760 (760)
T 2vnu_D          747 DPITSKRKAELLLK  760 (760)
T ss_dssp             -----CCEEEC---
T ss_pred             CccccCCcEEEEeC
Confidence            87   689999875

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

Probab=96.39  E-value=0.0039  Score=71.69  Aligned_cols=70  Identities=10%  Similarity=0.067  Sum_probs=54.8

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC--CeEEEeeccccc--c-cc-----------CC----hhhhhhhcCCEEEEEEEEEE
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL--S-RV-----------NN----FTELKEKVGRRMYVQITRIN  354 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel~--~-rv-----------~~----~~~l~~~VGq~V~vkVl~ID  354 (483)
                      ..|+..+|+|+++.++|+||.+.  |++|+||.+++.  . ++           ++    ... ...+|++|+|+|..+|
T Consensus       885 ~~ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~-~~~lGD~V~VkV~~vd  963 (977)
T 2wp8_J          885 NNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPR-DVYVFDKVEVQVRSVM  963 (977)
T ss_dssp             HTTCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCE-EEETTCEEEEEECCCC
T ss_pred             ccceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCc-EEccCCEEEEEEEEEc
Confidence            34999999999999999999994  799999999984  2 11           11    112 2379999999999998


Q ss_pred             CC---CCceeechh
Q 011538          355 ED---TNDLILSER  365 (483)
Q Consensus       355 ~e---~~rLiLS~K  365 (483)
                      .+   +++|.||+|
T Consensus       964 ~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          964 DPITSKRKAELLLK  977 (977)
T ss_dssp             CSSSCCCCCCEEEC
T ss_pred             CcccCCCceEEEeC
Confidence            63   378888875

>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=91.72  E-value=0.44  Score=39.95  Aligned_cols=57  Identities=9%  Similarity=0.051  Sum_probs=48.5

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc-----cC-cccccCCCCEEEEE
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----TS-VSDLLNEGERVKVL  430 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i-----~~-~~~~~kvGd~VkVk  430 (483)
                      ...|+.+.+.|+++.+.++-|.+.+ |-.+.|+.+.|.|.+-     .. +++.+++||.|.|+
T Consensus        31 ~~~~~~~~AvV~~v~~~~~~v~~~~-g~~~~l~~~~~~WA~~~~~~~~~~~~~~l~~GdvI~V~   93 (106)
T 3d0f_A           31 GNSDDILAAVVLSATPGAVEAFRKN-GETIRITGDGLKAAHRFLSNDPKIGEKRIRPGALIRVK   93 (106)
T ss_dssp             CTTTTCEEEEEEEEETTEEEEEETT-SCEEEECGGGGSTTGGGTTTCTTTGGGSCCTTEEEEEE
T ss_pred             CccCCeEEEEEEEeCCCeEEEEEcC-CCeEEEcHHHChhhhhcccccccchhccCCCCCEEEEE
Confidence            3458999999999999999999976 5788899999999853     34 67789999999987

>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=89.76  E-value=0.53  Score=49.78  Aligned_cols=58  Identities=10%  Similarity=0.082  Sum_probs=44.3

Q ss_pred             CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSL  444 (483)
                      ++|+.+.|.|..+         .+  ..|++|++++..+  ......|++||.|+|+|.++| .+++|.+..
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 QPERVWDAVVVDR---------RG--AQATLLIPDLAFD--VQVNTPAAPGTALQVQFADIDLPQMRVRARS  460 (469)
T ss_dssp             CTTCCEEEEEEEE---------ET--TEEEEEEGGGTEE--EEEECCCCTTCEEEEEEEEEETTTTEEEEEE
T ss_pred             CCCCEEEEEEEEE---------eC--cEEEEEECCCCeE--EecCCcCCCCCEEEEEEEEEccCCCEEEEEE
Confidence            6799999987543         33  3788888888755  223467999999999999998 778887654

>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=88.33  E-value=1.3  Score=41.95  Aligned_cols=66  Identities=15%  Similarity=0.075  Sum_probs=46.7

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc--cccCc----------ccccCCCCEEEEEEEEEeCCC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT--RVTSV----------SDLLNEGERVKVLVVKSMFPD  438 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~--~i~~~----------~~~~kvGd~VkVkVi~vdek~  438 (483)
                      ...+|+++.|+|+.+++.|+.+-+.+. ...+|+...|..+  +..+-          .+.-++|+.|++||.+++.++
T Consensus       126 rPf~GevL~G~V~~~s~~~Ig~~~~G~-Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~~~~~~~  203 (214)
T 2rf4_A          126 QPQVGDVLEGYIFIQSASHIGLLIHDA-FNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTG  203 (214)
T ss_dssp             CCCTTCEEEEEECCCCSSCEEEEETTT-EEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEEEEECCS
T ss_pred             ecCCCCEEEEEEEEECCCcEEEEEeCC-EEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEEEEEecC
Confidence            467899999999999997777655553 6789999887532  11110          012246999999999987444

>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=88.01  E-value=0.99  Score=42.79  Aligned_cols=63  Identities=13%  Similarity=0.188  Sum_probs=45.0

Q ss_pred             hCCCeEEEEEEEEECCeEEEEE-CCeEEEeeccccc---cccCC--------h--hhhhhhcCCEEEEEEEEEECCCC
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELL---SRVNN--------F--TELKEKVGRRMYVQITRINEDTN  358 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I-~Gi~gFVP~Sel~---~rv~~--------~--~~l~~~VGq~V~vkVl~ID~e~~  358 (483)
                      ..|++++|+|+.+.+.|+.+-+ |-+.+|||...+.   ....+        +  ++- ..+|++|+|||..++..++
T Consensus       128 f~GevL~G~V~~~s~~~Ig~~~~G~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~-~~ig~~IRFrV~~~~~~~~  204 (214)
T 2rf4_A          128 QVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNG-EPIDGKLRFTVRNVHTTGR  204 (214)
T ss_dssp             CTTCEEEEEECCCCSSCEEEEETTTEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSC-CBCCSEEEEEEEEEECCSS
T ss_pred             CCCCEEEEEEEEECCCcEEEEEeCCEEEEEcHHHCCCcccccccccccCCCceEcCCC-CCCCCEEEEEEEEEEecCC
Confidence            6899999999999998877755 5588999999882   11111        0  000 1368999999999886443

>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=87.72  E-value=1.7  Score=36.11  Aligned_cols=63  Identities=21%  Similarity=0.205  Sum_probs=48.1

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEecc-CcCcccccCcccccCCCCEEEEEEEEEeC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHIS-NMSRTRVTSVSDLLNEGERVKVLVVKSMF  436 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiS-els~~~i~~~~~~~kvGd~VkVkVi~vde  436 (483)
                      ++.+|++.+|.|. +.++-.+|.+.++ |.+|++--. ++-.++..++++.+ +|.+|+|+|+.+|.
T Consensus        29 ~~~~g~VtkGiVy-~kd~~fyV~L~dY~glEaii~dYvnv~~dr~~klkkkL-VGKtIkVqVIRvD~   93 (102)
T 1jjg_A           29 DLSPGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADG   93 (102)
T ss_dssp             CCCSSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECS
T ss_pred             ccCCCceEeeEEE-EeCCEEEEEecCCCCceeeeehhhhhhHHHHHHHHHHh-cCceEEEEEEEecc
Confidence            6889999999886 5666778999876 789987432 33345666666666 79999999998863

>4b9w_A TDRD1, tudor domain-containing protein 1; replication; HET: 2MR; 2.10A {Mus musculus}

Probab=86.78  E-value=19  Score=33.06  Aligned_cols=170  Identities=14%  Similarity=0.051  Sum_probs=100.4

Q ss_pred             ccccccccCCCCCcEEEEEEEEEe-CCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecc
Q 011538          161 DKVSVEYYEPKPGDFVIGVVVSGN-ENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD  239 (483)
Q Consensus       161 ~~~~~~~~~ik~GdiV~G~Vv~V~-~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~  239 (483)
                      ..++.++.++.+|+.+...|+.+. ++..||.+-... .       .    ..+..+..+    ..++..          
T Consensus         4 ~~l~~~~~~l~~~~~~~V~Vt~v~sP~~Fyvq~~~~~-~-------~----~~l~~L~~~----l~~~~~----------   57 (201)
T 4b9w_A            4 EALEWTWVEFTVDETVDVVVCMMYSPGEFYCHFLKDD-A-------L----EKLDDLNQS----LADYCA----------   57 (201)
T ss_dssp             --CCCCBCCCCTTCEEEEEEEEEEETTEEEEEECCTT-H-------H----HHHHHHHHH----HHHHHH----------
T ss_pred             CcceeEEEEcCCCCEEEEEEEEEeCCCEEEEEECCCc-h-------H----HHHHHHHHH----HHHHHh----------
Confidence            456677888999999999999994 577888763210 0       0    011111111    111100          


Q ss_pred             ccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhHHHHHHhhCCCeEEEEEEEEECCe-EEEEE--
Q 011538          240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGG-LLTRI--  316 (483)
Q Consensus       240 d~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G-~fV~I--  316 (483)
                            .. ......+++|+..-|..   .                         ..|....|+|+++.+.| +.|.+  
T Consensus        58 ------~~-~~~~~~~~~G~~c~a~~---~-------------------------~d~~wyRa~V~~~~~~~~~~V~~vD  102 (201)
T 4b9w_A           58 ------QK-PPNGFKAEIGRPCCAFF---S-------------------------GDGNWYRALVKEILPSGNVKVHFVD  102 (201)
T ss_dssp             ------SS-SCCCCCCCTTCEEEEEE---T-------------------------TTTEEEEEEEEEECTTSCEEEEETT
T ss_pred             ------cC-CCCCCCCCCCCEEEEEE---C-------------------------CCCeEEEEEEEEECCCCeEEEEEEc
Confidence                  00 00112356777654431   1                         24678899999987665 55655  


Q ss_pred             CCeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhhhcCCCCCcEEEEEEEEEeCceEEEEEC
Q 011538          317 EGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIG  396 (483)
Q Consensus       317 ~Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e~~~l~vG~iv~G~V~~I~~~GaFV~I~  396 (483)
                      -|....+|.+++..-   +.++.....+-++|++-.+.+.++.  -|........++-.|..+.++|..+...+..|.+.
T Consensus       103 yG~~~~v~~~~l~~l---~~~f~~lP~qA~~c~L~~v~p~~~~--w~~ea~~~f~~l~~~k~l~~~V~~~~~~~~~V~L~  177 (201)
T 4b9w_A          103 YGNVEEVTTDQLQAI---LPQFLLLPFQGMQCWLVDIQPPNKH--WTKEATARFQACVVGLKLQARVVEITANGVGVELT  177 (201)
T ss_dssp             TCCEEEECGGGEEEC---CGGGGSSCBCCEEEEESSEECSSSS--CCHHHHHHHHHHHTTCCEEEEEEEEETTEEEEEEE
T ss_pred             cCCEEEEEHHHhccC---hHhHcccchhhEEEEEcCEEcCCCC--CCHHHHHHHHHHHCCCEEEEEEEEEeCCEEEEEEE
Confidence            377889999998321   1223335789999998888765432  12221111124456888999999999888888774

---

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	483
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	2e-11
d1e3pa2	62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	6e-09
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	8e-09
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	7e-08
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	0.002
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	6e-06
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	8e-06
d1kl9a2	86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	1e-05
d1wi5a_	119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	1e-05
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	1e-05
d2ahob2	84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	2e-05
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	8e-04

>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 = 57.1 bits (138), Expect = 2e-11
 Identities = 26/72 (36%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432
           +  G +  G V +I  +GA + IG   + GL+HIS ++  RV  V+D L  G+ V V V+
Sbjct: 3   IEVGRVYTGKVTRIVDFGAFVAIGG-GKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVL 61

Query: 433 KSMFPDKISLSI 444
           +     +I LSI
Sbjct: 62  EVDRQGRIRLSI 73

>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 = 50.1 bits (120), Expect = 6e-09
 Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 5/57 (8%)

Query: 381 GTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT----RVTSVSDLLNEGERVKVLVVK 433
           G+V K   +GA + +    + GLLHIS + +     RV +V D+L  G++V+V + +
Sbjct: 1   GSVVKTTTFGAFVSLLP-GKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAE 56

>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 = 50.7 bits (121), Expect = 8e-09
 Identities = 29/90 (32%), Positives = 51/90 (56%), Gaps = 4/90 (4%)

Query: 365 REAWATL-NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNE 423
           +E   +L +L+ G +LEG V  +  +GA + IG  ++ GL+HIS +S   V    +++  
Sbjct: 7   QEGVESLKDLKPGMVLEGVVTNVTNFGAFVDIGV-HQDGLVHISALSEKFVKDPYEVVKA 65

Query: 424 GERVKVLVVKSMFPD-KISLSIADLESEPG 452
           G+ VKV V++   P  ++ LS+   +  PG
Sbjct: 66  GDIVKVKVMEVDIPRNRVGLSMRMSD-TPG 94

>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 = 48.0 bits (114), Expect = 7e-08
 Identities = 11/78 (14%), Positives = 26/78 (33%), Gaps = 5/78 (6%)

Query: 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----TSVSDLLNEGERVKV 429
           + G ++ G ++ +      + I       +L + +            +  LL  G+ +K 
Sbjct: 6   QAGDVVIGLIQSVGIMNWFVDINS-PYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKA 64

Query: 430 LVVKSMFPDKISLSIADL 447
            VV         L++   
Sbjct: 65  KVVAFDKTRSPLLTVQGE 82

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 88

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 13/65 (20%), Positives = 26/65 (40%)

Query: 166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAE 225
           E Y P+ GD VIG++ S       V++ +  +  +  ++ L          +  L K  +
Sbjct: 1   EIYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGD 60

Query: 226 EFMVR 230
               +
Sbjct: 61  YIKAK 65

>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 = 42.3 bits (99), Expect = 6e-06
 Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 4/77 (5%)

Query: 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSV---SDLLNEGERVKVL 430
           +   ++ G V+ +  YG  + I        L  SN+    +         L+ G+ V   
Sbjct: 6   KINDIVIGLVEDVEIYGWVVDIKA-PYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIAR 64

Query: 431 VVKSMFPDKISLSIADL 447
           +          LS+   
Sbjct: 65  IENFDRSIDPVLSVKGK 81

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.2 bits (99), Expect = 8e-06
 Identities = 15/84 (17%), Positives = 35/84 (41%), Gaps = 13/84 (15%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS----------RTRVTSVSDLLNEGE 425
           G ++ G + ++     ++    S    +L +S+M+               ++   L EG+
Sbjct: 9   GDIVVGRITEVQQKRWKVETN-SRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGD 67

Query: 426 RVKVLVVKSMFPD-KISLSIADLE 448
            +    V+++F D  +SL    L+
Sbjct: 68  LISA-EVQAVFSDGAVSLHTRSLK 90

>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 = 41.5 bits (97), Expect = 1e-05
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 374 REGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432
               ++   V+ I   GA + + + +N  G++ +S +SR R+ S++ L+  G    V+V+
Sbjct: 12  EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVI 71

Query: 433 KSMFPD-KISLSI 444
           +       I LS 
Sbjct: 72  RVDKEKGYIDLSK 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 = 42.4 bits (99), Expect = 1e-05
 Identities = 20/82 (24%), Positives = 31/82 (37%), Gaps = 2/82 (2%)

Query: 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVL 430
            L+ G LL GTV  +  +G  + IG       L +       R  +    L  G+ +  +
Sbjct: 18  ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCI 77

Query: 431 VVK-SMFPDKISLSIADLESEP 451
           V K       +SLS+   E   
Sbjct: 78  VEKVKGNGGVVSLSVGHSEVST 99

>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 = 41.1 bits (96), Expect = 1e-05
 Identities = 13/79 (16%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS-RTRVTSVSDLLNEGERVKVLVV 432
             G ++ G ++++   G  + I        L +S           +++L+ G+ +   V+
Sbjct: 4   SVGDVVIGIIREVAANGWAVDIYS-PYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVL 62

Query: 433 KSMFPDKISLSIADLESEP 451
                 K++L++ D    P
Sbjct: 63  NIDPKMKVTLTMKDRICRP 81

>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 = 40.4 bits (94), Expect = 2e-05
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 375 EGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433
           EG +L  TVK+++ YG+ + + +       L  S +S   V ++ D+L E  +V V V++
Sbjct: 11  EGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIR 70

Query: 434 SMFPD-KISLSI 444
                  + +S+
Sbjct: 71  VDRRKGTVDVSL 82

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 106

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 36.9 bits (85), Expect = 8e-04
 Identities = 19/100 (19%), Positives = 42/100 (42%), Gaps = 19/100 (19%)

Query: 376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEG 424
             L+EG V  +  +G+ +R+G  +  GL+H+S +    V+               +L  G
Sbjct: 4   YELIEGEVVDVVEFGSFVRLGPLD--GLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIG 61

Query: 425 ERVKVLVV------KSMFPDKISLSIADLESEPGLFVSDK 458
           + V+  +V      +     KI+L++         ++ ++
Sbjct: 62  DYVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIEEE 101

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	483
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.72
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.66
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.63
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.61
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.59
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.56
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.47
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.46
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.42
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.38
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.35
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.34
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.32
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.24
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.21
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.14
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.14
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.11
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.03
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	99.02
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.0
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.99
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.82
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.8
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	98.72
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.59
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	98.59
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.56
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.48
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.47
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.34
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.34
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.33
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.29
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	98.07
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.83
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.76
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.36
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.25
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	96.13
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	92.86
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	92.51
d3d31a1	119	Sulfate/molybdate ABC transporter, ATP-binding pro	91.87
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	89.25
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	88.41
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	85.78
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	81.36

>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=99.72  E-value=2.1e-18  Score=138.06  Aligned_cols=75  Identities=35%  Similarity=0.588  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~  447 (483)
                      ++++|+++.|+|++|++||+||+|++ +++||||.++|+|.++.++++.|++||+|+|+|+++|+++||.||+|++
T Consensus         2 d~kvG~iv~G~V~~v~~~G~fV~l~~-~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~~~ri~LS~k~a   76 (76)
T d1sroa_           2 EIEVGRVYTGKVTRIVDFGAFVAIGG-GKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEA   76 (76)
T ss_dssp             CCCTTSEEEEEEEEEETTEEEEECSS-SCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCTTCCCEEEECCC
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEeCC-CCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECCCCCEEEEEEcC
Confidence            68999999999999999999999988 7999999999999999999999999999999999998778999999974

>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=99.66  E-value=1e-16  Score=133.16  Aligned_cols=80  Identities=33%  Similarity=0.544  Sum_probs=76.1

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCCC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~~  449 (483)
                      .++++|+++.|+|++|+++|+||+|++ +++||||.++++|.++.++++.|++||.|+|+|+++| +++||.||+|+. +
T Consensus        14 ~~~k~G~iv~g~V~~v~~~G~~V~l~~-~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~~i~LS~K~~-e   91 (94)
T d3bzka4          14 KDLKPGMVLEGVVTNVTNFGAFVDIGV-HQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMS-D   91 (94)
T ss_dssp             GGCCTTCEEEEEEEEEETTEEEEECSS-SSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEESCTT-C
T ss_pred             hcCCCCCEEEEEEEEEECcEEEEEeCC-CceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEEecc-C
Confidence            579999999999999999999999988 8999999999999999999999999999999999998 899999999975 7


Q ss_pred             CcC
Q 011538          450 EPG  452 (483)
Q Consensus       450 dPw  452 (483)
                      +|.
T Consensus        92 ~P~   94 (94)
T d3bzka4          92 TPG   94 (94)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            784

>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=99.63  E-value=3.8e-16  Score=127.43  Aligned_cols=74  Identities=24%  Similarity=0.322  Sum_probs=57.7

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD  446 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~  446 (483)
                      .++|+++.|+|++|+++|+||+|... |++||||.++++|.++.++.+.|++||.|+|+|+++| +++||.||+|+
T Consensus        11 p~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~ki~LS~Kq   86 (86)
T d1kl9a2          11 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEEECCCCEEEEEeeC
Confidence            36899999999999999999999632 7999999999999999999999999999999999998 88999999986

>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=99.61  E-value=4e-16  Score=126.56  Aligned_cols=74  Identities=26%  Similarity=0.444  Sum_probs=64.6

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD  446 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~  446 (483)
                      .++|+++.|+|++|+++|+||+|... |++||+|.++++|.++.++.+.|++||.|+|+|+++| ++++|.||+|+
T Consensus         9 p~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2           9 PSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             CCTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEEcC
Confidence            46899999999999999999999742 7999999999999999999999999999999999998 88999999985

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.59  E-value=1.5e-15  Score=122.82  Aligned_cols=79  Identities=16%  Similarity=0.243  Sum_probs=72.8

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccc-ccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCCCCc
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR-VTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP  451 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~-i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~~dP  451 (483)
                      .++|++|.|+|++++++|+||+|++ ++.||||.++++|.+ ..++++.|++||.|.|+|+++++++||.||+|+....|
T Consensus         3 Pk~Gd~V~G~V~~v~~~g~~V~i~~-~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~i~LS~k~~~~~k   81 (83)
T d2ba0a1           3 PSVGDVVIGIIREVAANGWAVDIYS-PYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRICRP   81 (83)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECSS-SSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCSSSCEE
T ss_pred             CCCCCEEEEEEEEEECCEEEEecCC-CeeEEEecccccccccccChhhhcccccEEEEEEEEECCCCCEEEEecCCCCCC
Confidence            4789999999999999999999998 799999999999875 67899999999999999999987789999999987766


Q ss_pred             C
Q 011538          452 G  452 (483)
Q Consensus       452 w  452 (483)
                      +
T Consensus        82 ~   82 (83)
T d2ba0a1          82 I   82 (83)
T ss_dssp             E
T ss_pred             C
Confidence            4

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.56  E-value=1.9e-15  Score=128.10  Aligned_cols=84  Identities=21%  Similarity=0.395  Sum_probs=74.7

Q ss_pred             CCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc-----------cCcccccCCCCEEEEEEEEEe-CCCe--
Q 011538          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDK--  439 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i-----------~~~~~~~kvGd~VkVkVi~vd-ek~r--  439 (483)
                      ++|++++|+|++|++||+||+|+  +++||||.++|+++++           .++.+.|++||.|+|+|+++| ++++  
T Consensus         2 ~~gei~~g~V~~v~~~G~FVel~--~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~~~~~~   79 (106)
T d1go3e1           2 EMYELIEGEVVDVVEFGSFVRLG--PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKR   79 (106)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECS--SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC----
T ss_pred             CCCCEEEEEEEEEeeeEEEEEee--CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchhhcccc
Confidence            68999999999999999999996  5899999999999877           478899999999999999998 5544  


Q ss_pred             ---EEEEEecCCCCcCccccccc
Q 011538          440 ---ISLSIADLESEPGLFVSDKE  459 (483)
Q Consensus       440 ---I~LSLK~~~~dPw~~l~~k~  459 (483)
                         |.||+|+...+||+.++++.
T Consensus        80 ~~~i~ls~K~~~~~~~e~~~~~~  102 (106)
T d1go3e1          80 GSKIALTMRQPYLGKLEWIEEEK  102 (106)
T ss_dssp             -CEEEEECCSTTCEEHHHHHHHH
T ss_pred             CceeecccccCCCCcchhhhhHh
Confidence               89999999999999877654

>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=99.47  E-value=2.4e-14  Score=116.81  Aligned_cols=74  Identities=18%  Similarity=0.173  Sum_probs=67.9

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc---CcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT---SVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~---~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~  447 (483)
                      .++|+++.|+|++|+++|+||+|++ +++||||.++++|+++.   ++++.|++||.|.|+|+++|+.+++.||+|+.
T Consensus         5 Pk~Gdiv~G~V~~i~~~g~fV~i~~-~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~i~LS~k~~   81 (87)
T d2je6i1           5 PKINDIVIGLVEDVEIYGWVVDIKA-PYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGK   81 (87)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECSS-SSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCST
T ss_pred             CCCCCEEEEEEEEEECCEEEEEeCC-CEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECCCCCEEEEEecC
Confidence            4689999999999999999999988 79999999999998664   57788999999999999999778999999975

>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=99.46  E-value=3.2e-14  Score=116.16  Aligned_cols=74  Identities=15%  Similarity=0.184  Sum_probs=68.1

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc----CcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT----SVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~----~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~  447 (483)
                      .++|++|.|+|++++++|+||+|++ +++||||.+++++.++.    ++++.|++||.|.|+|+++++++++.||+|+.
T Consensus         5 Pk~GdvV~G~V~~v~~~g~fV~i~~-~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~i~Ls~k~~   82 (88)
T d2z0sa1           5 PQAGDVVIGLIQSVGIMNWFVDINS-PYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGE   82 (88)
T ss_dssp             CCTTCCEEEEEEEECSSEEEEECSS-SSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSS
T ss_pred             CCCCCEEEEEEEEEECCeEEEEeCC-CeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECCCCCEEEEEecC
Confidence            5799999999999999999999988 79999999999998764    67788999999999999999778999999964

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

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=1e-13  Score=119.60  Aligned_cols=81  Identities=25%  Similarity=0.303  Sum_probs=72.6

Q ss_pred             cCCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc-cccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       371 ~~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~-~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      ..|++|+++.|+|++|+++|+||+|+..+++||||++++++. +..++.+.|++||.|+|+|++++ ++++|.||+|+..
T Consensus        17 ~~l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~k~~~   96 (119)
T d1wi5a_          17 EALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSE   96 (119)
T ss_dssp             TTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCCC
T ss_pred             hhcCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEEecHHH
Confidence            479999999999999999999999962279999999999987 47789999999999999999998 7789999999876


Q ss_pred             CCc
Q 011538          449 SEP  451 (483)
Q Consensus       449 ~dP  451 (483)
                      ...
T Consensus        97 ~~~   99 (119)
T d1wi5a_          97 VST   99 (119)
T ss_dssp             SCC
T ss_pred             hhh
Confidence            543

>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=99.38  E-value=6.3e-13  Score=107.96  Aligned_cols=71  Identities=18%  Similarity=0.361  Sum_probs=57.2

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC---CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~---Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~  366 (483)
                      +.|+++.|+|+++.++|+||++.   |++||||.+++ +.+..++.+.. .+||.|.|+|+++|++++++.||+|+
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 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLI-RIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC-------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEEe-ecccEEEEEEEEEECCCCEEEEEeeC
Confidence            58999999999999999999994   79999999999 77888888775 89999999999999999999999984

>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=99.35  E-value=3.4e-13  Score=107.32  Aligned_cols=72  Identities=19%  Similarity=0.278  Sum_probs=65.8

Q ss_pred             hhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       294 ~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      ++.|++++|+|+++.++|+||+++ |+.||||.+++ +.+..++++.. .+||+++|+|+++|+ ++|+.||+|++
T Consensus         3 ~kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~-~~G~~v~v~Vi~id~-~~ri~LS~k~a   76 (76)
T d1sroa_           3 IEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYL-QMGQEVPVKVLEVDR-QGRIRLSIKEA   76 (76)
T ss_dssp             CCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCSCHHHHC-CTTCEEEEEEEECCT-TCCCEEEECCC
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccCCHHHcc-CCCCEEEEEEEEECC-CCCEEEEEEcC
Confidence            478999999999999999999995 79999999999 78888998875 899999999999996 57899999864

>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=99.34  E-value=1e-12  Score=106.12  Aligned_cols=71  Identities=23%  Similarity=0.358  Sum_probs=61.8

Q ss_pred             hCCCeEEEEEEEEECCeEEEEEC---CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhh
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~---Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~  366 (483)
                      +.|++++|+|+++.++|+||+++   |++||+|.+++ +.+..++.+.. .+||.++|+|+++|++++++.||+|+
T Consensus        10 ~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~-~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2          10 SEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVL-KENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             CTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----CHHHHT-CSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccccceEe-ecccEEEEEEEEEECCCCEEEEEEcC
Confidence            58999999999999999999994   79999999999 77888888875 89999999999999999999999974

>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=99.32  E-value=1.3e-12  Score=107.88  Aligned_cols=85  Identities=16%  Similarity=0.075  Sum_probs=72.9

Q ss_pred             HHHHhhhHHHHHHhhCCCeEEEEEEEEECCeEEEEEC-CeEEEeecccc-ccccCChhhhhhhcCCEEEEEEEEEECCCC
Q 011538          281 LFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTN  358 (483)
Q Consensus       281 ~~~~~~w~~L~~~~k~GeiV~GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~  358 (483)
                      +...+.++.+. .++.|+++.|+|+++.++|+||+++ |+.||+|.+++ +.++.++.+.+ ++||.|.|+|+++|++++
T Consensus         4 a~~~~~ie~~~-~~k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~-~vGq~v~~~V~~id~~~~   81 (94)
T d3bzka4           4 AEFQEGVESLK-DLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVV-KAGDIVKVKVMEVDIPRN   81 (94)
T ss_dssp             HHHHHTCCCGG-GCCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSCHHHHC-CTTCEEEEEEEEEETTTT
T ss_pred             hHHHhhhhHHh-cCCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccChhhhh-ccCcEEEEEEEEEECCCC
Confidence            33344444443 4589999999999999999999995 79999999999 77888888875 899999999999999999


Q ss_pred             ceeechhhH
Q 011538          359 DLILSEREA  367 (483)
Q Consensus       359 rLiLS~K~~  367 (483)
                      ++.||+|+.
T Consensus        82 ~i~LS~K~~   90 (94)
T d3bzka4          82 RVGLSMRMS   90 (94)
T ss_dssp             EEEEESCTT
T ss_pred             EEEEEEecc
Confidence            999999864

>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=99.24  E-value=7.6e-14  Score=107.22  Aligned_cols=58  Identities=34%  Similarity=0.545  Sum_probs=36.1

Q ss_pred             EEEEEEeCceEEEEECCCceEEEEeccCcCcc----cccCcccccCCCCEEEEEEEEEeCCCe
Q 011538          381 GTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT----RVTSVSDLLNEGERVKVLVVKSMFPDK  439 (483)
Q Consensus       381 G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~----~i~~~~~~~kvGd~VkVkVi~vdek~r  439 (483)
                      |+|++|++|||||+|++ +++||||+|+|+|.    ++.++++.|++||+|+|+|+++|+++|
T Consensus         1 G~V~~i~~fG~FV~l~~-g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~~r   62 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLP-GKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGK   62 (62)
T ss_dssp             CBEEECC-CSCEECCC----CCCCC-------------------CCSSCBCCCCCCCCCSSCC
T ss_pred             CEEEEEEeceEEEEecC-CceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCCCC
Confidence            78999999999999998 89999999999864    788999999999999999999985544

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.21  E-value=4.1e-12  Score=105.22  Aligned_cols=74  Identities=16%  Similarity=0.243  Sum_probs=64.6

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcc----------cccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT----------RVTSVSDLLNEGERVKVLVVKSMFPDKISL  442 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~----------~i~~~~~~~kvGd~VkVkVi~vdek~rI~L  442 (483)
                      .++|++|.|+|+++.++|+||+|+. +.+|+||+|+++|.          +..++++.|++||.|.|+|++++.++++.|
T Consensus         6 P~vGdiV~G~V~~v~~~g~~V~I~~-~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~dg~i~L   84 (95)
T d2nn6h1           6 GEVGDIVVGRITEVQQKRWKVETNS-RLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSL   84 (95)
T ss_dssp             CCSSBCCCEEEEEEETTEEEEECSS-SSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTEEEE
T ss_pred             CCCCCEEEEEEEEEecCcEEEEeCC-CceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECCCCCEEE
Confidence            4689999999999999999999987 68999999999763          334567889999999999999998899999


Q ss_pred             EEecC
Q 011538          443 SIADL  447 (483)
Q Consensus       443 SLK~~  447 (483)
                      |+|..
T Consensus        85 s~r~~   89 (95)
T d2nn6h1          85 HTRSL   89 (95)
T ss_dssp             ECCSS
T ss_pred             Eeccc
Confidence            99864

>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=99.14  E-value=9.5e-11  Score=94.06  Aligned_cols=77  Identities=21%  Similarity=0.286  Sum_probs=64.2

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      |.+++||+|.|+|.+++++|+||+++.+..|+||.+|++....          .                          
T Consensus         1 Y~Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~----------~--------------------------   44 (83)
T d2ba0a1           1 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKP----------N--------------------------   44 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCT----------T--------------------------
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEecCCCeeEEEeccccccccc----------c--------------------------
Confidence            4578999999999999999999999999999999999863210          0                          


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~  281 (483)
                       .+....|++||.|.|+|+..+.++++.||+|..
T Consensus        45 -~~~~~~~~vGd~V~~kV~~vd~~~~i~LS~k~~   77 (83)
T d2ba0a1          45 -KKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDR   77 (83)
T ss_dssp             -SCGGGTCCTTCEEEEEEEEECTTCCEEEECCSS
T ss_pred             -cChhhhcccccEEEEEEEEECCCCCEEEEecCC
Confidence             011245899999999999988889999999864

>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=99.14  E-value=6.9e-11  Score=95.86  Aligned_cols=81  Identities=22%  Similarity=0.224  Sum_probs=66.3

Q ss_pred             cccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecccccccc
Q 011538          166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS  245 (483)
Q Consensus       166 ~~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~  245 (483)
                      ++|.+++||+|.|+|++++++|+||+++.+.+|+||.+|+...+.           .+                      
T Consensus         1 s~Y~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~-----------~~----------------------   47 (87)
T d2je6i1           1 SFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSI-----------NV----------------------   47 (87)
T ss_dssp             SCCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCC-----------CT----------------------
T ss_pred             CcccCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCcee-----------cc----------------------
Confidence            457799999999999999999999999999999999999864210           00                      


Q ss_pred             CCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538          246 GGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (483)
Q Consensus       246 ~~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~  281 (483)
                        ..+....+++||.|.|+|+..|.++++.||+|..
T Consensus        48 --~~~~~~~~~~Gd~v~~kV~~vd~~~~i~LS~k~~   81 (87)
T d2je6i1          48 --GEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGK   81 (87)
T ss_dssp             --TCCCSSSCCTTCEEEEEEEEEETTEEEEEECCST
T ss_pred             --ccccchhhcccceEEEEEEEECCCCCEEEEEecC
Confidence              0112356899999999999988889999999864

>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=99.11  E-value=1.2e-10  Score=94.61  Aligned_cols=81  Identities=20%  Similarity=0.282  Sum_probs=66.3

Q ss_pred             ccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccC
Q 011538          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (483)
Q Consensus       167 ~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~  246 (483)
                      .|.+++||+|.|+|++++++|+||+++...+|+||.+|++..+.+                                  .
T Consensus         2 ~Y~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~~~----------------------------------~   47 (88)
T d2z0sa1           2 IYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFN----------------------------------P   47 (88)
T ss_dssp             CCCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCC----------------------------------T
T ss_pred             CcCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCccccc----------------------------------c
Confidence            477899999999999999999999999999999999998643100                                  0


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (483)
Q Consensus       247 ~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~  281 (483)
                      ...+....+++||.|.|+|++.|.++++.||+|..
T Consensus        48 ~~~~~~~~~~vGd~V~~kV~~vd~~~~i~Ls~k~~   82 (88)
T d2z0sa1          48 AVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGE   82 (88)
T ss_dssp             TTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSS
T ss_pred             cccchhhhcccCcEEEEEEEEECCCCCEEEEEecC
Confidence            00122456899999999999998889999999864

>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=99.03  E-value=2e-10  Score=96.70  Aligned_cols=72  Identities=17%  Similarity=0.247  Sum_probs=58.8

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeecccc-cccc-----------CChhhhhhhcCCEEEEEEEEEECCCCc---
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRV-----------NNFTELKEKVGRRMYVQITRINEDTND---  359 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv-----------~~~~~l~~~VGq~V~vkVl~ID~e~~r---  359 (483)
                      +.|++++|+|+++.++|+||++++++||||.++| ++++           .++.... .+||.|+++|++||.++++   
T Consensus         2 ~~gei~~g~V~~v~~~G~FVel~~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~-~~Gd~v~vkV~~vd~~~~~~~~   80 (106)
T d1go3e1           2 EMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVL-EIGDYVRARIVAISLKAERKRG   80 (106)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC--CEEETTTCCEE-CTTCEEEEEEEEEECCC-----
T ss_pred             CCCCEEEEEEEEEeeeEEEEEeeCeEEEEEeecccCceeeeccceeEEeecccccce-eecceEEEEEEEEchhhccccC
Confidence            5799999999999999999999999999999999 4443           2333333 7999999999999988776   


Q ss_pred             --eeechhhH
Q 011538          360 --LILSEREA  367 (483)
Q Consensus       360 --LiLS~K~~  367 (483)
                        +.+|+|+.
T Consensus        81 ~~i~ls~K~~   90 (106)
T d1go3e1          81 SKIALTMRQP   90 (106)
T ss_dssp             CEEEEECCST
T ss_pred             ceeecccccC
Confidence              67787753

>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=99.02  E-value=5.1e-10  Score=91.11  Aligned_cols=68  Identities=12%  Similarity=0.131  Sum_probs=58.7

Q ss_pred             CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccccc------------CcccccCCCCEEEEEEEEEe-CCCeEE
Q 011538          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT------------SVSDLLNEGERVKVLVVKSM-FPDKIS  441 (483)
Q Consensus       375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~------------~~~~~~kvGd~VkVkVi~vd-ek~rI~  441 (483)
                      .|+.++|+|++|+++|+||+|.+.+++||+|+++|.++++.            +....|++||+|+|+|+++| ++++|.
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            47889999999999999999976579999999999988542            23457999999999999998 788886


Q ss_pred             E
Q 011538          442 L  442 (483)
Q Consensus       442 L  442 (483)
                      +
T Consensus        83 ~   83 (87)
T d2ix0a3          83 A   83 (87)
T ss_dssp             E
T ss_pred             E
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=99.00  E-value=8.3e-11  Score=100.98  Aligned_cols=74  Identities=22%  Similarity=0.240  Sum_probs=63.4

Q ss_pred             HhhCCCeEEEEEEEEECCeEEEEEC--CeEEEeecccc-cc-ccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhH
Q 011538          293 IKQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (483)
Q Consensus       293 ~~k~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel-~~-rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~  367 (483)
                      .++.|++++|+|+++.++|+||+++  +++||||.+++ +. +.+++.+.+ ++||.|.|+|+++|++++++.||+|+.
T Consensus        18 ~l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~-~vGq~v~~~V~~vd~~~~~i~LS~k~~   95 (119)
T d1wi5a_          18 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKL-KVGQYLNCIVEKVKGNGGVVSLSVGHS   95 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCC-CTTCEEEEEEEECCTTSCEEEEECCCC
T ss_pred             hcCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhccccccCCHHHhc-ccceEEEEEEEEEeCCCCEEEEEecHH
Confidence            3589999999999999999999994  79999999999 32 344444433 799999999999999999999999864

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.99  E-value=1.4e-09  Score=88.66  Aligned_cols=66  Identities=18%  Similarity=0.291  Sum_probs=58.1

Q ss_pred             CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccc----------cCcccccCCCCEEEEEEEEEe-CCCeEEE
Q 011538          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----------TSVSDLLNEGERVKVLVVKSM-FPDKISL  442 (483)
Q Consensus       375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i----------~~~~~~~kvGd~VkVkVi~vd-ek~rI~L  442 (483)
                      +|++++|+|++++++|+||+++.  ++||+|+++|.+++.          .+....++.||.|+|||++++ ++++|..
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg~--~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~i~~   79 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVGP--MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHA   79 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETT--EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTEEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEEcC--eEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccCccEE
Confidence            69999999999999999999974  799999999987743          345668999999999999998 7888865

>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=98.82  E-value=8.8e-09  Score=84.34  Aligned_cols=75  Identities=12%  Similarity=0.187  Sum_probs=62.2

Q ss_pred             CCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCccc-c-----------cCcccccCCCCEEEEEEEEEe-CCCeEE
Q 011538          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR-V-----------TSVSDLLNEGERVKVLVVKSM-FPDKIS  441 (483)
Q Consensus       375 vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~-i-----------~~~~~~~kvGd~VkVkVi~vd-ek~rI~  441 (483)
                      .|++++|+|++++++|+||+++.  ++||+|.++|.+++ +           .+....|+.||.|++||++++ +.++|.
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg~--~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~I~   81 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIGP--MSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIF   81 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETT--EEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEecC--ceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCcce
Confidence            59999999999999999999974  79999999999875 2           344567999999999999997 788885


Q ss_pred             EEEecCCCCcCc
Q 011538          442 LSIADLESEPGL  453 (483)
Q Consensus       442 LSLK~~~~dPw~  453 (483)
                      .-  ....+||.
T Consensus        82 ~i--gt~~~d~L   91 (94)
T d2c35b1          82 AI--GSLMDDYL   91 (94)
T ss_dssp             EE--EECCSTTC
T ss_pred             EE--EEccCCCc
Confidence            42  35556664

>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=98.80  E-value=5e-09  Score=85.28  Aligned_cols=74  Identities=11%  Similarity=0.004  Sum_probs=67.7

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCC
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLE  448 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~~  448 (483)
                      .++||+|.|+|++++.+|+||+|+. ...|+||.+++. .+.++.+..+++||.|.|||.+++..+++.||+.+..
T Consensus         4 P~~GD~ViG~V~~~~~~~~~VdI~s-~~~a~L~~~~f~-g~~k~~r~~l~~GD~V~arV~~v~~~~~~~Lscvd~~   77 (88)
T d2nn6g1           4 PVKGDHVIGIVTAKSGDIFKVDVGG-SEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSC   77 (88)
T ss_dssp             CCSSEEEEEEEEEEETTEEEEECSS-SSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCTTSCCEEECSBTT
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEcCC-CeeEEEeHHHcC-ccccccCcccCCCCEEEEEEEEeCCCCCEEEEEEccc
Confidence            4789999999999999999999998 689999999995 5788889999999999999999998899999998653

>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=98.72  E-value=6.2e-09  Score=85.65  Aligned_cols=87  Identities=23%  Similarity=0.239  Sum_probs=63.5

Q ss_pred             ccCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccC
Q 011538          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (483)
Q Consensus       167 ~~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~  246 (483)
                      -|.+++||+|.|+|+++.+++++|+|+...+|+||++++....   .. .......+..+                    
T Consensus         3 ~Y~P~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~---~~-~rr~~~~~~~~--------------------   58 (95)
T d2nn6h1           3 RYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPG---GE-LRRRSAEDELA--------------------   58 (95)
T ss_dssp             CCCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-----------------CHH--------------------
T ss_pred             cccCCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccc---cc-cccccchhhhh--------------------
Confidence            3568899999999999999999999999999999999985210   00 00000000000                    


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (483)
Q Consensus       247 ~~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~  281 (483)
                          ....+++||.|.|+|++.+.+|++.||+|..
T Consensus        59 ----~~~~~~~Gd~V~~kV~~v~~dg~i~Ls~r~~   89 (95)
T d2nn6h1          59 ----MRGFLQEGDLISAEVQAVFSDGAVSLHTRSL   89 (95)
T ss_dssp             ----HHHHSCSSCEECCEEEEEETTTEEEEECCSS
T ss_pred             ----hhhhcccccEEEEEEEEECCCCCEEEEeccc
Confidence                1234899999999999998899999999864

>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=98.59  E-value=4.5e-08  Score=79.81  Aligned_cols=74  Identities=9%  Similarity=0.005  Sum_probs=68.0

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~LSLK~~  447 (483)
                      -++||+|.|+|+++...++||+|+. ...|++|.+...+...++.+..+++||.|-|||.+++.++++.||+++.
T Consensus         5 P~~gD~ViG~V~~~~~~~~~vdI~~-~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~~~~~~Lsc~~~   78 (90)
T d2ja9a1           5 PSVNDFVIGVIIGTFSDSYKVSLQN-FSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDS   78 (90)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEESST-TSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCTTSCCEEESSCT
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEcCC-cchhhhhhhhccCccccccCCccCCCCEEEEEEEEECCCCCEEEEEecc
Confidence            4789999999999999999999987 5899999998888888999999999999999999999888999998753

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

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

Probab=98.59  E-value=6.1e-10  Score=85.00  Aligned_cols=55  Identities=22%  Similarity=0.329  Sum_probs=35.0

Q ss_pred             EEEEEEECCeEEEEEC-CeEEEeecccc-c----cccCChhhhhhhcCCEEEEEEEEEECCC
Q 011538          302 VKFTEWNTGGLLTRIE-GLRAFLPKAEL-L----SRVNNFTELKEKVGRRMYVQITRINEDT  357 (483)
Q Consensus       302 GkV~~v~k~G~fV~I~-Gi~gFVP~Sel-~----~rv~~~~~l~~~VGq~V~vkVl~ID~e~  357 (483)
                      |+|+++.++|+||+++ |++||||.|+| +    .+++++++.. ++||+|+|+|+++|+++
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~~~~~~v~~~~~~~-~~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVL-GVGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC-------------------C-CSSCBCCCCCCCCCSSC
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHcccccccccccCHHHhc-CCCCEEEEEEEEEcCCC
Confidence            7899999999999995 89999999999 3    3667787765 89999999999999754

>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=98.56  E-value=1.3e-07  Score=76.73  Aligned_cols=75  Identities=21%  Similarity=0.344  Sum_probs=63.1

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      |.+++||+|.|+|+++..++++|||+....|+||.+++...                        +              
T Consensus         2 Y~P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~g~------------------------~--------------   43 (88)
T d2nn6g1           2 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGA------------------------T--------------   43 (88)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCC------------------------S--------------
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcCcc------------------------c--------------
Confidence            56889999999999999999999999999999999887321                        0              


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~  281 (483)
                       .+.++.+++||.|.|+|...+.++++.||...+
T Consensus        44 -k~~r~~l~~GD~V~arV~~v~~~~~~~Lscvd~   76 (88)
T d2nn6g1          44 -KRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDS   76 (88)
T ss_dssp             -SCSSSSSCTTCEEEEEEEECCTTSCCEEECSBT
T ss_pred             -cccCcccCCCCEEEEEEEEeCCCCCEEEEEEcc
Confidence             112466899999999999989999999997543

>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=98.48  E-value=1.9e-07  Score=75.49  Aligned_cols=66  Identities=23%  Similarity=0.319  Sum_probs=54.0

Q ss_pred             CCCeEEEEEEEEECCeEEEEEC--CeEEEeecccc-ccccC------------ChhhhhhhcCCEEEEEEEEEECCCCce
Q 011538          296 LNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRVN------------NFTELKEKVGRRMYVQITRINEDTNDL  360 (483)
Q Consensus       296 ~GeiV~GkV~~v~k~G~fV~I~--Gi~gFVP~Sel-~~rv~------------~~~~l~~~VGq~V~vkVl~ID~e~~rL  360 (483)
                      .|+..+|+|+++.++|+||++.  +++||||.+.| +++..            +.+. .+++||+|+++|+++|+++++|
T Consensus         3 ~~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~-~~~~Gd~V~V~v~~vd~~~r~I   81 (87)
T d2ix0a3           3 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGET-VYKVTDVIDVTIAEVRMETRSI   81 (87)
T ss_dssp             SCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEE-EEETTCEEEEEEEEEETTTTEE
T ss_pred             CCCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCCCceEEEeccceEEEEEEcccE-EEECCCEEEEEEEEEecccCeE
Confidence            5788999999999999999993  79999999999 43321            0111 2479999999999999999988


Q ss_pred             ee
Q 011538          361 IL  362 (483)
Q Consensus       361 iL  362 (483)
                      .+
T Consensus        82 ~~   83 (87)
T d2ix0a3          82 IA   83 (87)
T ss_dssp             EE
T ss_pred             EE
Confidence            65

>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=98.47  E-value=2.1e-07  Score=75.36  Aligned_cols=66  Identities=12%  Similarity=0.136  Sum_probs=52.4

Q ss_pred             CCCeEEEEEEEEECCeEEEEECCeEEEeecccc-ccccCChhh---------hhhhcCCEEEEEEEEEECCCCcee
Q 011538          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTE---------LKEKVGRRMYVQITRINEDTNDLI  361 (483)
Q Consensus       296 ~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel-~~rv~~~~~---------l~~~VGq~V~vkVl~ID~e~~rLi  361 (483)
                      .|++++|+|++++++|+||+++.++||+|.++| ++..-+...         ....+|+.|+++|+.+|.+.+++.
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~i~   78 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIH   78 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEEcCeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccCccE
Confidence            599999999999999999999999999999999 332211110         123689999999999998877763

>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=98.34  E-value=1.1e-06  Score=71.45  Aligned_cols=76  Identities=22%  Similarity=0.310  Sum_probs=62.3

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccccccccCC
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~~~~~  247 (483)
                      |.+++||+|.|+|+.+..++++||||....|++|.++..+..                                      
T Consensus         3 Y~P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g~--------------------------------------   44 (90)
T d2ja9a1           3 YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNA--------------------------------------   44 (90)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTC--------------------------------------
T ss_pred             ccCCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCcc--------------------------------------
Confidence            557899999999999999999999999899998876654320                                      


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 011538          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (483)
Q Consensus       248 ~~~~~~~~kVGd~V~v~Vi~~d~~G~iiLS~k~~  281 (483)
                      ..+.++.+++||.|.|+|...+.++.+.||.+..
T Consensus        45 ~k~~r~~l~~GDlV~arV~~v~~~~~~~Lsc~~~   78 (90)
T d2ja9a1          45 SKKNRPTLQVGDLVYARVCTAEKELEAEIECFDS   78 (90)
T ss_dssp             CSSSCCCCCTTCEEEEEEEECCTTSCCEEESSCT
T ss_pred             ccccCCccCCCCEEEEEEEEECCCCCEEEEEecc
Confidence            0112466899999999999999999999998644

>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=98.34  E-value=1.6e-06  Score=67.66  Aligned_cols=63  Identities=25%  Similarity=0.297  Sum_probs=54.4

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEe-CCC--eEEEE
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD--KISLS  443 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vd-ek~--rI~LS  443 (483)
                      =++|+++.|+|.++.+..++|+++  +.+|+||.+|..      |.+.|++||.|+|.|.+|. +.+  .|.||
T Consensus         6 ~~~geiv~G~V~r~~~~~~~Vdlg--~~eaiLp~~eqi------p~E~~~~Gdrik~~i~~V~~~~kgpqI~lS   71 (72)
T d1hh2p1           6 ELKGTVTTAEVIRVMGEWADIRIG--KLETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVS   71 (72)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEET--TEEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEE
T ss_pred             hccCcEEEEEEEEEcCCCEEEEEC--CcEEECCHHHcC------CCCCCCCCCEEEEEEEEEEEcCCCCeEEEe
Confidence            468999999999999999999998  589999999975      5789999999999999996 332  56665

>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=98.33  E-value=1e-06  Score=68.76  Aligned_cols=64  Identities=22%  Similarity=0.171  Sum_probs=53.8

Q ss_pred             hCCCeEEEEEEEEECCeEEEEECCeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCC--ceeech
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTN--DLILSE  364 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~--rLiLS~  364 (483)
                      +.|++++|+|.++.+++++|++++.+|+||.+++..     .+. +.+|+.|+|.|.+|+...+  +|+|||
T Consensus         7 ~~geiv~G~V~r~~~~~~~Vdlg~~eaiLp~~eqip-----~E~-~~~Gdrik~~i~~V~~~~kgpqI~lSR   72 (72)
T d1hh2p1           7 LKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWIP-----GEE-IKAGDLVKVYIIDVVKTTKGPKILVSR   72 (72)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTEEEEEEGGGSCT-----TCC-CCTTCEEEEEEEEEEEETTEEEEEEES
T ss_pred             ccCcEEEEEEEEEcCCCEEEEECCcEEECCHHHcCC-----CCC-CCCCCEEEEEEEEEEEcCCCCeEEEeC
Confidence            689999999999999999999999999999999831     111 2699999999999975543  678876

>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=98.29  E-value=1.1e-06  Score=71.60  Aligned_cols=71  Identities=20%  Similarity=0.271  Sum_probs=54.6

Q ss_pred             CCCeEEEEEEEEECCeEEEEECCeEEEeeccccc-cc-c-CCh---------hhhhhhcCCEEEEEEEEEECCCCcee--
Q 011538          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL-SR-V-NNF---------TELKEKVGRRMYVQITRINEDTNDLI--  361 (483)
Q Consensus       296 ~GeiV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~-~r-v-~~~---------~~l~~~VGq~V~vkVl~ID~e~~rLi--  361 (483)
                      .|++++|+|++++++|+||+++.++||+|.++|. +. . .+.         ......+|+.|++||+.++.+.+++.  
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~I~~i   83 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAI   83 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEEEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEecCceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCcceEE
Confidence            5999999999999999999999999999999993 32 1 111         11123789999999999988777653  


Q ss_pred             echhh
Q 011538          362 LSERE  366 (483)
Q Consensus       362 LS~K~  366 (483)
                      .++++
T Consensus        84 gt~~~   88 (94)
T d2c35b1          84 GSLMD   88 (94)
T ss_dssp             EECCS
T ss_pred             EEccC
Confidence            44443

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.07  E-value=4.1e-06  Score=71.82  Aligned_cols=74  Identities=15%  Similarity=0.125  Sum_probs=61.8

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCC-------ceEEEEeccCcC--cccccCcccccCCCCEEEEEEEEEeC-CCeEEE
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDS-------NRSGLLHISNMS--RTRVTSVSDLLNEGERVKVLVVKSMF-PDKISL  442 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~-------gi~GLlhiSels--~~~i~~~~~~~kvGd~VkVkVi~vde-k~rI~L  442 (483)
                      .++|++|.|+|+++.+..++|+|...       .+.|++|.+++.  +....++.+.|++||.|+|+|+++.+ +..+.|
T Consensus         5 P~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~~~~L   84 (125)
T d2nn6i1           5 PDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLL   84 (125)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCccEEE
Confidence            46899999999999999999999321       467999999984  34556788999999999999999864 456899


Q ss_pred             EEec
Q 011538          443 SIAD  446 (483)
Q Consensus       443 SLK~  446 (483)
                      |+++
T Consensus        85 st~~   88 (125)
T d2nn6i1          85 TTAE   88 (125)
T ss_dssp             ECCS
T ss_pred             EecC
Confidence            9876

>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=97.83  E-value=2.3e-05  Score=61.45  Aligned_cols=64  Identities=23%  Similarity=0.403  Sum_probs=52.0

Q ss_pred             CCCcEEEEEEEEEeCce----EEEEECC--CceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeC--C-CeEEEE
Q 011538          374 REGTLLEGTVKKIYPYG----AQIRIGD--SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMF--P-DKISLS  443 (483)
Q Consensus       374 ~vG~iv~G~V~~I~~~G----aFV~I~~--~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vde--k-~rI~LS  443 (483)
                      ++|+++.|+|.++....    ++|+|+.  .+++|+||.+|.-      |.+.|+.||.|+|.|.++..  + -.|.||
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqi------p~E~y~~Gdrik~~i~~V~~~~kGp~IilS   75 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITLS   75 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEEE
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcC------CCcccCCCCEEEEEEEEEEecCCCCEEEEe
Confidence            58999999999996532    8999972  1699999999975      56899999999999999962  2 266665

>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=97.76  E-value=2.4e-05  Score=61.33  Aligned_cols=64  Identities=27%  Similarity=0.310  Sum_probs=50.7

Q ss_pred             CCCcEEEEEEEEEeCC----eEEEEeC---CceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeecccccc
Q 011538          171 KPGDFVIGVVVSGNEN----KLDVNVG---ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA  243 (483)
Q Consensus       171 k~GdiV~G~Vv~V~~~----gv~VdiG---~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d~~~  243 (483)
                      +.|++|.|+|.+++.+    .++||+|   .+.+|+||.+|..|.                                   
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqip~-----------------------------------   47 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPG-----------------------------------   47 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSCTT-----------------------------------
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcCCC-----------------------------------
Confidence            5799999999999754    3899998   469999999998753                                   


Q ss_pred             ccCCCCCCCCcccCCCEEEEEEEEEc---CCCcEEEEe
Q 011538          244 MSGGSGPGRPVVETGTVLFAEVLGRT---LSGRPLLST  278 (483)
Q Consensus       244 ~~~~~~~~~~~~kVGd~V~v~Vi~~d---~~G~iiLS~  278 (483)
                               ..|+.||.|.|.|....   ..-.++||+
T Consensus        48 ---------E~y~~Gdrik~~i~~V~~~~kGp~IilSR   76 (76)
T d2asba1          48 ---------ESYEHGNRLRCYVVGVTRGAREPLITLSR   76 (76)
T ss_dssp             ---------CCCCTTCEEEEEEEEEECCSSSCEEEEES
T ss_pred             ---------cccCCCCEEEEEEEEEEecCCCCEEEEeC
Confidence                     23789999999999843   234567774

>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=97.36  E-value=0.0002  Score=57.28  Aligned_cols=57  Identities=28%  Similarity=0.546  Sum_probs=48.5

Q ss_pred             cEEEEEEEEEeC--ceEEEEECCCceEEEEeccCcCcccc---------cCcccccCCCCEEEEEEEEE
Q 011538          377 TLLEGTVKKIYP--YGAQIRIGDSNRSGLLHISNMSRTRV---------TSVSDLLNEGERVKVLVVKS  434 (483)
Q Consensus       377 ~iv~G~V~~I~~--~GaFV~I~~~gi~GLlhiSels~~~i---------~~~~~~~kvGd~VkVkVi~v  434 (483)
                      .|+.|+|.+|.+  .+|||+|+. +..||||.+++.+.+.         .+..+.+++||.|-|.|++=
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~-~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke   69 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE   69 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSS-SSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEEC
T ss_pred             CcEEEEEEEecCCceEEEEEeCC-CccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeec
Confidence            579999999998  589999998 7999999999876643         24567899999999999863

>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=97.25  E-value=0.0005  Score=58.42  Aligned_cols=77  Identities=23%  Similarity=0.211  Sum_probs=53.7

Q ss_pred             CCCCCcEEEEEEEEEeCCeEEEEeC--------CceeeEeecccccccccchhhhhhhhhhhhhhHHhhcccceeeeccc
Q 011538          169 EPKPGDFVIGVVVSGNENKLDVNVG--------ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDD  240 (483)
Q Consensus       169 ~ik~GdiV~G~Vv~V~~~gv~VdiG--------~k~~G~lp~sEl~~~~~~e~~~l~~d~~~~~~e~~~~g~v~vv~~~d  240 (483)
                      =+++||+|.|+|+++.+..+.|+|.        ....|+++.+++...   +                          .|
T Consensus         4 vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~t---e--------------------------~d   54 (125)
T d2nn6i1           4 LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRAT---E--------------------------KD   54 (125)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTC---S--------------------------SC
T ss_pred             CCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccc---h--------------------------hh
Confidence            4688999999999999999999983        234566666665321   0                          01


Q ss_pred             cccccCCCCCCCCcccCCCEEEEEEEEEcCC-CcEEEEehHH
Q 011538          241 AIAMSGGSGPGRPVVETGTVLFAEVLGRTLS-GRPLLSTRRL  281 (483)
Q Consensus       241 ~~~~~~~~~~~~~~~kVGd~V~v~Vi~~d~~-G~iiLS~k~~  281 (483)
                      .       .+....|++||.|.|+|++.... ..+.||.+..
T Consensus        55 ~-------~~m~~~fr~GDiV~A~Vis~~~~~~~~~Lst~~~   89 (125)
T d2nn6i1          55 K-------VEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAEN   89 (125)
T ss_dssp             C-------CCGGGTCCSSSEEEEEEEEEETTTTEEEEECCSS
T ss_pred             h-------hhHHHhcCCCCEEEEEEEEccCCCccEEEEecCC
Confidence            0       11134589999999999986443 3578998764

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=96.13  E-value=0.0092  Score=47.28  Aligned_cols=34  Identities=21%  Similarity=0.217  Sum_probs=30.2

Q ss_pred             cEEEEEEEEEeC--CeEEEEeCCceeeEeecccccc
Q 011538          174 DFVIGVVVSGNE--NKLDVNVGADLLGTMLTKEVLP  207 (483)
Q Consensus       174 diV~G~Vv~V~~--~gv~VdiG~k~~G~lp~sEl~~  207 (483)
                      +|-.|+|.+|.+  +.+|||+|.+..||||.+++.+
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~   37 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAR   37 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCG
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccce
Confidence            467899999998  5899999999999999999864

>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=92.86  E-value=0.17  Score=39.11  Aligned_cols=74  Identities=24%  Similarity=0.257  Sum_probs=57.2

Q ss_pred             CCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEecc-CcCcccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCC
Q 011538          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHIS-NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (483)
Q Consensus       373 l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhiS-els~~~i~~~~~~~kvGd~VkVkVi~vd-ek~rI~LSLK~~~  448 (483)
                      ..+|++.+|+|. +.++-.+|.+.+. |.++++--+ ++-.++..++++.+ +|.+|+|+|+.+| -++.|.+.-|.+-
T Consensus         6 PnigdVtkGiVy-~kd~~fyV~L~dY~g~ea~l~dy~~~~~d~~~klk~kL-VGKtIkvqVIR~d~lKGYIDVr~~~~~   82 (85)
T d1luza_           6 PNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKRMC   82 (85)
T ss_dssp             CCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEEEC
T ss_pred             CCCCceeeeEEE-EeCCEEEEEecCCCCceEEeeehhhhhhHHHHHHHHHh-cCceEEEEEEEEcceeeEEEehhhhhh
Confidence            358999999886 5666778999876 789987432 33344566666666 7999999999998 7899999988754

>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=92.51  E-value=0.13  Score=40.82  Aligned_cols=62  Identities=21%  Similarity=0.235  Sum_probs=48.7

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCC-ceEEEEec-cCcCcccccCcccccCCCCEEEEEEEEEe
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHI-SNMSRTRVTSVSDLLNEGERVKVLVVKSM  435 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~-gi~GLlhi-Sels~~~i~~~~~~~kvGd~VkVkVi~vd  435 (483)
                      ++.+|++.+|+|+ +.++-.+|.+.++ |.++++-- -++-.++..++++.+ +|.+|+|+|+.+|
T Consensus        29 ~~~~G~V~kGiVy-~rd~~fyV~L~dY~g~eail~dY~n~~~dr~~klkkkL-VGKTIkVqVIRvD   92 (102)
T d1jjga_          29 DLSPGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRAD   92 (102)
T ss_dssp             CCCSSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEEC
T ss_pred             ccCCCcEeeeEEE-EeCCEEEEEecCCCCceeeeeehhhhhHHHHHHHHHHh-cCceEEEEEEEec
Confidence            6889999999886 5667778999876 78888533 344455667777766 7999999999986

>d3d31a1 b.40.6.3 (A:230-348) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: All beta proteins
fold: OB-fold
superfamily: MOP-like
family: ABC-transporter additional domain
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=91.87  E-value=1.5  Score=34.21  Aligned_cols=104  Identities=16%  Similarity=0.221  Sum_probs=64.6

Q ss_pred             eEEEEEEEEECCeEEEEECCeEEEeeccccccccCChhhhhhhcCCEEEEEEEEEECCCCceeechhhHhhhcCCCCCcE
Q 011538          299 PIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTL  378 (483)
Q Consensus       299 iV~GkV~~v~k~G~fV~I~Gi~gFVP~Sel~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K~~~e~~~l~vG~i  378 (483)
                      +++|+|++...+.+.+.+++....+|..           +  ..|+.+.+.   |.++  .|.++....    .-...-.
T Consensus         4 ~l~g~v~~~~~~~~~v~~~~~~l~~~~~-----------~--~~g~~v~~~---iRPE--~i~l~~~~~----~~~~~N~   61 (119)
T d3d31a1           4 VLKGRVISAEQGLLRIRVGEVVIDAAGD-----------M--EVGDQVYAF---LRPE--NIALSKSST----QSSIRNS   61 (119)
T ss_dssp             EEEEEEEEEETTEEEEEETTEEEEEESS-----------C--CTTCEEEEE---ECGG--GEEEESSCC----CBSCSEE
T ss_pred             EEEEEEEEecCCEEEEEECCEEEECCCC-----------C--CCCCEEEEE---EchH--Hcccccccc----ccccceE
Confidence            6899999999999999999877666521           1  368887654   4444  355554321    1112247


Q ss_pred             EEEEEEEEeCceEEEEE--CC-CceEEEEeccCcCcccccCcccccCCCCEEEEEE
Q 011538          379 LEGTVKKIYPYGAQIRI--GD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLV  431 (483)
Q Consensus       379 v~G~V~~I~~~GaFV~I--~~-~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkV  431 (483)
                      +.|+|..+...|..+.+  .. ..+...+......       ...+++||+|.+.+
T Consensus        62 l~g~V~~~~~~G~~~~v~l~~g~~~~~~v~~~~~~-------~~~l~~G~~V~v~~  110 (119)
T d3d31a1          62 LQGRVTEAWVLGALVRVKVDCGVPLNVLITRRSAE-------EMELSPGVQIYARF  110 (119)
T ss_dssp             EEEEEEEEEECSSEEEEEEESSSEEEEEEETTHHH-------HSCCCTTCEEEEEE
T ss_pred             EEEEEEEEEECCCeEEEEEEeCCEEEEEEecCchh-------hcCcCCCCEEEEEE
Confidence            99999999988865444  21 1233333322211       13488999998865

>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=89.25  E-value=0.53  Score=35.23  Aligned_cols=49  Identities=20%  Similarity=0.201  Sum_probs=39.9

Q ss_pred             CCCCCcEEEEEEEEEeCceEEEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEE
Q 011538          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS  434 (483)
Q Consensus       372 ~l~vG~iv~G~V~~I~~~GaFV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~v  434 (483)
                      ..++|++-+|.+.+-...|+||+|+-   +-+...           ...|.+|+.+.+||.++
T Consensus         7 ~p~vGEiReG~~~rr~~~g~~vDiGl---D~la~~-----------k~~~~~~~r~tfrIvs~   55 (71)
T d1k3ra1           7 KPVTGEYRQGLTVKRVKKGTLVDIGA---DKLALC-----------REKLTVNRIMSFRVVRL   55 (71)
T ss_dssp             SCCTTCEEEEEEEEECSSSEEEESSS---SCEEEC-----------SSCCCSSCEEEEEEEEC
T ss_pred             CCcccceeeEEEEEecCCcEEEEecC---Cceeee-----------ecccccCcEEEEEEEEc
Confidence            47899999999999999999999974   333332           23588999999999986

>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=88.41  E-value=0.94  Score=33.82  Aligned_cols=31  Identities=29%  Similarity=0.461  Sum_probs=27.8

Q ss_pred             cCCCCCcEEEEEEEEEeCCeEEEEeCCceee
Q 011538          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLG  198 (483)
Q Consensus       168 ~~ik~GdiV~G~Vv~V~~~gv~VdiG~k~~G  198 (483)
                      ..++.|++=+|-+++....|+|||||.+..+
T Consensus         6 g~p~vGEiReG~~~rr~~~g~~vDiGlD~la   36 (71)
T d1k3ra1           6 GKPVTGEYRQGLTVKRVKKGTLVDIGADKLA   36 (71)
T ss_dssp             SSCCTTCEEEEEEEEECSSSEEEESSSSCEE
T ss_pred             CCCcccceeeEEEEEecCCcEEEEecCCcee
Confidence            4688999999999999999999999987655

>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=85.78  E-value=1.1  Score=34.34  Aligned_cols=68  Identities=15%  Similarity=0.273  Sum_probs=46.4

Q ss_pred             hCCCeEEEEEEEEECCeEEEEE---CCeEEEeeccc-c-ccccCChhhhhhhcCCEEEEEEEEEECCCCceeechh
Q 011538          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAE-L-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (483)
Q Consensus       295 k~GeiV~GkV~~v~k~G~fV~I---~Gi~gFVP~Se-l-~~rv~~~~~l~~~VGq~V~vkVl~ID~e~~rLiLS~K  365 (483)
                      ..|++.+|.|.- .++-+.|.+   .|.+|++-..- + .+++.+.++-  .+|..|+++|+++|.-++-+-++.|
T Consensus         7 nigdVtkGiVy~-kd~~fyV~L~dY~g~ea~l~dy~~~~~d~~~klk~k--LVGKtIkvqVIR~d~lKGYIDVr~~   79 (85)
T d1luza_           7 NAGDVIKGRVYE-KDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDK--LVGKTVKVKVIRVDYTKGYIDVNYK   79 (85)
T ss_dssp             CTTCEEEEEEEE-ETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHH--HTTCEEEEEEEEEETTTTEEEEEEE
T ss_pred             CCCceeeeEEEE-eCCEEEEEecCCCCceEEeeehhhhhhHHHHHHHHH--hcCceEEEEEEEEcceeeEEEehhh
Confidence            578888988763 344566777   36788765332 2 2344444443  6999999999999998887766554

>d1c9oa_ b.40.4.5 (A:) Major cold shock protein {Bacillus caldolyticus [TaxId: 1394]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Bacillus caldolyticus [TaxId: 1394]

Probab=81.36  E-value=5.5  Score=28.73  Aligned_cols=57  Identities=19%  Similarity=0.240  Sum_probs=39.4

Q ss_pred             EEEEEEEeC-ceE-EEEECCCceEEEEeccCcCcccccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 011538          380 EGTVKKIYP-YGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL  442 (483)
Q Consensus       380 ~G~V~~I~~-~Ga-FV~I~~~gi~GLlhiSels~~~i~~~~~~~kvGd~VkVkVi~vdek~rI~L  442 (483)
                      .|+|+-..+ .|. ||...+ |-+-|+|.|.+.....    ..+..||.|.+.+.. .+++.-..
T Consensus         3 ~G~Vk~fn~~kGfGFI~~d~-g~DiF~H~s~l~~~~~----~~L~~G~~V~f~~~~-~~~G~~A~   61 (66)
T d1c9oa_           3 RGKVKWFNNEKGYGFIEVEG-GSDVFVHFTAIQGEGF----KTLEEGQEVSFEIVQ-GNRGPQAA   61 (66)
T ss_dssp             EEEEEEEETTTTEEEEEETT-EEEEEEEGGGBCSSSC----CCCCTTCEEEEEEEE-ETTEEEEE
T ss_pred             CeEEEEEECCCCEEEEEecC-CceEEEEehhcccccC----CcCCCCCEEEEEEEE-CCCCCEEE
Confidence            688988853 333 566666 7899999999964322    347899999998864 34444333