Citrus Sinensis ID: 010232

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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-------490-------500-------510----
Protein Sequence
MQTPVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCANWKWFRFEQDS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccHHHccccccccccccccEEEEEEccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccHHHHccccccccccccccHHHHcccccccccccccccccccccccccccccccccccEEEEEEEEEEccEEEEEccccccccEEccccccccHHHHHHHHHHcccccccEEEEEEEEEEcccccEEccccccccccccccccEEEEEEEEEcccccEEEEHHHHHHHHHHHHHHHHHHccccEEEEEEEEEEcEEEEEEccEEEEEcccccccccccccccccccccEEEEEEEEEEcccccEEEEHHHHHHHHccccccEEEEEEEEEEccEEEEEcccccccccEEEEccccccccccccccccccEEEEEEEEcccccEEEEEccccccccccccccccccccEEEEEEEEEccccccEEccccccccccccccccccccEEccEEEEEEEccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEEEcccccccccEEEcccccccccccccccccccccEEEcccEEEEEEcccccccccccEEccccccccccEcHHHHHHccccccccccccccEEEcccccHHHHHHHHHHHHHHHHcccccccEEEEEEEEEEcccEEEEEcccccccEcHHHccccccccccEEEEEcccEEEEEEEEEcccccEEEEHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEEEccEEEEEcccccccEEEEEcccEEEEEEEEEcccccEEEEHHHHHcccHHHHHHHHcccccEEEEEEEEEEccEEEEEcccccEEEEccccccccccccccEEEcccEEEEEEEEEcccccEEEEEHHHHHHHHHcccccEEEEEEEEEccccEEEEEcccccEEEEEEEcccHccccccccEEEcccEEEEEEEccccccEEEEcHHHccccHHHHHHHHcccccEEEEEEEEEccccEEEEEcccccEEEEEEccccccccccccccccEEEccc
Coil and Loop (DISEMBL)
MQTPVQACKSFTFtllnsapplstcsfvqngnakyplqqsrkfhSFAASFRFLRSThivfcsqkdvfddlssaqfpenveneglegneelellnkpnlvpisngvasevdkksekpdeeealapflkffkprdsaeeveeegsevgvsresidvddkvgedkvsveyyepkpgdFVIGVVVSgnenkldvNVGADLLGTmltkevlplYDKEMDFLLCDLKKDAEEFMVRgkmgivkdddaiamsggsgpgrpvveTGTVLFAEVLGrtlsgrpllsTRRLFRKMAWHRVRQIKQLnepievkftewntggllTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLRegtllegtvkkiypygaqirigdsnrsgllhisnmsrtRVTSVSDLLNEGERVKVLVVKSmfpdkislsiadlesepglfvsdkerVFSEAEEMAKKYRqklpavsvspkseslptdtppfdseasmcaNWKWFRFEQDS
Flexible Loop (DISEMBL)
MQTPVQACKSFTFtllnsapplSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVasevdkksekpdeeealapflkffkprDSAEeveeegsevgvsresidvddkvgeDKVSveyyepkpgdFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVlgrtlsgrpllstrRLFRKMAWHRVRQikqlnepievkftewntgGLLTRIEGLRAFlpkaellsrvnnftelkekvgrrMYVQItrinedtndliLSEREAWATLNlregtllegtvkkIYPYGAQIRIGDSNRSGLLHISNMSRTRVtsvsdllnegERVKVLVVKSMFPDKISlsiadlesepglfvsDKERVFSEAEEMAKKyrqklpavsvspkseslptdtppfdseASMCANWKWFRFEQDS
Low Complexity Region (SEG)
MQTPVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPenveneglegneelellnkpnlvpISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAeeveeegsevgvsresIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCANWKWFRFEQDS
Disordered region (IsUnstruct)
******ACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDL********************************************************************************************VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA********RPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL*****************************************************MCANWKWFRF****
Disordered Region (DISOPRED)
*******CKSFTFTLLNSAPP******************************FLRSTHIVF**********************************************************************************************************YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCANWKWFRFEQ**
Disordered Region (DISEMBL)
MQTPVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVA************EEALAPFLKFFKPR*****************ESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKERVFSEAEEM**************************FDSEASMCANWKWFRFEQDS
Disordered Region (DISPRO)
****VQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCANWKW*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQTPVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFxxxxxxxxxxxxxxxxxxxxxLPAVSVSPKSESLPTDTPPFDSEASMCANWKWFRFEQDS
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	514	2.2.26 [Sep-21-2011]
P29344	411	30S ribosomal protein S1,	N/A	no	0.404	0.506	0.313	2e-26
P73530	328	30S ribosomal protein S1	N/A	no	0.408	0.640	0.352	4e-25
P46228	307	30S ribosomal protein S1	yes	no	0.387	0.648	0.382	8e-25
P74142	305	30S ribosomal protein S1	N/A	no	0.449	0.757	0.295	3e-21
O33698	295	30S ribosomal protein S1	no	no	0.387	0.674	0.311	3e-19
P51345	263	30S ribosomal protein S1,	N/A	no	0.303	0.593	0.315	1e-17
Q1XDE2	263	30S ribosomal protein S1,	N/A	no	0.303	0.593	0.309	1e-16
O06147	481	30S ribosomal protein S1	yes	no	0.338	0.361	0.286	9e-14
O06000	382	30S ribosomal protein S1	yes	no	0.332	0.447	0.291	4e-13
P14129	568	30S ribosomal protein S1	yes	no	0.449	0.406	0.274	5e-13

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

 Score =  120 bits (302), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 68/217 (31%), Positives = 129/217 (59%), Gaps = 9/217 (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 IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV-KSMFPDKISLSIADLESEP 451
           I IG  N  GLLH+S +S  RV+ ++ +L  G+ +KV+++       ++SLS   LE  P
Sbjct: 278 IDIGGIN--GLLHVSQISHDRVSDIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP 335

Query: 452 GLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESL 488
           G  + + + VF +AEEMA+ +RQ++       +++ L
Sbjct: 336 GDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARADML 372

Actively engaged in the initiation complex formation via a strong mRNA-binding activity. Possesses a poly(A)-binding activity which might play a role as a control element in chloroplast mRNA translation.
Spinacia oleracea (taxid: 3562)

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

 Score =  116 bits (291), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 80/227 (35%), Positives = 123/227 (54%), Gaps = 17/227 (7%)

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 LESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTP 493
           LE EPG  + D++ V   A+EMA+ +RQK  A     +++ +P + P
Sbjct: 266 LEPEPGAMLKDRDLVNEMADEMAEIFRQKRLA-----EAQGIPYEPP 307

Binds mRNA.

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

>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 =  115 bits (288), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 80/209 (38%), Positives = 117/209 (55%), Gaps = 10/209 (4%)

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 ESEPGLFVSDKERVFSEAEEMAKKYRQKL 476
           E EPG  V + E V+ +AEEMA +YR+KL
Sbjct: 268 EPEPGDMVRNPEVVYEKAEEMAAQYREKL 296

Binds mRNA.

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

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

 Score =  103 bits (257), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 76/257 (29%), Positives = 129/257 (50%), Gaps = 26/257 (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 SEPGLFVSDKERVFSEA 465
           + PG  V   + + ++A
Sbjct: 266 TYPGELVEKFDEMMADA 282

Binds mRNA.

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

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

 Score = 97.1 bits (240), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 65/209 (31%), Positives = 112/209 (53%), Gaps = 10/209 (4%)

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 ESEPGLFVSDKERVFSEAEEMAKKYRQKL 476
           E+ PG  + +   + + A + A++ R++L
Sbjct: 264 ENHPGEILENVAELQASAADRAERARKQL 292

Binds mRNA.

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

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

 Score = 92.0 bits (227), 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|Q1XDE2|RR1_PORYE 30S ribosomal protein S1, chloroplastic OS=Porphyra yezoensis GN=rps1 PE=3 SV=2

 Score = 88.2 bits (217), Expect = 1e-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 = 79.0 bits (193), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 55/192 (28%), Positives = 103/192 (53%), Gaps = 18/192 (9%)

Query: 272 GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR 331
           GR +LS +R   + AW  +  +K+ +E ++    E   GGL+  I GLR FLP +  L  
Sbjct: 98  GRLILSKKRAQYERAWGTIEALKEKDEAVKGTVIEVVKGGLILDI-GLRGFLPAS--LVE 154

Query: 332 VNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATL-----------NLREGTLLE 380
           +    +L+  +G+ +  +I  ++++ N+++LS R AW              NL++GT+ +
Sbjct: 155 MRRVRDLQPYIGKEIEAKIIELDKNRNNVVLS-RRAWLEQTQSEVRSEFLNNLQKGTIRK 213

Query: 381 GTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFPDK 439
           G V  I  +GA + +G  +  GL+H+S +S   +   S+++  G+ V V V+   M  ++
Sbjct: 214 GVVSSIVNFGAFVDLGGVD--GLVHVSELSWKHIDHPSEVVQVGDEVTVEVLDVDMDRER 271

Query: 440 ISLSIADLESEP 451
           +SLS+   + +P
Sbjct: 272 VSLSLKATQEDP 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 = 105/189 (55%), 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 NFTELKEKVGRRMYVQITRINEDTNDLILSEREAW----------ATLNLREGTLLEGTV 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 = 76.3 bits (186), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 73/266 (27%), Positives = 129/266 (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-VNNFTELKEKVGRRMYVQITRINEDTNDLILS----------ERE 366
           G  AFLP++++  R + + T L          +I ++++   ++++S          E+ 
Sbjct: 132 GAVAFLPRSQVDIRPIRDVTPLMHN---PQPFEILKMDKRRGNIVVSRRTVLEESRAEQR 188

Query: 367 AWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGER 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	514
255572295	476	conserved hypothetical protein [Ricinus	0.889	0.960	0.747	0.0
359495207	513	PREDICTED: uncharacterized protein LOC10	0.949	0.951	0.693	0.0
449446381	530	PREDICTED: 30S ribosomal protein S1 homo	0.892	0.866	0.714	0.0
297739376	435	unnamed protein product [Vitis vinifera]	0.803	0.949	0.744	1e-180
449527959	529	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.891	0.865	0.681	1e-176
356534027	513	PREDICTED: uncharacterized protein LOC10	0.902	0.904	0.655	1e-166
297839005	501	predicted protein [Arabidopsis lyrata su	0.854	0.876	0.642	1e-163
334183835	500	small subunit ribosomal protein S1 [Arab	0.854	0.878	0.646	1e-162
224066601	486	predicted protein [Populus trichocarpa]	0.891	0.942	0.592	1e-160
422778917	487	plastid S1 binding domain protein precur	0.828	0.874	0.630	1e-155

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

 Score =  694 bits (1791), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 344/460 (74%), Positives = 401/460 (87%), Gaps = 3/460 (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 VTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYR 473
           VT+VSDLL   ERVKVLVVKSMFPDKISLSIADLESEPGLFVS+KE+VF+EAEEMAKKYR
Sbjct: 377 VTAVSDLLKVDERVKVLVVKSMFPDKISLSIADLESEPGLFVSNKEKVFAEAEEMAKKYR 436

Query: 474 QKLPAVSVSPKSESLPTDTPPFDSEASMCANWKWFRFEQD 513
           QKLPAV  + KS +  + T  FD EA+M ANWKWF+FE+D
Sbjct: 437 QKLPAVLATRKSATPLSSTLTFDDEATMYANWKWFKFERD 476

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 =  680 bits (1754), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/513 (69%), Positives = 415/513 (80%), Gaps = 25/513 (4%)

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  +S     G PVVETGTVLFAEVLGRTLSGRPLLSTRR FR++AWHRVRQIKQLNEPI
Sbjct: 239 A--LSRVPMQGSPVVETGTVLFAEVLGRTLSGRPLLSTRRFFRRIAWHRVRQIKQLNEPI 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 LNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVS 480
           L   E+VKV+VVKSMFP+KI+LSIADLESEPGLF+S+KE+VFS+AEEMAKKYRQKLPAV+
Sbjct: 417 LTVDEKVKVMVVKSMFPNKIALSIADLESEPGLFLSNKEKVFSDAEEMAKKYRQKLPAVT 476

Query: 481 VSPKSESLPTDTPPFDSEASMCANWKWFRFEQD 513
            + K E LPTD  PF  EAS+ ANW+WF+FE+D
Sbjct: 477 ATRKLEPLPTDALPFHDEASLYANWRWFKFERD 509

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 =  662 bits (1708), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 330/462 (71%), Positives = 396/462 (85%), Gaps = 3/462 (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 RTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAK 470
           R RVTSVSDLL+ GE+V VLVVKSMFPDKISLSIADLESEPGLF+++KE+VFSEA+ MAK
Sbjct: 429 RARVTSVSDLLSVGEKVNVLVVKSMFPDKISLSIADLESEPGLFITNKEKVFSEAKIMAK 488

Query: 471 KYRQKLPAVSVSPKSESLPTDTPPFDSEASMCANWKWFRFEQ 512
           KYRQ+LP++    + ++ PT   PF++E+SM ANWKWF+FE+
Sbjct: 489 KYRQRLPSLDGILRPKTAPTTDLPFENESSMYANWKWFKFER 530

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 =  638 bits (1645), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 320/430 (74%), Positives = 370/430 (86%), Gaps = 17/430 (3%)

Query: 89  ELELLNKPNLVPISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVE----EEGSE 144
            LELL KP+ VP++NG AS++D + +KPD++EALAPFLKFFKPR+S+EE      E+GSE
Sbjct: 14  HLELLGKPSPVPLNNGSASDIDSELKKPDKDEALAPFLKFFKPRESSEEANGASGEDGSE 73

Query: 145 VGVSRESIDVDDKVGEDK-VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTK 203
           +  S          G  K VSVEYYEPKPGDFV+GVVVSGNENKLDVNVGADLLGTMLTK
Sbjct: 74  ISES----------GSTKLVSVEYYEPKPGDFVVGVVVSGNENKLDVNVGADLLGTMLTK 123

Query: 204 EVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFA 263
           EVLPLYDKEM++LLCD++KDAEEFMV GKM IV++DDA  +S     G PVVETGTVLFA
Sbjct: 124 EVLPLYDKEMEYLLCDVEKDAEEFMVHGKMSIVRNDDA--LSRVPMQGSPVVETGTVLFA 181

Query: 264 EVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFL 323
           EVLGRTLSGRPLLSTRR FR++AWHRVRQIKQLNEPIEV+ TEWNTGGLLTRIEGLRAFL
Sbjct: 182 EVLGRTLSGRPLLSTRRFFRRIAWHRVRQIKQLNEPIEVRITEWNTGGLLTRIEGLRAFL 241

Query: 324 PKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTV 383
           PKAELL+RV +FTELKE VGRR+YVQITRI+E  NDLILSE++AW   +L+EGTLLEGTV
Sbjct: 242 PKAELLNRVKSFTELKENVGRRLYVQITRIDEAKNDLILSEKDAWEKSHLQEGTLLEGTV 301

Query: 384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLS 443
           KKI+PYGAQI IG+SNRSGLLHISN++R RVTSVSDLL   E+VKV+VVKSMFP+KI+LS
Sbjct: 302 KKIFPYGAQIMIGESNRSGLLHISNITRARVTSVSDLLTVDEKVKVMVVKSMFPNKIALS 361

Query: 444 IADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCA 503
           IADLESEPGLF+S+KE+VFS+AEEMAKKYRQKLPAV+ + K E LPTD  PF  EAS+ A
Sbjct: 362 IADLESEPGLFLSNKEKVFSDAEEMAKKYRQKLPAVTATRKLEPLPTDALPFHDEASLYA 421

Query: 504 NWKWFRFEQD 513
           NW+WF+FE+D
Sbjct: 422 NWRWFKFERD 431

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  623 bits (1607), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 315/462 (68%), Positives = 384/462 (83%), Gaps = 4/462 (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 RTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAK 470
           R RVTSVSDLL+ GE+V VLVVKSMFPDKISLSIADLESEPGLF+++KE+VFSEA+ MAK
Sbjct: 428 RARVTSVSDLLSVGEKVNVLVVKSMFPDKISLSIADLESEPGLFITNKEKVFSEAKIMAK 487

Query: 471 KYRQKLPAVSVSPKSESLPTDTPPFDSEASMCANWKWFRFEQ 512
           KYRQ+LP++    + ++ PT   PF++E+SM ANWKWF+FE+
Sbjct: 488 KYRQRLPSLDGIFRPKTAPTTDLPFENESSMYANWKWFKFER 529

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  592 bits (1525), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 321/490 (65%), Positives = 380/490 (77%), Gaps = 26/490 (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 SIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMC 502
           SIADLESEPGLF+S+KERV+ EA+ MAKKY+QKLP    + + E LPT   PF++EA + 
Sbjct: 445 SIADLESEPGLFLSNKERVYMEADMMAKKYKQKLPPSVTTQRLEPLPTSALPFENEA-LY 503

Query: 503 ANWKWFRFEQ 512
           +NWKWF+FE+
Sbjct: 504 SNWKWFKFEK 513

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 =  581 bits (1498), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 305/475 (64%), Positives = 365/475 (76%), Gaps = 36/475 (7%)

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 KERVFSEAEEMAKKYRQKLPAVSVSPKSESLP-TDTPPFDSEASMCANWKWFRFE 511
           +E+VF+EAEEMAKKYR+K+P+V+ S  S+  P T + P   +  + ANW WF+FE
Sbjct: 445 REKVFTEAEEMAKKYREKMPSVATSAISDHPPITSSFPQGKDEEIYANWDWFKFE 499

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 =  579 bits (1493), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 306/473 (64%), Positives = 366/473 (77%), Gaps = 34/473 (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 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+ +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

Query: 460 RVFSEAEEMAKKYRQKLPAVSVSPKSESLP-TDTPPFDSEASMCANWKWFRFE 511
           +VF+EAEEMAKKYR+K+P V+ SP S+  P T + P   +  + ANW+WF+FE
Sbjct: 446 KVFTEAEEMAKKYREKMPLVATSPISDRPPITSSFPQGKDEEIYANWEWFKFE 498

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 =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 315/532 (59%), Positives = 379/532 (71%), Gaps = 74/532 (13%)

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++NR  
Sbjct: 332 GRQIYVLIKRINESNNELILSEREAWEMINLREGTLLEGTVKKLFPYGAQVRIGETNR-- 389

Query: 403 LLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKERVF 462
                          SDLL   E+VKVLV KSMFPDKISLSIADLESEPGLFVS+KE+VF
Sbjct: 390 ---------------SDLLKVDEKVKVLVAKSMFPDKISLSIADLESEPGLFVSNKEKVF 434

Query: 463 SEAEEMAKKYRQKLPAVSVSPKSESLPT-DTPPFDSEASMCANWKWFRFEQD 513
           +EAEEMAKKYRQKLPA S + K E  P+ +    D+EA++ ANWKWF+FE++
Sbjct: 435 AEAEEMAKKYRQKLPASSTNLKPEIPPSKNALSSDTEATLYANWKWFKFEKE 486

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 =  553 bits (1426), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 298/473 (63%), Positives = 356/473 (75%), Gaps = 47/473 (9%)

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

Query: 460 RVFSEAEEMAKKYRQKLPAVSVSPKSESLP-TDTPPFDSEASMCANWKWFRFE 511
           +VF+EAEEMAKKYR+K+P V+ SP S+  P T + P   +  + ANW+WF+FE
Sbjct: 433 KVFTEAEEMAKKYREKMPLVATSPISDRPPITSSFPQGKDEEIYANWEWFKFE 485

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	514
TAIR|locus:2145860	416	RPS1 "ribosomal protein S1" [A	0.404	0.5	0.336	1.3e-25
UNIPROTKB|O06147	481	rpsA "30S ribosomal protein S1	0.373	0.399	0.289	6.1e-14
TIGR_CMR|BA_1519	382	BA_1519 "ribosomal protein S1"	0.441	0.594	0.282	1e-13
TAIR|locus:2095203	392	AT3G23700 [Arabidopsis thalian	0.334	0.438	0.320	4.7e-12
TIGR_CMR|GSU_2603	586	GSU_2603 "ribosomal protein S1	0.359	0.315	0.323	9e-12
TIGR_CMR|GSU_1200	402	GSU_1200 "ribosomal protein S1	0.287	0.368	0.331	6.8e-11
TIGR_CMR|NSE_0408	553	NSE_0408 "ribosomal protein S1	0.391	0.363	0.273	1.1e-10
TIGR_CMR|ECH_0402	567	ECH_0402 "putative ribosomal p	0.383	0.347	0.294	1.1e-10
TIGR_CMR|SPO_0802	558	SPO_0802 "ribosomal protein S1	0.424	0.390	0.263	4.4e-10
TIGR_CMR|APH_0273	542	APH_0273 "ribosomal protein S1	0.406	0.385	0.289	4.5e-10

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

 Score = 301 (111.0 bits), Expect = 1.3e-25, P = 1.3e-25
 Identities = 73/217 (33%), Positives = 125/217 (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 GLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESL 488
             G  + + + VF +AEEMA+ +RQ++       +++ L
Sbjct:   339 GDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARADML 375

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 = 6.1e-14, Sum P(2) = 6.1e-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 = 195 (73.7 bits), Expect = 1.0e-13, Sum P(2) = 1.0e-13
 Identities = 70/248 (28%), Positives = 126/248 (50%)

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 EGERVKVLVVKSMFPD--KISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVS 480
             +G++VKV V+ S+  D  +ISLSI   +  P   V  + +     E + K+       V 
Sbjct:   234 QGQKVKVKVL-SVDADTQRISLSIKAAQPGPWENVGGEVKAGDIREGVVKRLVTFGAFVE 292

Query:   481 VSPKSESL 488
             + P  E L
Sbjct:   293 ILPGVEGL 300

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

GO:0006412 "translation" evidence=ISS

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

 Score = 192 (72.6 bits), Expect = 4.7e-12, Sum P(2) = 4.7e-12
 Identities = 60/187 (32%), Positives = 94/187 (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 GLFVSDK 458
              L   DK
Sbjct:   277 LLETLDK 283

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 = 191 (72.3 bits), Expect = 9.0e-12, P = 9.0e-12
 Identities = 65/201 (32%), Positives = 101/201 (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 SLSIADLESEPGLFVSDKERV 461
             SL +  +  +P L V  K +V
Sbjct:   281 SLGLKQITPDPWLAVEQKFQV 301

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

GO:0006412 "translation" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

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

 Score = 180 (68.4 bits), Expect = 6.8e-11, P = 6.8e-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 = 1.1e-10, Sum P(2) = 1.1e-10
 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|ECH_0402 ECH_0402 "putative ribosomal protein S1" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 181 (68.8 bits), Expect = 1.1e-10, P = 1.1e-10
 Identities = 65/221 (29%), Positives = 112/221 (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-SMFPDKISLSIADLESEPGLFVSDKERVFS 463
             G+ VK  ++K      KISL +  LE  P   +  K  V S
Sbjct:   283 GQTVKTKIIKIDRENKKISLGVKQLEESPWSNIEKKYPVDS 323

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 = 4.4e-10, Sum P(2) = 4.4e-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

TIGR_CMR|APH_0273 APH_0273 "ribosomal protein S1" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 175 (66.7 bits), Expect = 4.5e-10, P = 4.5e-10
 Identities = 68/235 (28%), Positives = 117/235 (49%)

Query:   249 GPGRPVVETGTV--LFAEVL-GRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIE-VKF 304
             G G+  +E G+   L+ E   G+  SG  +LS  +  R   W ++ Q    N  IE V F
Sbjct:    71 GEGKQDIEVGSKVKLYLEKTEGK--SGSVVLSREKAVRDELWQKLEQAAAENLDIEGVIF 128

Query:   305 TEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS 363
                  G     + G+ AFLP + + L +V + T L   +G++   +I ++++   ++++S
Sbjct:   129 GSIKCG-FTVDVGGVVAFLPASHVGLRQVKDITPL---LGKKQKFRILKMDKKQGNVVVS 184

Query:   364 ER----EAWATLN------LREGTLLEGTVKKIYPYGAQIRIGDSNR----SGLLHISNM 409
              +    E+ A         L EG+++EG VK I  YG  I I +S       GLLHI+++
Sbjct:   185 RKAVLEESLADAKDSFLSTLEEGSIVEGKVKSITKYGVFIEIHESPTVGVVDGLLHITDI 244

Query:   410 SRTRVTSVSDLLNEGERVKVLVVKSMFPD-KISLSIADLESEPGLFVSDKERVFS 463
             S +RV+  S + + G+ V+  +++    + KISL +  LE  P   V ++  V S
Sbjct:   245 SWSRVSHPSAVFSCGQTVRAKIIRIDRENRKISLGVKQLEESPWANVEERYPVGS 299

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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	514
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	3e-35
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	3e-28
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	6e-27
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	9e-27
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	6e-24
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	2e-17
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	1e-15
cd04465	67	cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec	2e-13
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	4e-13
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	6e-13
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	7e-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	4e-12
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	1e-11
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	1e-11
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	1e-11
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	2e-11
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	9e-11
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	2e-10
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	3e-10
COG1098	129	COG1098, VacB, Predicted RNA binding protein (cont	3e-10
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	6e-10
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	2e-09
pfam00575	74	pfam00575, S1, S1 RNA binding domain	5e-09
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	3e-08
PRK05807	136	PRK05807, PRK05807, hypothetical protein; Provisio	4e-08
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	7e-08
PRK07252	120	PRK07252, PRK07252, hypothetical protein; Provisio	8e-08
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	9e-08
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	1e-07
cd05686	73	cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-b	2e-07
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	3e-07
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	1e-06
PRK08059	123	PRK08059, PRK08059, general stress protein 13; Val	2e-06
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	1e-05
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	3e-05
PRK03987	262	PRK03987, PRK03987, translation initiation factor	3e-05
PRK08582	139	PRK08582, PRK08582, hypothetical protein; Provisio	6e-05
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	4e-04
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	6e-04
pfam00575	74	pfam00575, S1, S1 RNA binding domain	0.002
COG2183	780	COG2183, Tex, Transcriptional accessory protein [T	0.002
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	0.002

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

 Score =  133 bits (337), Expect = 3e-35
 Identities = 83/212 (39%), Positives = 122/212 (57%), Gaps = 12/212 (5%)

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 LESEPGLFVSDKERVFSEAEEMAKKYRQKLPA 478
           LE EPG  + D ++VF +AEEMA KYRQ L A
Sbjct: 267 LEPEPGDMLKDPQKVFDKAEEMAAKYRQMLLA 298

Length = 318

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

 Score =  115 bits (291), 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|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score =  113 bits (286), Expect = 6e-27
 Identities = 92/334 (27%), Positives = 146/334 (43%), Gaps = 59/334 (17%)

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 VSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESL 488
           +  K  V  + E            V +    E L
Sbjct: 271 IEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGL 304

Length = 541

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

 Score =  113 bits (286), Expect = 9e-27
 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|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score =  104 bits (263), Expect = 6e-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 = 85.2 bits (211), 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 = 71.2 bits (175), Expect = 1e-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|239911 cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain

 Score = 64.8 bits (159), Expect = 2e-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 = 71.2 bits (175), Expect = 4e-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|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional

 Score = 70.5 bits (173), Expect = 6e-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|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

 Score = 70.7 bits (174), Expect = 7e-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 = 62.3 bits (152), 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 = 61.5 bits (150), Expect = 4e-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|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 67.0 bits (165), 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|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|239918 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

 Score = 59.5 bits (145), Expect = 1e-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 = 59.6 bits (145), Expect = 2e-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 = 9e-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 = 62.2 bits (152), 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 = 56.1 bits (136), Expect = 3e-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 = 57.7 bits (140), Expect = 3e-10
 Identities = 34/117 (29%), Positives = 52/117 (44%), Gaps = 13/117 (11%)

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

Query: 436 FPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDT 492
              KISLSI  LE EP            E +    ++ +  P          L    
Sbjct: 65  ENGKISLSIRKLEEEP------------EKQHRKPRFSKSRPKEGFETLLSRLLKWI 109

Length = 129

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

 Score = 54.9 bits (133), Expect = 6e-10
 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|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|216000 pfam00575, S1, S1 RNA binding domain

 Score = 52.3 bits (126), Expect = 5e-09
 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|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 55.9 bits (136), Expect = 3e-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|235614 PRK05807, PRK05807, hypothetical protein; Provisional

 Score = 51.7 bits (124), Expect = 4e-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|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

 Score = 54.6 bits (132), Expect = 7e-08
 Identities = 39/162 (24%), Positives = 69/162 (42%), Gaps = 18/162 (11%)

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-KISLSIADLESEPGLFVSDKERVFSEAEEMAKK 471
           V+       +ISL I  LE  P          + E  E  KK
Sbjct: 418 VLAVDKEKERISLGIKQLEESP----------WEEFSEKYKK 449

Length = 541

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

 Score = 50.5 bits (121), Expect = 8e-08
 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|233102 TIGR00717, rpsA, ribosomal protein S1

 Score = 54.4 bits (131), Expect = 9e-08
 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|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 379 LEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK-SMFP 437
           + G V  I  +G  + + D    GL+HIS +S   V   S++   G+ V+V V++     
Sbjct: 1   VTGKVVSITKFGVFVELED-GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEK 59

Query: 438 DKISLS 443
            +ISLS
Sbjct: 60  GRISLS 65

Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold. Length = 65

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

 Score = 52.8 bits (127), Expect = 3e-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|239899 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

 Score = 45.7 bits (109), Expect = 1e-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|181215 PRK08059, PRK08059, general stress protein 13; Validated

 Score = 47.0 bits (112), Expect = 2e-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|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|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha; Validated

 Score = 45.2 bits (108), Expect = 3e-05
 Identities = 28/91 (30%), Positives = 49/91 (53%), Gaps = 16/91 (17%)

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

Query: 432 VKSMFPDK--ISLSIADLESEPGLFVSDKER 460
           V    P K  I LS+          V++ +R
Sbjct: 68  VD---PRKGHIDLSLKR--------VNEHQR 87

Length = 262

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

 Score = 42.7 bits (101), Expect = 6e-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|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 42.8 bits (102), 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|216000 pfam00575, S1, S1 RNA binding domain

 Score = 36.5 bits (85), Expect = 0.002
 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

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

 Score = 40.5 bits (94), Expect = 0.002
 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	514
PRK07400	318	30S ribosomal protein S1; Reviewed	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	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
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	100.0
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	100.0
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.98
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.96
PRK07400	318	30S ribosomal protein S1; Reviewed	99.91
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.73
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.68
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.67
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.66
PRK08582	139	hypothetical protein; Provisional	99.58
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.55
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.52
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.49
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.47
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.46
PRK08059	123	general stress protein 13; Validated	99.45
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.43
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.43
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.43
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
PRK07252	120	hypothetical protein; Provisional	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	99.41
PRK05807	136	hypothetical protein; Provisional	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	99.38
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.37
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	99.37
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.35
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.34
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.33
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	99.3
PHA02945	88	interferon resistance protein; Provisional	99.28
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	99.26
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.24
PRK03987	262	translation initiation factor IF-2 subunit alpha;	99.22
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.22
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.22
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.21
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.2
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.19
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.19
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.18
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.16
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.16
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.15
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.15
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.14
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.11
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.11
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.08
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	99.08
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.08
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.08
COG2183	780	Tex Transcriptional accessory protein [Transcripti	99.05
PRK09202	470	nusA transcription elongation factor NusA; Validat	99.04
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.03
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.03
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	99.02
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.01
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.01
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.97
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.97
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.95
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	98.94
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	98.94
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.93
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.93
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.92
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.92
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	98.92
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	98.9
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	98.87
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	98.87
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.86
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	98.84
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.81
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.8
PRK07252	120	hypothetical protein; Provisional	98.8
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.8
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	98.8
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.79
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.79
PRK08582	139	hypothetical protein; Provisional	98.79
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.77
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	98.76
TIGR01953	341	NusA transcription termination factor NusA. This m	98.74
PRK05807	136	hypothetical protein; Provisional	98.74
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.73
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.7
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	98.69
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.68
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.66
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	98.66
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.64
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.64
PRK08059	123	general stress protein 13; Validated	98.62
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.62
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.62
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.61
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	98.6
PHA02945	88	interferon resistance protein; Provisional	98.57
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.52
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.49
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.48
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.47
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.46
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.45
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.42
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.38
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	98.38
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.33
PRK11642	813	exoribonuclease R; Provisional	98.33
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.31
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.3
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.28
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.28
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.26
COG2183	780	Tex Transcriptional accessory protein [Transcripti	98.24
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.22
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.19
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	98.17
TIGR01953	341	NusA transcription termination factor NusA. This m	98.15
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.13
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.11
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.02
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.0
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	97.92
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.92
KOG2916	304	consensus Translation initiation factor 2, alpha s	97.81
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	97.78
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.74
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.74
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	97.73
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	97.7
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.66
PRK05054	644	exoribonuclease II; Provisional	97.65
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.55
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.53
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.47
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.43
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	97.42
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.41
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.4
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.39
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	97.37
PRK12329	449	nusA transcription elongation factor NusA; Provisi	97.35
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	97.28
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.15
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	97.12
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	97.12
COG0557	706	VacB Exoribonuclease R [Transcription]	97.08
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.07
PRK11642	813	exoribonuclease R; Provisional	97.03
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	97.02
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	96.95
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.85
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	96.84
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	96.79
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	96.73
PRK10811	1068	rne ribonuclease E; Reviewed	95.83
KOG2916	304	consensus Translation initiation factor 2, alpha s	95.8
PRK11712	489	ribonuclease G; Provisional	95.58
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	95.55
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	95.36
PRK05054	644	exoribonuclease II; Provisional	95.2
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	95.07
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	94.67
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	94.59
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	94.5
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	93.76
KOG3013	301	consensus Exosomal 3'-5' exoribonuclease complex,	93.61
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	93.56
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	93.21
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	92.88
COG0557	706	VacB Exoribonuclease R [Transcription]	91.2
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	90.92
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	90.82
PRK12442	87	translation initiation factor IF-1; Reviewed	90.3
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	89.68
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	89.67
PRK10811	1068	rne ribonuclease E; Reviewed	88.77
TIGR00008	68	infA translation initiation factor IF-1. This fami	88.45
PRK11712	489	ribonuclease G; Provisional	88.27
KOG1004	230	consensus Exosomal 3'-5' exoribonuclease complex s	87.98
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	86.27
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	83.11
cd05700	65	S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a t	80.41

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1e-46  Score=387.62  Aligned_cols=281  Identities=34%  Similarity=0.480  Sum_probs=252.8

Q ss_pred             chhhhhchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhcccee
Q 010232          156 DKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI  235 (514)
Q Consensus       156 ~~~~~~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v  235 (514)
                      ..+|+++|+.+.+.+++|++|.|+|++++++|+|||+|++..||||.+|++..+           ..++           
T Consensus        15 ~~~f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~-----------~~~~-----------   72 (318)
T PRK07400         15 HEDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINR-----------VEGP-----------   72 (318)
T ss_pred             HHHHHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccc-----------ccCH-----------
Confidence            367999998766779999999999999999999999999999999999985321           0111           


Q ss_pred             eeccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEE
Q 010232          236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT  314 (514)
Q Consensus       236 ~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fV  314 (514)
                                      ...+++|+.|.|.|++.+ .+++++||+|+......|+.+.++++.|+++.|+|++++++|++|
T Consensus        73 ----------------~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V  136 (318)
T PRK07400         73 ----------------EEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALV  136 (318)
T ss_pred             ----------------HHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEE
Confidence                            234789999999999965 578999999999878899999999999999999999999999999


Q ss_pred             EECCEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh---hccCCCCceEEEEEEEEecceE
Q 010232          315 RIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA---TLNLREGTLLEGTVKKIYPYGA  391 (514)
Q Consensus       315 di~Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~---~~~l~~G~iV~G~V~~I~~~Ga  391 (514)
                      +++|++||||.++++.+.  ..+.  .+|+.+.|+|+++|+++++|+||+|.++.   ...+++|+++.|+|++|++||+
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            999999999999994331  2222  59999999999999999999999997653   2479999999999999999999


Q ss_pred             EEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhhhHHHHHHH
Q 010232          392 QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVFSEAEEMAK  470 (514)
Q Consensus       392 FV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~a~  470 (514)
                      ||+++  |+.||+|+++++|.++.++.+.|++||.|+|+|+++| ++++|.||+|++.++||+++.+++.++.+|++||.
T Consensus       213 fV~i~--gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~~~~~~~~~~~~~~~~~  290 (318)
T PRK07400        213 FIDIG--GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDPQKVFDKAEEMAA  290 (318)
T ss_pred             EEEEC--CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeccccChhhhhhhHHHHHHHHHHHHH
Confidence            99996  6999999999999999999999999999999999998 78999999999999999999999999999999999


Q ss_pred             HHHhhCccCC
Q 010232          471 KYRQKLPAVS  480 (514)
Q Consensus       471 ~~~~kl~~~~  480 (514)
                      ++++++.+..
T Consensus       291 ~~~~~~~~~~  300 (318)
T PRK07400        291 KYRQMLLAQA  300 (318)
T ss_pred             HHHHHhhhhh
Confidence            9999998774

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

Probab=100.00  E-value=1.2e-47  Score=411.82  Aligned_cols=281  Identities=30%  Similarity=0.397  Sum_probs=253.8

Q ss_pred             hhhhchh---ccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccce
Q 010232          158 VGEDKVS---VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMG  234 (514)
Q Consensus       158 ~~~~~~~---~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~  234 (514)
                      .|++.+.   .+.+.+++|++|.|+|+++++++++||+|++.+|++|.+|+....                         
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            3445554   456789999999999999999999999999999999999985320                         


Q ss_pred             eeeccccccccCCCCCCCCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEE
Q 010232          235 IVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLL  313 (514)
Q Consensus       235 v~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~-d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~f  313 (514)
                                      ....+++||.+.+.|... +.+|+++||++++....+|..|.++++.|+++.|+|+..+++|++
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                            022588999999999984 567899999999999999999999999999999999999999999


Q ss_pred             EEECCEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh----------hccCCCCceEEEE
Q 010232          314 TRIEGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGT  382 (514)
Q Consensus       314 Vdi~Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~----------~~~l~~G~iV~G~  382 (514)
                      |+++|++||+|.|++. +++++...   ++|.++.++|+++|.+++++++|+|..++          ...+++|++|+|+
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   58999999999999999999999998765          2489999999999


Q ss_pred             EEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhh
Q 010232          383 VKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERV  461 (514)
Q Consensus       383 V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v  461 (514)
                      |++|++|||||+|+  |++||+|+++|||.|+.+|++++++||+|+|+|+++| +++||+||||++.++||+.+.+++++
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 89999999999999999999988864


Q ss_pred             hhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232          462 FSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN  504 (514)
Q Consensus       462 ~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~  504 (514)
                                          |++++|+|+++.|||+|++.+.-
T Consensus       278 --------------------g~~v~G~Vt~i~~~GafVei~~G  300 (541)
T COG0539         278 --------------------GDKVEGKVTNLTDYGAFVEIEEG  300 (541)
T ss_pred             --------------------CCEEEEEEEEeecCcEEEEecCC
Confidence                                88999999999999999987653

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=5.6e-44  Score=384.36  Aligned_cols=286  Identities=24%  Similarity=0.378  Sum_probs=252.6

Q ss_pred             chhhhhchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhcccee
Q 010232          156 DKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI  235 (514)
Q Consensus       156 ~~~~~~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v  235 (514)
                      .++|.++++..+..++.|++|+|+|++++++|++||||++.+|+||.+|++...           ..++           
T Consensus        19 ~e~f~~~~e~~~~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~-----------~~~~-----------   76 (486)
T PRK07899         19 AEDFLAAIDKTIKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKH-----------DVDP-----------   76 (486)
T ss_pred             HHHHHHHHHHHHhcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccc-----------cCCh-----------
Confidence            367999998888889999999999999999999999999999999999985320           0111           


Q ss_pred             eeccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEE
Q 010232          236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT  314 (514)
Q Consensus       236 ~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fV  314 (514)
                                      ...+++|+.|+|.|++.+ .+|+++||++++.....|..+.++++.|++++|+|+++.++|++|
T Consensus        77 ----------------~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~V  140 (486)
T PRK07899         77 ----------------NEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLIL  140 (486)
T ss_pred             ----------------hhcCCCCCEEEEEEEEEECCCCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEE
Confidence                            234799999999999865 678999999999888999999999999999999999999999999


Q ss_pred             EECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh--------h--ccCCCCceEEEEE
Q 010232          315 RIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA--------T--LNLREGTLLEGTV  383 (514)
Q Consensus       315 di~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~--------~--~~l~~G~iV~G~V  383 (514)
                      ++ |++||||.+++ +.++.++..   ++|+.|.|+|+++|+++++++||+|..++        .  ..+++|+++.|+|
T Consensus       141 dl-Gi~gflP~Sel~~~~~~~~~~---~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V  216 (486)
T PRK07899        141 DI-GLRGFLPASLVEMRRVRDLQP---YIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVV  216 (486)
T ss_pred             EE-CCEEEEEhhHhcccccCChhh---cCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEE
Confidence            99 89999999999 555555544   59999999999999999999999995322        1  3799999999999


Q ss_pred             EEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhh
Q 010232          384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVF  462 (514)
Q Consensus       384 ~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~  462 (514)
                      ++++++|+||+|+  |+.||||+|+|+|.++.+|.+.|++||.|+|+|+++| +++||.||+|++.++||..+.++    
T Consensus       217 ~~i~~~G~FVdlg--gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~----  290 (486)
T PRK07899        217 SSIVNFGAFVDLG--GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFART----  290 (486)
T ss_pred             EEEECCeEEEEEC--CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHh----
Confidence            9999999999996  6999999999999999999999999999999999998 78999999999999999654433    


Q ss_pred             hHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhcc
Q 010232          463 SEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCANW  505 (514)
Q Consensus       463 ~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~~  505 (514)
                                      ..+|.++.|+|+++.|||.|+.++..+
T Consensus       291 ----------------~~vG~vv~G~V~~I~~fGvFVeL~~gi  317 (486)
T PRK07899        291 ----------------HAIGQIVPGKVTKLVPFGAFVRVEEGI  317 (486)
T ss_pred             ----------------cCCCCEEEEEEEEEeccEEEEEeCCCc
Confidence                            246899999999999999999987543

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

Probab=100.00  E-value=2.8e-42  Score=370.45  Aligned_cols=284  Identities=21%  Similarity=0.262  Sum_probs=253.4

Q ss_pred             hhhhhchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceee
Q 010232          157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV  236 (514)
Q Consensus       157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~  236 (514)
                      -+..+.|......+..|.+|.|+|+...++|+.|+++. ..||||.+++....                           
T Consensus        90 ~~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~g-vr~FlP~S~v~~r~---------------------------  141 (541)
T COG0539          90 AERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEG-VRAFLPGSLVDVRP---------------------------  141 (541)
T ss_pred             HHHHHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEECC-EEEeccHHHhcccc---------------------------
Confidence            46777787777888899999999999999999999964 89999999984220                           


Q ss_pred             eccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHH---hhhhHHHhhhcCCCEEEEEEEEEECCeE
Q 010232          237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRK---MAWHRVRQIKQLNEPIEVKFTEWNTGGL  312 (514)
Q Consensus       237 ~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~---~~w~~l~~~~k~GeiV~GkV~~v~~~G~  312 (514)
                             +.      .....+|..+.+.|+..| .++++++|+|.....   .....+.+.++.|++++|+|++++++|+
T Consensus       142 -------v~------d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~Ga  208 (541)
T COG0539         142 -------VR------DLDPLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGA  208 (541)
T ss_pred             -------cc------cccccCCceEEEEEEEEccccCcEEEEhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcE
Confidence                   00      112358999999999987 578999999988653   2334455667999999999999999999


Q ss_pred             EEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----hhhh--ccCCCCceEEEEEEE
Q 010232          313 LTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLEGTVKK  385 (514)
Q Consensus       313 fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~~~~--~~l~~G~iV~G~V~~  385 (514)
                      ||+++|++||+|.++| |.++.+|.++. ++||+|+|+|+++|++++||.||+|+    ||+.  ..+.+|+.+.|+|++
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 99999999999999999999999996    6765  479999999999999


Q ss_pred             EecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhhhH
Q 010232          386 IYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVFSE  464 (514)
Q Consensus       386 I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~  464 (514)
                      +++|||||++.+ |++||+|+|||||.+...|++++++||+|.|+|+.+| +++||+||||++..|||+.+.++++    
T Consensus       288 i~~~GafVei~~-GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~~~----  362 (541)
T COG0539         288 LTDYGAFVEIEE-GVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHP----  362 (541)
T ss_pred             eecCcEEEEecC-CccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeeehhhhcChhhhhhhhcC----
Confidence            999999999999 9999999999999999999999999999999999999 8899999999999999999887765    


Q ss_pred             HHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhh
Q 010232          465 AEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCA  503 (514)
Q Consensus       465 ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~  503 (514)
                                      +|++++|.+++..+||+|+.++.
T Consensus       363 ----------------~g~~v~g~v~~~t~~g~fv~le~  385 (541)
T COG0539         363 ----------------VGDVVEGKVKSITDFGAFVELEG  385 (541)
T ss_pred             ----------------CCCeEEEEEeeecccceEEccCC
Confidence                            58899999999999999999987

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=8.9e-41  Score=367.59  Aligned_cols=283  Identities=25%  Similarity=0.378  Sum_probs=252.5

Q ss_pred             chhhhhchhccc--cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccc
Q 010232          156 DKVGEDKVSVEY--YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKM  233 (514)
Q Consensus       156 ~~~~~~~~~~~~--~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~  233 (514)
                      .++|+++++.+.  +++++|++|+|+|++++++|++||+|.+.+||||.+|+.+..                        
T Consensus        12 ~~~f~~~l~~~~~~~~~~~G~~v~G~V~~v~~~~~~Vdig~k~~g~lp~~e~~~~~------------------------   67 (565)
T PRK06299         12 EESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQ------------------------   67 (565)
T ss_pred             hHHHHHHHHhhcccccCCCCCEEEEEEEEEECCEEEEEeCCCeEEEEEHHHhcCcc------------------------
Confidence            368999998876  779999999999999999999999999999999999984210                        


Q ss_pred             eeeeccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeE
Q 010232          234 GIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL  312 (514)
Q Consensus       234 ~v~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~  312 (514)
                                       ....+++|++++|.|++.+ .+|+++||++++.....|+.+.++++.|++++|+|++++++|+
T Consensus        68 -----------------~~~~~~vG~~i~~~V~~~~~~~~~i~lS~k~~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~  130 (565)
T PRK06299         68 -----------------GELEVKVGDEVEVYVERIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGF  130 (565)
T ss_pred             -----------------ccccCCCCCEEEEEEEEEECCCCcEEEechHHHHHHHHHHHHHHhhCCCEEEEEEEEEECCEE
Confidence                             0234789999999999965 5789999999999999999999999999999999999999999


Q ss_pred             EEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh----------hccCCCCceEEE
Q 010232          313 LTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEG  381 (514)
Q Consensus       313 fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~----------~~~l~~G~iV~G  381 (514)
                      +|+++|++||||.+++ +.+..++.   .++|+++.|+|+++|++++++++|+|.+++          ...+++|+++.|
T Consensus       131 ~V~~~g~~gfip~s~~~~~~~~~~~---~~vG~~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g  207 (565)
T PRK06299        131 TVDLNGVEAFLPGSQVDVRPVRDTD---PLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEG  207 (565)
T ss_pred             EEEECCEEEEEEHHHccCcCCCChH---HhCCCEEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEE
Confidence            9999999999999999 44555543   359999999999999999999999997642          137999999999


Q ss_pred             EEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhh
Q 010232          382 TVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKER  460 (514)
Q Consensus       382 ~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~  460 (514)
                      +|++++++|+||+++  |+.||+|+++++|.++.+|.+.|++||+|+|+|+++| +++||.||+|.+.++||+.+.+.  
T Consensus       208 ~V~~v~~~G~~V~i~--g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~~~~--  283 (565)
T PRK06299        208 VVKNITDYGAFVDLG--GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKK--  283 (565)
T ss_pred             EEEEEeCCeEEEEEC--CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHHHhh--
Confidence            999999999999997  6999999999999999999999999999999999998 78999999999999999875432  


Q ss_pred             hhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232          461 VFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN  504 (514)
Q Consensus       461 v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~  504 (514)
                                        ..+|..+.|+|.++.+||.|+++...
T Consensus       284 ------------------~~~G~~v~g~V~~i~~~G~fV~l~~~  309 (565)
T PRK06299        284 ------------------YPVGSKVKGKVTNITDYGAFVELEEG  309 (565)
T ss_pred             ------------------CCCCCEEEEEEEEEeCCeEEEEeCCC
Confidence                              34799999999999999999988654

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=4.7e-40  Score=346.62  Aligned_cols=284  Identities=30%  Similarity=0.420  Sum_probs=249.9

Q ss_pred             hhhhhchhccccCCCCCCEEEEEEEEEeCCeEEEEe-CCceeEEeecccccccccchhhhhhhhhchhhhHHhhhcccee
Q 010232          157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNV-GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI  235 (514)
Q Consensus       157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdI-G~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v  235 (514)
                      .+|++.+. ...++++|++|+|+|++++++|++|++ |.+.+|+||.+|+....           .++            
T Consensus         3 ~~~~~~~~-~~~~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~-----------~~~------------   58 (390)
T PRK06676          3 EEFEESLN-SVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDH-----------IED------------   58 (390)
T ss_pred             HHHHHHhh-hhhcccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhcccc-----------ccC------------
Confidence            57888887 788999999999999999999999999 88999999999985310           011            


Q ss_pred             eeccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEE
Q 010232          236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT  314 (514)
Q Consensus       236 ~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fV  314 (514)
                                     ....+++|+.|+|+|+..+ .+++++||++++.....|+.+.++++.|++++|+|+++.++|++|
T Consensus        59 ---------------~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V  123 (390)
T PRK06676         59 ---------------INDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVV  123 (390)
T ss_pred             ---------------cccccCCCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEE
Confidence                           1235799999999999976 567899999999888899999999999999999999999999999


Q ss_pred             EECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh----------hccCCCCceEEEEE
Q 010232          315 RIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGTV  383 (514)
Q Consensus       315 di~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~----------~~~l~~G~iV~G~V  383 (514)
                      +++|++||||++++ +.+..++.+   ++|+.+.|+|+++|++++++.||+|.+..          ...+++|+++.|+|
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 555566654   48999999999999999999999996422          13689999999999


Q ss_pred             EEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhh
Q 010232          384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVF  462 (514)
Q Consensus       384 ~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~  462 (514)
                      ++++++|+||+++  ++.||||.++++|.++.++.+.|++||.|+|+|+.++ +++||.||+|++.++||..+.+     
T Consensus       201 ~~v~~~G~fV~l~--~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~-----  273 (390)
T PRK06676        201 ARLTDFGAFVDIG--GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEE-----  273 (390)
T ss_pred             EEEecceEEEEeC--CeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchh-----
Confidence            9999999999996  6999999999999999999999999999999999998 7899999999999999975432     


Q ss_pred             hHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232          463 SEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN  504 (514)
Q Consensus       463 ~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~  504 (514)
                                     ...+|.++.|+|.++.|||.|++++..
T Consensus       274 ---------------~~~~G~~v~g~V~~i~~~G~fV~l~~g  300 (390)
T PRK06676        274 ---------------KLPEGDVIEGTVKRLTDFGAFVEVLPG  300 (390)
T ss_pred             ---------------hhcCCcEEEEEEEEEeCceEEEEECCC
Confidence                           345689999999999999999988743

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=3e-40  Score=357.86  Aligned_cols=282  Identities=24%  Similarity=0.336  Sum_probs=246.2

Q ss_pred             hhhhhchhccccC----CCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhcc
Q 010232          157 KVGEDKVSVEYYE----PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGK  232 (514)
Q Consensus       157 ~~~~~~~~~~~~~----ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~  232 (514)
                      .+|+++|+.+.++    +++|++|+|+|++++++|++||+|++.+|+||.+|+...               .        
T Consensus        15 ~~f~~~l~~~~~~~~~~~~~G~~v~G~V~~v~~~~v~Vdig~k~eg~ip~~e~~~~---------------~--------   71 (491)
T PRK13806         15 ESFAELLEAYEGERKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDA---------------D--------   71 (491)
T ss_pred             HHHHHHHHhhhhhccccCCCCCEEEEEEEEEECCEEEEEECCCcEEEEEHHHhcCc---------------c--------
Confidence            5799999876543    999999999999999999999999999999999997421               0        


Q ss_pred             ceeeeccccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeE
Q 010232          233 MGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL  312 (514)
Q Consensus       233 ~~v~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~  312 (514)
                                        ....+++|+.|++.|++.+ ++.++||++.. ....|+.+.++++.|++++|+|++++++|+
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                              0123789999999999765 35789997644 467999999999999999999999999999


Q ss_pred             EEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh----------hccCCCCceEEE
Q 010232          313 LTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEG  381 (514)
Q Consensus       313 fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~----------~~~l~~G~iV~G  381 (514)
                      +|+++|++||||.+++ +.+..++..   .+|+++.|+|+++|+++++++||+|+.++          ...+++|++++|
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 555666655   49999999999999999999999996532          136999999999


Q ss_pred             EEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CC----CeEEEEEecCcCCCCcccc
Q 010232          382 TVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP----DKISLSIADLESEPGLFVS  456 (514)
Q Consensus       382 ~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~----~rI~LSlK~l~~~P~~~~~  456 (514)
                      +|++++++|+||+|++ |+.||||+|+++|.++.++.+.|++||.|+|+|++++ ++    +||.||+|++.++||+.+.
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 44    4899999999999997765


Q ss_pred             chhhhhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhcc
Q 010232          457 DKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCANW  505 (514)
Q Consensus       457 ~k~~v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~~  505 (514)
                      ++                    ..+|+.++|+|+++.|||+|+++....
T Consensus       288 ~~--------------------~~~G~~v~G~V~~v~~~G~fV~l~~gv  316 (491)
T PRK13806        288 DR--------------------LKAGDKVTGKVVRLAPFGAFVEILPGI  316 (491)
T ss_pred             cc--------------------CCCCCEEEEEEEEEeCceEEEEeCCCc
Confidence            44                    356999999999999999999997543

>TIGR00717 rpsA ribosomal protein S1

Probab=100.00  E-value=1.9e-38  Score=345.40  Aligned_cols=279  Identities=25%  Similarity=0.391  Sum_probs=245.8

Q ss_pred             hhhhchhccc--cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhcccee
Q 010232          158 VGEDKVSVEY--YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI  235 (514)
Q Consensus       158 ~~~~~~~~~~--~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v  235 (514)
                      +|+++++.++  ..+++|++|.|+|+++++++++||+|++.+|+||.+|+...                           
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            5888887663  46999999999999999999999999999999999888421                           


Q ss_pred             eeccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEE
Q 010232          236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT  314 (514)
Q Consensus       236 ~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fV  314 (514)
                                      +..+++||.|.+.|++.+ ..|+++||.++......|..+..+++.|++++|+|++++++|++|
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                            134789999999999854 579999999999888899999999999999999999999999999


Q ss_pred             EECCEEEEEeccccccc-cCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh----------hccCCCCceEEEEE
Q 010232          315 RIEGLRAFLPKAELLSR-VNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA----------TLNLREGTLLEGTV  383 (514)
Q Consensus       315 di~Gi~gFVP~sel~~~-i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~----------~~~l~~G~iV~G~V  383 (514)
                      +++|++||||.+++..+ .++..   .++|+++.|+|+++|+.++++++|+|+++.          ...+++|++++|+|
T Consensus       119 ~i~g~~~flP~s~~~~~~~~~~~---~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V  195 (516)
T TIGR00717       119 DLNGVEAFLPGSQVDVKPIKDLD---SLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVV  195 (516)
T ss_pred             EECCEEEEEeHHHhcCcccCchh---hhCCCEEEEEEEEEECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEE
Confidence            99999999999999533 23322   259999999999999999999999997642          13799999999999


Q ss_pred             EEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhh
Q 010232          384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVF  462 (514)
Q Consensus       384 ~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~  462 (514)
                      +++.++|+||+++  |++||+|.++++|.++.++.+.|++||+|.|+|+.+| +++++.||+|.+.++||+.+.      
T Consensus       196 ~~i~~~G~~V~l~--g~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~------  267 (516)
T TIGR00717       196 KNITDFGAFVDLG--GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIE------  267 (516)
T ss_pred             EEEECCeEEEEEC--CEEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHH------
Confidence            9999999999996  6999999999999999999999999999999999998 788999999999988886532      


Q ss_pred             hHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232          463 SEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN  504 (514)
Q Consensus       463 ~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~  504 (514)
                                    ....+|+.++|+|+++.+||+|+++...
T Consensus       268 --------------~~~~~G~i~~g~V~~v~~~G~fV~l~~~  295 (516)
T TIGR00717       268 --------------KKFPVGDKITGRVTNLTDYGVFVEIEEG  295 (516)
T ss_pred             --------------hhccCCCEEEEEEEEeeCCcEEEEeCCC
Confidence                          2235799999999999999999988644

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=3.2e-38  Score=358.12  Aligned_cols=312  Identities=21%  Similarity=0.297  Sum_probs=259.8

Q ss_pred             CCCCCChhhhhhhhhccccCCC--ChHHHhhhccccccccccccc--cchhhhhchhcc-ccCCCCCCEEEEEEEEEeCC
Q 010232          112 KSEKPDEEEALAPFLKFFKPRD--SAEEVEEEGSEVGVSRESIDV--DDKVGEDKVSVE-YYEPKPGDFVIGVVVSGNEN  186 (514)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~-~~~ik~GdiV~G~Vv~v~~~  186 (514)
                      .+..++-+|.+.=.++..+.+.  .+|        ..+  ++.++  ..---..+++.+ +..+++|++|+|+|++++++
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            3567889999998898888765  111        111  11111  111223455555 57899999999999999999


Q ss_pred             eEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCCCCCCCCcccCCCEEEEEEE
Q 010232          187 KLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVL  266 (514)
Q Consensus       187 Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl  266 (514)
                      ++|||+|++.+|++|.+|+.                                              ..+++||+|+|.|+
T Consensus       336 ~v~VdiG~K~eGiI~~~E~~----------------------------------------------~~~kvGd~i~~~V~  369 (863)
T PRK12269        336 TVFVDIGGKSEGRVPVEEFE----------------------------------------------APPKAGDGVRVYVE  369 (863)
T ss_pred             EEEEEeCCCceEEeEHHHhc----------------------------------------------cCCCCCCEEEEEEE
Confidence            99999999999999988872                                              11479999999999


Q ss_pred             EEcCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEE--CCeEEEEEC-CEEEEEeccccc-cccCChhhHhhhc
Q 010232          267 GRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN--TGGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKV  342 (514)
Q Consensus       267 ~~d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~--~~G~fVdi~-Gi~gFVP~sel~-~~i~~~~el~~~V  342 (514)
                      +.+.+| ++||.+++.....|+.+.++++.|++|+|+|++++  ++|++|+++ |++||||.+|+. ....++..   .+
T Consensus       370 ~~~~~~-~~LS~~~~~~~~~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~~~~~~~---~v  445 (863)
T PRK12269        370 RVTPYG-PELSKTKADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPES---LI  445 (863)
T ss_pred             EEcCCc-eEEEehHhhhhHHHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhccccccchHH---hC
Confidence            876666 89999999989999999999999999999999984  589999996 799999999994 33344433   58


Q ss_pred             CCEEEEEEEEEeC-----CCCceEeehhhhhhh----------ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEee
Q 010232          343 GRRMYVQITRINE-----DTNDLILSEREAWAT----------LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHIS  407 (514)
Q Consensus       343 Gq~V~vkVl~vD~-----e~~rIiLS~K~~~~~----------~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~S  407 (514)
                      |++++|+|+++|+     +++++++|+|++++.          .++++|++|.|+|++++++|+||+++  |++||||+|
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     346899999975321          36889999999999999999999996  699999999


Q ss_pred             ccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhhhHHHHHHHHHHhhCccCCCCCccc
Q 010232          408 NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSE  486 (514)
Q Consensus       408 els~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~a~~~~~kl~~~~~g~~~e  486 (514)
                      +++|.++.+|.+.+++||+|+|+|+++| +++||.||+|++.++||..+.++                    ..+|++++
T Consensus       524 eiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~--------------------~~vG~iV~  583 (863)
T PRK12269        524 DMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENK--------------------FGVNDVVK  583 (863)
T ss_pred             hccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhcc--------------------CCCCCEEE
Confidence            9999999999999999999999999998 78999999999999999776554                    35799999


Q ss_pred             CCCCCCCCCCCccchhhcc
Q 010232          487 SLPTDTPPFDSEASMCANW  505 (514)
Q Consensus       487 ~~v~~~~pfg~~~~~~~~~  505 (514)
                      |+|.++.|||+|+++..+.
T Consensus       584 G~V~~I~~fG~fVeL~~gv  602 (863)
T PRK12269        584 GRVTKIADFGAFIELAEGI  602 (863)
T ss_pred             EEEEEEeCCeEEEEecCCc
Confidence            9999999999999997554

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=1.1e-38  Score=361.85  Aligned_cols=283  Identities=16%  Similarity=0.236  Sum_probs=244.8

Q ss_pred             hhhchhccccCCCCCCEEEEEEEEEe--CCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceee
Q 010232          159 GEDKVSVEYYEPKPGDFVIGVVVSGN--ENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV  236 (514)
Q Consensus       159 ~~~~~~~~~~~ik~GdiV~G~Vv~v~--~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~  236 (514)
                      ..+.|+.-...++.|++|+|+|++++  ++|++||+|++.+||||.+|+....           .++             
T Consensus       385 ~~~~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~-----------~~~-------------  440 (863)
T PRK12269        385 RLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQK-----------VDA-------------  440 (863)
T ss_pred             hhHHHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhcccc-----------ccc-------------
Confidence            34556655667889999999999985  4799999998999999999983210           000             


Q ss_pred             eccccccccCCCCCCCCcccCCCEEEEEEEEEc------CCCcEEEEehHHHHHhhhhHHHhhh---cCCCEEEEEEEEE
Q 010232          237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT------LSGRPLLSTRRLFRKMAWHRVRQIK---QLNEPIEVKFTEW  307 (514)
Q Consensus       237 ~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d------~~grliLS~kk~~~~~~w~~l~~~~---k~GeiV~GkV~~v  307 (514)
                                      ....+|+.+++.|+..+      .++++++|+|++..+..|+.+.+++   +.|+++.|+|.++
T Consensus       441 ----------------~~~~vG~~ie~~V~~~~~~~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i  504 (863)
T PRK12269        441 ----------------PESLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSF  504 (863)
T ss_pred             ----------------hHHhCCCeEEEEEEEEecccccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEE
Confidence                            11247999999999854      3468999999998888888877665   4799999999999


Q ss_pred             ECCeEEEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----hhhh--ccCCCCceEE
Q 010232          308 NTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLE  380 (514)
Q Consensus       308 ~~~G~fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~~~~--~~l~~G~iV~  380 (514)
                      .++|+||+++|++||||.+++ +.++.++.+.. ++||+++|+|+++|++++++.||+|+    +|..  ..+++|++++
T Consensus       505 ~~~G~fVdl~Gv~Gfvp~SeiS~~~v~~~~~~~-kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~  583 (863)
T PRK12269        505 TSFGAFIDLGGFDGLLHVNDMSWGHVARPREFV-KKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVK  583 (863)
T ss_pred             eCCcEEEEECCEEEEEEchhccccccCCHHHhc-cCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEE
Confidence            999999999999999999999 77888888765 89999999999999999999999995    4543  3699999999


Q ss_pred             EEEEEEecceEEEEECCCceEEEEEeecccc-ccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccch
Q 010232          381 GTVKKIYPYGAQIRIGDSNRSGLLHISNMSR-TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDK  458 (514)
Q Consensus       381 G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~-~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k  458 (514)
                      |+|+++++||+||++++ |++||+|+|+++| .++.+|.+.|++||+|+|+|+.+| +++||.||+|++.+|||+.+.++
T Consensus       584 G~V~~I~~fG~fVeL~~-gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~  662 (863)
T PRK12269        584 GRVTKIADFGAFIELAE-GIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEAR  662 (863)
T ss_pred             EEEEEEeCCeEEEEecC-CceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHHHh
Confidence            99999999999999998 8999999999999 689999999999999999999998 78999999999999999887543


Q ss_pred             hhhhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhh
Q 010232          459 ERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCA  503 (514)
Q Consensus       459 ~~v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~  503 (514)
                                          ..+|+.++|+|+++.+||.|++++.
T Consensus       663 --------------------~~vG~~v~G~V~~i~~~G~fV~l~~  687 (863)
T PRK12269        663 --------------------YPVGARFTRRIVKVTNAGAFIEMEE  687 (863)
T ss_pred             --------------------CCCCCEEEEEEEEEecceEEEEeCC
Confidence                                3579999999999999999999864

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=4.6e-38  Score=340.84  Aligned_cols=279  Identities=22%  Similarity=0.265  Sum_probs=240.1

Q ss_pred             hhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccc
Q 010232          163 VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAI  242 (514)
Q Consensus       163 ~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~  242 (514)
                      |......++.|++|+|+|.++.++|++|+++ +..||||.+++....           .+++                  
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            3333445678999999999999999999997 589999999984210           0111                  


Q ss_pred             cccCCCCCCCCcccCCCEEEEEEEEEcC-CCcEEEEehHHHH---HhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC-
Q 010232          243 AMSGGSGPGRPVVETGTVLFAEVLGRTL-SGRPLLSTRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-  317 (514)
Q Consensus       243 ~l~~~~~~~~~~~~vGd~V~v~Vl~~d~-~grliLS~kk~~~---~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~-  317 (514)
                                .. .+|+.+.|.|+..|. +++++||++....   ...|+.+...++.|++++|+|+++.++|+||+++ 
T Consensus       156 ----------~~-~vG~~i~~~V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~  224 (491)
T PRK13806        156 ----------ES-YVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAP  224 (491)
T ss_pred             ----------HH-cCCCeEEEEEEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCC
Confidence                      11 289999999999874 6789999988753   4678888788999999999999999999999995 


Q ss_pred             CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCC----CceEeehhhh----hhh--ccCCCCceEEEEEEEE
Q 010232          318 GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDT----NDLILSEREA----WAT--LNLREGTLLEGTVKKI  386 (514)
Q Consensus       318 Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~----~rIiLS~K~~----~~~--~~l~~G~iV~G~V~~I  386 (514)
                      |++||||.+++ +.++.++.+++ ++|+.++|+|+++|.++    +||.||+|++    |..  ..+++|+++.|+|+++
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            79999999999 77777887764 89999999999999876    4799999964    543  3799999999999999


Q ss_pred             ecceEEEEECCCceEEEEEeecccc-ccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhhhH
Q 010232          387 YPYGAQIRIGDSNRSGLLHISNMSR-TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVFSE  464 (514)
Q Consensus       387 ~~~GaFV~I~~~gi~GLvh~Sels~-~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~  464 (514)
                      ++||+||++++ |++||+|+|+|+| .++.++.+.|++||.|+|+|+.+| +++||.||+|++..+||+.+.+.+     
T Consensus       304 ~~~G~fV~l~~-gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~-----  377 (491)
T PRK13806        304 APFGAFVEILP-GIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERF-----  377 (491)
T ss_pred             eCceEEEEeCC-CcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecccChhHHhhhhC-----
Confidence            99999999988 8999999999999 578899999999999999999998 789999999999999998876543     


Q ss_pred             HHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232          465 AEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN  504 (514)
Q Consensus       465 ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~  504 (514)
                                     .+|+.++|+|+++.|||+|++++..
T Consensus       378 ---------------~vG~~v~G~V~~i~~~G~FV~l~~g  402 (491)
T PRK13806        378 ---------------APGTTVTGTVEKRAQFGLFVNLAPG  402 (491)
T ss_pred             ---------------CCCCEEEEEEEEEecCceEEEcCCC
Confidence                           4699999999999999999998743

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

Probab=100.00  E-value=4.1e-37  Score=343.30  Aligned_cols=285  Identities=29%  Similarity=0.398  Sum_probs=249.2

Q ss_pred             hhhhhchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceee
Q 010232          157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV  236 (514)
Q Consensus       157 ~~~~~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~  236 (514)
                      .++.+.|+.....+++|++|+|+|.+++++|+||++|.+.+|+||.+|+...           ...++            
T Consensus       287 ~~~~~~~~~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~-----------~~~~~------------  343 (647)
T PRK00087        287 NEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLD-----------EISSL------------  343 (647)
T ss_pred             HHHHHHHHHHHhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccc-----------ccCCh------------
Confidence            4555666778889999999999999999999999999999999999998521           00111            


Q ss_pred             eccccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEE
Q 010232          237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR  315 (514)
Q Consensus       237 ~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVd  315 (514)
                                     ...+++|+.|+|+|++.+ .+|+++||++++.....|+.+.++++.|+++.|+|+++.++|++|+
T Consensus       344 ---------------~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~  408 (647)
T PRK00087        344 ---------------KESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVD  408 (647)
T ss_pred             ---------------hhccCCCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEE
Confidence                           235899999999999965 6899999999998888999999999999999999999999999999


Q ss_pred             ECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCc-eEeehhhhhh----------hccCCCCceEEEEE
Q 010232          316 IEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTND-LILSEREAWA----------TLNLREGTLLEGTV  383 (514)
Q Consensus       316 i~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~r-IiLS~K~~~~----------~~~l~~G~iV~G~V  383 (514)
                      ++|++||||.+++ +.+..++..   ++|+.+.|+|+++|+++++ +.+|+|.++.          ..++++|+++.|+|
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 455556544   4999999999999999998 9999997642          13689999999999


Q ss_pred             EEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhh
Q 010232          384 KKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVF  462 (514)
Q Consensus       384 ~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~  462 (514)
                      ++++++|+||++ + ++.||+|+|+++|.++.++.+.|++||.|+|+|++++ ++++|.||+|++.++||..+.+     
T Consensus       486 ~~v~~~G~fV~l-~-gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~-----  558 (647)
T PRK00087        486 KRLTDFGAFVDI-G-GVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEE-----  558 (647)
T ss_pred             EEEeCCcEEEEE-C-CEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhh-----
Confidence            999999999999 5 7999999999999999999999999999999999998 7899999999999999965422     


Q ss_pred             hHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232          463 SEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN  504 (514)
Q Consensus       463 ~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~  504 (514)
                                     ...+|..+.|+|.++.+||.|+.++.+
T Consensus       559 ---------------~~~~G~~v~g~V~~i~~~G~fV~l~~~  585 (647)
T PRK00087        559 ---------------KYPVGSIVLGKVVRIAPFGAFVELEPG  585 (647)
T ss_pred             ---------------hccCCeEEEEEEEEEECCeEEEEECCC
Confidence                           235689999999999999999988643

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1.2e-35  Score=326.94  Aligned_cols=281  Identities=20%  Similarity=0.290  Sum_probs=242.5

Q ss_pred             chhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccc
Q 010232          162 KVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA  241 (514)
Q Consensus       162 ~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~  241 (514)
                      .+...+.++++|+++.|+|+++++.|+||++| +.+|+||.+|+...           ...++                 
T Consensus       191 ~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~-----------~~~~~-----------------  241 (565)
T PRK06299        191 EREELLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWK-----------RVNHP-----------------  241 (565)
T ss_pred             HHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhccc-----------ccCCH-----------------
Confidence            44555678999999999999999999999998 89999999998521           01111                 


Q ss_pred             ccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC-CE
Q 010232          242 IAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GL  319 (514)
Q Consensus       242 ~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi  319 (514)
                                ...+++||.|.|+|+..| .++++.||++.... ..|..+...++.|+++.|+|+++.++|+||+++ |+
T Consensus       242 ----------~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~-~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v  310 (565)
T PRK06299        242 ----------SEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGE-DPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGI  310 (565)
T ss_pred             ----------hhcCCCCCEEEEEEEEEeCCCCeEEEEEEeccc-ChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCC
Confidence                      234899999999999987 47899999998764 689999888999999999999999999999995 79


Q ss_pred             EEEEecccc-cc-ccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh----hhh--ccCCCCceEEEEEEEEecceE
Q 010232          320 RAFLPKAEL-LS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA----WAT--LNLREGTLLEGTVKKIYPYGA  391 (514)
Q Consensus       320 ~gFVP~sel-~~-~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~----~~~--~~l~~G~iV~G~V~~I~~~Ga  391 (514)
                      .||+|.+++ +. +..++.+.. .+|+.|.|+|+++|+++++|.||+|+.    |..  ..+++|++|.|+|++++++|+
T Consensus       311 ~Glv~~sel~~~~~~~~~~~~~-~~G~~v~v~V~~id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~  389 (565)
T PRK06299        311 EGLVHVSEMSWTKKNKHPSKVV-SVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGA  389 (565)
T ss_pred             EEEEEHHHcCccccccCHHHhc-CCCCEEEEEEEEEcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceE
Confidence            999999999 43 345665543 799999999999999999999999853    442  368899999999999999999


Q ss_pred             EEEECCCceEEEEEeeccccccc-cCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhhhHHHHHH
Q 010232          392 QIRIGDSNRSGLLHISNMSRTRV-TSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVFSEAEEMA  469 (514)
Q Consensus       392 FV~I~~~gi~GLvh~Sels~~~v-~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~a  469 (514)
                      ||++++ ++.||+|+++++|.+. .++.+.|++||.|+|+|+.+| +++||.||+|++..+||..+.+            
T Consensus       390 fV~l~~-~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~------------  456 (565)
T PRK06299        390 FVGLEG-GIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAK------------  456 (565)
T ss_pred             EEECCC-CCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHh------------
Confidence            999998 7999999999999887 889999999999999999998 7899999999999999964322            


Q ss_pred             HHHHhhCccCCCCCcccCCCCCCCCCCCccchhhc
Q 010232          470 KKYRQKLPAVSVSPKSESLPTDTPPFDSEASMCAN  504 (514)
Q Consensus       470 ~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~~~  504 (514)
                              ....|+++.|+|.++.++|.|+.++.+
T Consensus       457 --------~~~~G~vV~G~V~~v~~~G~fV~l~~g  483 (565)
T PRK06299        457 --------KHKKGSIVTGTVTEVKDKGAFVELEDG  483 (565)
T ss_pred             --------hcCCCCEEEEEEEEEecCceEEecCCC
Confidence                    246799999999999999999998743

>TIGR00717 rpsA ribosomal protein S1

Probab=100.00  E-value=7.4e-35  Score=317.19  Aligned_cols=278  Identities=17%  Similarity=0.239  Sum_probs=237.3

Q ss_pred             chhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccc
Q 010232          162 KVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA  241 (514)
Q Consensus       162 ~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~  241 (514)
                      .|....+.++.|++|+|+|++++++|++|++| +.+||||.+++....           .+                   
T Consensus        90 ~~~~l~~a~~~g~~v~g~V~~~~~~g~~V~i~-g~~~flP~s~~~~~~-----------~~-------------------  138 (516)
T TIGR00717        90 LWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLN-GVEAFLPGSQVDVKP-----------IK-------------------  138 (516)
T ss_pred             HHHHHHHHhhCCCeEEEEEEEEECCEEEEEEC-CEEEEEeHHHhcCcc-----------cC-------------------
Confidence            44444456678999999999999999999998 789999999974210           00                   


Q ss_pred             ccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHH---hhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC
Q 010232          242 IAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRK---MAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE  317 (514)
Q Consensus       242 ~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~---~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~  317 (514)
                                .....+|+.++++|+..+ ..+++++|+|.+...   ..|..+...++.|++++|+|+++.++|+||+++
T Consensus       139 ----------~~~~~vG~~i~~~v~~~~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~  208 (516)
T TIGR00717       139 ----------DLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLG  208 (516)
T ss_pred             ----------chhhhCCCEEEEEEEEEECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC
Confidence                      112468999999999976 467899999987533   457777778899999999999999999999999


Q ss_pred             CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----hhhh--ccCCCCceEEEEEEEEecce
Q 010232          318 GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLEGTVKKIYPYG  390 (514)
Q Consensus       318 Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~~~~--~~l~~G~iV~G~V~~I~~~G  390 (514)
                      |++||||.+++ +.+..++.++. ++|+.+.|+|+++|++++++.+|+|.    +|+.  ..+++|+++.|+|++++++|
T Consensus       209 g~~g~lp~~e~s~~~~~~~~~~~-~vG~~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~~~~~~~G~i~~g~V~~v~~~G  287 (516)
T TIGR00717       209 GVDGLLHITDMSWKRVKHPSEYV-KVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYG  287 (516)
T ss_pred             CEEEEEEHHHcCCCCCCCHHHhc-cCCCEEEEEEEEEECCCCcEEEEEEecchhHHHHHHhhccCCCEEEEEEEEeeCCc
Confidence            99999999999 67777777654 79999999999999999999999985    4554  36899999999999999999


Q ss_pred             EEEEECCCceEEEEEeeccccc-cccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccchhhhhhHHHHH
Q 010232          391 AQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDKERVFSEAEEM  468 (514)
Q Consensus       391 aFV~I~~~gi~GLvh~Sels~~-~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~  468 (514)
                      +||++++ ++.||+|+++++|. ...++.+.+++||.|+|+|+.+| +++++.||+|++..+||..+.+           
T Consensus       288 ~fV~l~~-~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~-----------  355 (516)
T TIGR00717       288 VFVEIEE-GIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEE-----------  355 (516)
T ss_pred             EEEEeCC-CCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHH-----------
Confidence            9999988 89999999999986 46778888999999999999998 7899999999999999865321           


Q ss_pred             HHHHHhhCccCCCCCcccCCCCCCCCCCCccchh
Q 010232          469 AKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMC  502 (514)
Q Consensus       469 a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~  502 (514)
                               ...+|+.+.|+|+++.+||.|+++.
T Consensus       356 ---------~~~~G~~v~g~V~~v~~~G~fV~l~  380 (516)
T TIGR00717       356 ---------KHPVGDRVTGKIKKITDFGAFVELE  380 (516)
T ss_pred             ---------hCCCCCEEEEEEEEEecceEEEECC
Confidence                     2357999999999999999999886

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

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=2.2e-34  Score=310.09  Aligned_cols=248  Identities=20%  Similarity=0.271  Sum_probs=212.4

Q ss_pred             hhchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecc
Q 010232          160 EDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD  239 (514)
Q Consensus       160 ~~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~  239 (514)
                      .+.|+......+.|++|+|+|+++.++|++|++|  ..||||.+++....           ..+                
T Consensus       110 ~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~VdlG--i~gflP~Sel~~~~-----------~~~----------------  160 (486)
T PRK07899        110 ERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDIG--LRGFLPASLVEMRR-----------VRD----------------  160 (486)
T ss_pred             cchHHHHHHHhcCCCEEEEEEEEEECCeEEEEEC--CEEEEEhhHhcccc-----------cCC----------------
Confidence            3455543334468999999999999999999995  68999999874210           000                


Q ss_pred             ccccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHH---HhhhhHHHhhhcCCCEEEEEEEEEECCeEEEE
Q 010232          240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR  315 (514)
Q Consensus       240 d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~---~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVd  315 (514)
                                   ..-.+|+.|.|+|+..| .+++++||+|....   ...|+.+...++.|+++.|+|+++.++|+||+
T Consensus       161 -------------~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVd  227 (486)
T PRK07899        161 -------------LQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVD  227 (486)
T ss_pred             -------------hhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEE
Confidence                         01148999999999987 46789999987543   35788888889999999999999999999999


Q ss_pred             ECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----hhhh--ccCCCCceEEEEEEEEec
Q 010232          316 IEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLEGTVKKIYP  388 (514)
Q Consensus       316 i~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~~~~--~~l~~G~iV~G~V~~I~~  388 (514)
                      ++|++||||.+++ +.++.++.++. .+||.|+|+|+++|+++++|.||+|.    +|..  ..+.+|+++.|+|+++++
T Consensus       228 lggv~Glv~~Sels~~~v~~~~~~~-kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~  306 (486)
T PRK07899        228 LGGVDGLVHVSELSWKHIDHPSEVV-EVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVP  306 (486)
T ss_pred             ECCEEEEEEHHHCCCcccCCHHHhc-CCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEec
Confidence            9999999999999 77888887764 89999999999999999999999995    4643  257899999999999999


Q ss_pred             ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCC
Q 010232          389 YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEP  451 (514)
Q Consensus       389 ~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P  451 (514)
                      +|+||++.+ |+.||+|++++++.++.++.+.|++||+|+|+|+++| +++||.||+|++.++-
T Consensus       307 fGvFVeL~~-gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~~~~~~  369 (486)
T PRK07899        307 FGAFVRVEE-GIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQANEGV  369 (486)
T ss_pred             cEEEEEeCC-CcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEEEcccCC
Confidence            999999988 8999999999999999999999999999999999998 8999999999887643

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=3.8e-34  Score=301.78  Aligned_cols=255  Identities=25%  Similarity=0.329  Sum_probs=219.9

Q ss_pred             hchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccc
Q 010232          161 DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDD  240 (514)
Q Consensus       161 ~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d  240 (514)
                      +.|......++.|+++.|+|+++.++|++|+++ +..||||.+|+....           ..++                
T Consensus        94 ~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~-G~~gflp~~el~~~~-----------~~~~----------------  145 (390)
T PRK06676         94 KAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVE-GVRGFIPASLISTRF-----------VEDF----------------  145 (390)
T ss_pred             hhHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCcc-----------CCCh----------------
Confidence            345545556789999999999999999999995 459999999985320           0001                


Q ss_pred             cccccCCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHHHHH---hhhhHHHhhhcCCCEEEEEEEEEECCeEEEEE
Q 010232          241 AIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRK---MAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI  316 (514)
Q Consensus       241 ~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~~~~---~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi  316 (514)
                                  .. .+|+.+.|+|+..| ..+++.||++.+...   ..|..+...++.|++++|+|+++.++|+||++
T Consensus       146 ------------~~-~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l  212 (390)
T PRK06676        146 ------------SD-FKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDI  212 (390)
T ss_pred             ------------HH-cCCCEEEEEEEEEECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEe
Confidence                        11 28999999999977 467899999987443   57888878889999999999999999999999


Q ss_pred             CCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----hhhh--ccCCCCceEEEEEEEEecc
Q 010232          317 EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLEGTVKKIYPY  389 (514)
Q Consensus       317 ~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~~~~--~~l~~G~iV~G~V~~I~~~  389 (514)
                      +|++||||.+++ +.++.++.+.. .+|+.|+|+|+.+|+++++|.+|+|.    +|..  ..+++|+++.|+|++++++
T Consensus       213 ~~v~g~v~~sels~~~~~~~~~~~-~vGd~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~~  291 (390)
T PRK06676        213 GGVDGLVHISELSHERVEKPSEVV-SVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDF  291 (390)
T ss_pred             CCeEEEEEHHHcCccccCCHHHhc-CCCCEEEEEEEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeCc
Confidence            999999999999 66677777664 79999999999999999999999985    3543  3689999999999999999


Q ss_pred             eEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCccccch
Q 010232          390 GAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLFVSDK  458 (514)
Q Consensus       390 GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~~~~k  458 (514)
                      |+||++.+ |+.||+|+|++++.++.++.+.|++||.|+|+|+++| +++||.||+|++..+||..+.++
T Consensus       292 G~fV~l~~-gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~~~~~~~~~~~~  360 (390)
T PRK06676        292 GAFVEVLP-GVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEEEDRR  360 (390)
T ss_pred             eEEEEECC-CCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEecccChhhhhhhh
Confidence            99999998 8999999999999999999999999999999999998 88999999999999999987655

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

Probab=99.98  E-value=9.7e-31  Score=292.18  Aligned_cols=251  Identities=24%  Similarity=0.339  Sum_probs=214.0

Q ss_pred             hchhccccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccc
Q 010232          161 DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDD  240 (514)
Q Consensus       161 ~~~~~~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d  240 (514)
                      ..|......+++|+++.|+|+++.++|++|++|. .+||||.+|+...+           .+++                
T Consensus       378 ~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lgg-i~gfiP~sel~~~~-----------~~d~----------------  429 (647)
T PRK00087        378 KAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGG-VRAFLPASHVELGY-----------VEDL----------------  429 (647)
T ss_pred             hHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHhCccc-----------cCCH----------------
Confidence            3444444557899999999999999999999986 89999999985321           0011                


Q ss_pred             cccccCCCCCCCCcccCCCEEEEEEEEEcC-CCc-EEEEehHHHH---HhhhhHHHhhhcCCCEEEEEEEEEECCeEEEE
Q 010232          241 AIAMSGGSGPGRPVVETGTVLFAEVLGRTL-SGR-PLLSTRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR  315 (514)
Q Consensus       241 ~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~-~gr-liLS~kk~~~---~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVd  315 (514)
                                  .. .+|+.+.|+|+..|. +++ +.+|++....   ...|....+.++.|+++.|+|+++.++|+||+
T Consensus       430 ------------~~-~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~  496 (647)
T PRK00087        430 ------------SE-YKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVD  496 (647)
T ss_pred             ------------HH-hCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEE
Confidence                        11 289999999999774 667 9999988753   23455565667899999999999999999999


Q ss_pred             ECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----hhhh--ccCCCCceEEEEEEEEec
Q 010232          316 IEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----AWAT--LNLREGTLLEGTVKKIYP  388 (514)
Q Consensus       316 i~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~~~~--~~l~~G~iV~G~V~~I~~  388 (514)
                      ++|++||||.+++ +.++.++.+.. .+|+.+.++|+++|++++++.+|+|+    +|..  ..+++|+++.|+|+++++
T Consensus       497 l~gv~Gll~~sels~~~~~~~~~~~-~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~  575 (647)
T PRK00087        497 IGGVDGLLHVSEISWGRVEKPSDVL-KVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAP  575 (647)
T ss_pred             ECCEEEEEEHHHcCccccCCHHHhc-CCCCEEEEEEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEEC
Confidence            9999999999999 66777776654 89999999999999999999999996    4543  368999999999999999


Q ss_pred             ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCCCcc
Q 010232          389 YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEPGLF  454 (514)
Q Consensus       389 ~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P~~~  454 (514)
                      +|+||++.+ ++.||+|++++++.++.++.+.|++||.|+|+|+++| +++||.||+|++.++|++.
T Consensus       576 ~G~fV~l~~-~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~~~~~~~~  641 (647)
T PRK00087        576 FGAFVELEP-GVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEPGDI  641 (647)
T ss_pred             CeEEEEECC-CCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeecccCcccc
Confidence            999999988 8999999999999999999999999999999999998 7899999999999999443

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

Probab=99.96  E-value=4.9e-28  Score=238.31  Aligned_cols=250  Identities=18%  Similarity=0.119  Sum_probs=209.3

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCce-eEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232          169 EPKPGDFVIGVVVSGNENKLDVNVGADL-LGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (514)
Q Consensus       169 ~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~-~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~  247 (514)
                      .+++|+++++.|++.++.|+|++-|... .-++|.++.-                                         
T Consensus         2 ~~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~-----------------------------------------   40 (287)
T COG2996           2 MIKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPE-----------------------------------------   40 (287)
T ss_pred             cccccceEEEEEEEeeceeEEEecCCCceEEeccccCCc-----------------------------------------
Confidence            4679999999999999999999987653 4444544331                                         


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEE-CCeEEEEEC-CEEEEEec
Q 010232          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN-TGGLLTRIE-GLRAFLPK  325 (514)
Q Consensus       248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~-~~G~fVdi~-Gi~gFVP~  325 (514)
                          ....++||.|.+++| .|.++|+++|++.+...           .|+.-.++|++++ +-|+||++| .-+.|||.
T Consensus        41 ----~~e~evGdev~vFiY-~D~~~rl~aTt~~p~~t-----------vg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~  104 (287)
T COG2996          41 ----EDELEVGDEVTVFIY-VDSEDRLIATTREPKAT-----------VGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPL  104 (287)
T ss_pred             ----CCccccCcEEEEEEE-ECCCCceeheeecceEe-----------ecceeEEEEEEEcCCcceEEecCCCcceeeeh
Confidence                123689999999999 89999999999988754           8999999999999 779999993 24899999


Q ss_pred             cccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh--hhhh--ccC---CCCceEEEEEEEEecceEEEEECCC
Q 010232          326 AELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE--AWAT--LNL---REGTLLEGTVKKIYPYGAQIRIGDS  398 (514)
Q Consensus       326 sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~--~~~~--~~l---~~G~iV~G~V~~I~~~GaFV~I~~~  398 (514)
                      +++..    .++++.++|+++.|+++ +|+.+ ||....+.  .++.  ...   -.++.+.|+|+++...|.||.+++ 
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----LKSLWPQKGDKLLVYLY-VDKKG-RIWGTLAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITEN-  177 (287)
T ss_pred             hhccc----ccccCCCCCCEEEEEEE-EccCC-cEEEEecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcC-
Confidence            99842    12344579999999998 77654 88877763  2221  122   359999999999999999999988 


Q ss_pred             ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCCCCccccchhhhhhHHHHHHHHHHhhCcc
Q 010232          399 NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPA  478 (514)
Q Consensus       399 gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~a~~~~~kl~~  478 (514)
                      ++.||||.||..        ..++.|++++++|+.++++++|.||++             ....+.+++.|+.+...|..
T Consensus       178 ~~~GfIh~sEr~--------~~prlG~~l~~rVi~~reDg~lnLSl~-------------p~~~E~l~~daq~Il~yL~~  236 (287)
T COG2996         178 GYLGFIHKSERF--------AEPRLGERLTARVIGVREDGKLNLSLR-------------PRAHEMLDEDAQMILTYLES  236 (287)
T ss_pred             CeEEEEcchhhc--------ccccCCceEEEEEEEEccCCeeecccc-------------cccHHhhhhhHHHHHHHHHH
Confidence            899999999987        568999999999999999999999994             45567788999999999999


Q ss_pred             CCCCCcccCCCCCCCCCCCccchhhccceeeeecC
Q 010232          479 VSVSPKSESLPTDTPPFDSEASMCANWKWFRFEQD  513 (514)
Q Consensus       479 ~~~g~~~e~~v~~~~pfg~~~~~~~~~~~~~~~~~  513 (514)
                      .+          |++||+|+|+|++|.+.|+|||-
T Consensus       237 ~g----------G~mpf~DKSsPEdIk~~FgiSKg  261 (287)
T COG2996         237 NG----------GFMPFNDKSSPEDIKATFGISKG  261 (287)
T ss_pred             cC----------CccccCCCCCHHHHHHHhCcCHH
Confidence            99          99999999999999999999984

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.91  E-value=1.1e-23  Score=217.15  Aligned_cols=190  Identities=18%  Similarity=0.204  Sum_probs=159.8

Q ss_pred             HHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEECC-EEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCce
Q 010232          283 RKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEG-LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDL  360 (514)
Q Consensus       283 ~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~G-i~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rI  360 (514)
                      ....|+.....++.|++++|+|+++.++|++|++++ .+||||.+++ +.+..++.++. .+|+.+.|+|+++|.+++++
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            344555554557999999999999999999999975 8999999999 66777777764 79999999999999999999


Q ss_pred             Eeehhh-----hhhhc--cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEE
Q 010232          361 ILSERE-----AWATL--NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK  433 (514)
Q Consensus       361 iLS~K~-----~~~~~--~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~  433 (514)
                      +||+|+     +|+..  ....|++|.|+|+++.++|+||+++  |+.||||+|+++|.+..   +.+ +|+.|.++|++
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---EEL-VGEELPLKFLE  170 (318)
T ss_pred             EEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC--CEEEEEEHHHcCccCCc---ccc-CCCEEEEEEEE
Confidence            999985     35542  4567999999999999999999996  79999999999986533   334 99999999999


Q ss_pred             Ee-CCCeEEEEEecCcCCCCccccchhhhhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCccchh
Q 010232          434 SM-FPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEASMC  502 (514)
Q Consensus       434 vd-e~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~~~~  502 (514)
                      +| +++||.||+|....++                       .+....+|++++|+|+++.+||.|++..
T Consensus       171 id~~~~~i~lS~K~~~~~~-----------------------~~~~~k~G~vv~G~V~~I~~~G~fV~i~  217 (318)
T PRK07400        171 VDEERNRLVLSHRRALVER-----------------------KMNRLEVGEVVVGTVRGIKPYGAFIDIG  217 (318)
T ss_pred             EEcccCEEEEEhhHhhhhh-----------------------hhccCCCCCEEEEEEEEEECCeEEEEEC
Confidence            98 7899999998654311                       2455778999999999999999999864

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

Probab=99.73  E-value=2.6e-18  Score=151.71  Aligned_cols=81  Identities=38%  Similarity=0.594  Sum_probs=77.6

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCCC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP  451 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~P  451 (514)
                      .+++|++++|+|++|++|||||.|++ |-.||||+|++++.|++++.+++++||.|+|+|+.+|++++|+||||.++..|
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            47899999999999999999999999 89999999999999999999999999999999999999999999999999877


Q ss_pred             Cc
Q 010232          452 GL  453 (514)
Q Consensus       452 ~~  453 (514)
                      -.
T Consensus        81 e~   82 (129)
T COG1098          81 EK   82 (129)
T ss_pred             cc
Confidence            54

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.68  E-value=3.8e-17  Score=167.41  Aligned_cols=116  Identities=21%  Similarity=0.273  Sum_probs=101.8

Q ss_pred             cCC-CCceEEEEEEEEecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232          372 NLR-EGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (514)
Q Consensus       372 ~l~-~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~  448 (514)
                      .+. +|++|.|+|++|++||+||.|.++ |++||||+|+|||.++.++++++++||.|.|+|+++| ++++|.||+|++.
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            344 899999999999999999999632 7999999999999999999999999999999999998 8899999999999


Q ss_pred             CCCCccccchhhhhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCC-CCCccc-hhhccce
Q 010232          449 SEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPP-FDSEAS-MCANWKW  507 (514)
Q Consensus       449 ~~P~~~~~~k~~v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~p-fg~~~~-~~~~~~~  507 (514)
                      ++||..+.++++.                    |..+++++..+.. ||.+.+ +|..+-|
T Consensus        93 ~~pw~~~~e~~~~--------------------g~~v~~~V~~ia~~~g~~~eely~~i~~  133 (319)
T PTZ00248         93 PEDIEACEEKFSK--------------------SKKVHSIMRHIAQKHGMSVEELYTKIIW  133 (319)
T ss_pred             cchHHHHHHhCcC--------------------CCEEEEEEEEchhhcCCCHHHHHHHHHH
Confidence            9999988777654                    7788888888865 888876 5555544

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

Probab=99.67  E-value=8.9e-16  Score=175.77  Aligned_cols=244  Identities=22%  Similarity=0.285  Sum_probs=192.2

Q ss_pred             cccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecc-cccccccchhhhhhhhhchhhhHHhhhccceeeeccccccc
Q 010232          166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTK-EVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAM  244 (514)
Q Consensus       166 ~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~s-El~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l  244 (514)
                      ......+|++..|+|..++++++.|+.+.+..|-...- ++...+           ..+|                    
T Consensus      1061 ~~k~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~-----------~~~P-------------------- 1109 (1710)
T KOG1070|consen 1061 SDKNPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSY-----------SMTP-------------------- 1109 (1710)
T ss_pred             CCCCCCcchhhcceeeeeccceeEEecCCccccceEEeeehhccc-----------cCCh--------------------
Confidence            34455589999999999999998999988877733222 322110           0011                    


Q ss_pred             cCCCCCCCCcccCCCEEEEEEEEEcC-CCcEEEEeh-------HHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEE
Q 010232          245 SGGSGPGRPVVETGTVLFAEVLGRTL-SGRPLLSTR-------RLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI  316 (514)
Q Consensus       245 ~~~~~~~~~~~~vGd~V~v~Vl~~d~-~grliLS~k-------k~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi  316 (514)
                             ...+..++.+.+.++.++. ++.+-||.+       .+.....--...+.++.|+++.|.|..+.+.|+|+.+
T Consensus      1110 -------~~~f~~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~l 1182 (1710)
T KOG1070|consen 1110 -------VEHFTKIQIVYVCVLSVSALNKGLELSLRESRTKITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIAL 1182 (1710)
T ss_pred             -------HHhcccccEEEEEEEEEecccccceeecccccccCccccccCCcccchhhcccCceeEEEEEEecCCcEEEEE
Confidence                   1235677889999998774 444888888       3332222222356779999999999999999999999


Q ss_pred             C-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh---------hhhccCCCCceEEEEEEE
Q 010232          317 E-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA---------WATLNLREGTLLEGTVKK  385 (514)
Q Consensus       317 ~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~---------~~~~~l~~G~iV~G~V~~  385 (514)
                      . ++.||+|++++ ......++... .+|+.+.++|+.+|+..+|+-+|.|..         .....++.|+...|+|..
T Consensus      1183 s~~v~a~v~is~~~ds~~k~w~k~~-~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~ 1261 (1710)
T KOG1070|consen 1183 SRKVEAFVPISGLSDSFEKEWEKHL-PVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEV 1261 (1710)
T ss_pred             ccceEEEEEccccccchhhhhhccC-CccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccceEEE
Confidence            6 69999999999 44444455443 799999999999999999999999842         223479999999999999


Q ss_pred             EecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232          386 IYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (514)
Q Consensus       386 I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~  448 (514)
                      +.++|.||+++.+ +..|++|++++.+.+..+....+..|+.|+|.+++++ +.+||.|.+|..-
T Consensus      1262 ~~~~G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~~~V~a~~lk~~~ek~rIsl~~k~s~ 1326 (1710)
T KOG1070|consen 1262 VDPFGLFIKLDVTVNMVGLCHISEEADDRGENITALYYAGDRVKACVLKEDSEKKRISLGLKSSY 1326 (1710)
T ss_pred             ecCCceEEEecCcceecccccceeecchhhhhcccceeccceeeeEeeeccchhhhhhhhhhhhc
Confidence            9999999999885 3699999999999999999999999999999999998 8899999998764

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

Probab=99.66  E-value=3.3e-16  Score=179.26  Aligned_cols=195  Identities=20%  Similarity=0.249  Sum_probs=166.8

Q ss_pred             CcccCCCEEEEEEEEEcC-CCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEE--CCEEEEEeccccc
Q 010232          253 PVVETGTVLFAEVLGRTL-SGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAELL  329 (514)
Q Consensus       253 ~~~~vGd~V~v~Vl~~d~-~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi--~Gi~gFVP~sel~  329 (514)
                      +.+++|.++.++|..+-. +..+++|.++......+.++.+ ++.|+.|.|+|..+.+.|+.|.+  +.+.|++|..++.
T Consensus       466 ~~~e~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~nD-I~iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hls  544 (1710)
T KOG1070|consen  466 PIYEVGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVND-IEIGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLS  544 (1710)
T ss_pred             CceecCCcccCccceecccCcEEEEEEehHhhccccccccc-ccccceeeeEEEEecCCcEEEEEecCceeeecChHhhh
Confidence            568899999999998654 4455788887766555555544 79999999999999999999998  3499999999995


Q ss_pred             cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh---------hccCCCCceEEEEEEEEecceEEEEECCCce
Q 010232          330 SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA---------TLNLREGTLLEGTVKKIYPYGAQIRIGDSNR  400 (514)
Q Consensus       330 ~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~---------~~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi  400 (514)
                      +....+....+.+|..++++|+.++...+++.|++|..+-         ..+..+|.++.|+|..+.++|+||.+.+ |+
T Consensus       545 d~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~~~~~~g~~V~F~g-~l  623 (1710)
T KOG1070|consen  545 DHPLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLCAIKENGAFVTFTG-GL  623 (1710)
T ss_pred             hcccccccceeeeccccEEEEEEEEccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEeeeccCCeEEEecC-cc
Confidence            4433344444579999999999999999999999997542         2468899999999999999999999999 89


Q ss_pred             EEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcC
Q 010232          401 SGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (514)
Q Consensus       401 ~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~  449 (514)
                      +||.|.++++++++.++++.|.+||+|.|+|.++| +++||.+++|+..+
T Consensus       624 sGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~~  673 (1710)
T KOG1070|consen  624 SGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASSC  673 (1710)
T ss_pred             ccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhhh
Confidence            99999999999999999999999999999999998 88999999987654

>PRK08582 hypothetical protein; Provisional

Probab=99.58  E-value=1.9e-14  Score=132.08  Aligned_cols=82  Identities=30%  Similarity=0.497  Sum_probs=77.7

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCCC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP  451 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~P  451 (514)
                      .+++|++|.|+|++|+++|+||+|++ ++.||||+|++++.++.++.+.|++||.|+|+|++++.+++|.||+|++.++|
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 89999999999999999999999999999999999986699999999999999


Q ss_pred             Ccc
Q 010232          452 GLF  454 (514)
Q Consensus       452 ~~~  454 (514)
                      |..
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=99.55  E-value=1.3e-15  Score=156.05  Aligned_cols=136  Identities=16%  Similarity=0.256  Sum_probs=119.5

Q ss_pred             CCCEEEEEEEEEECCeEEEEE---CCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----h
Q 010232          296 LNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----A  367 (514)
Q Consensus       296 ~GeiV~GkV~~v~~~G~fVdi---~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----~  367 (514)
                      .|++|.|+|+++.++|+||++   +|++||||.|++ +.++.+++++. ++|+++.|+|+++|+++++|.||.|+    +
T Consensus        17 ~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~v-kvGd~v~vkVl~VD~ekg~IdLS~K~v~~~p   95 (319)
T PTZ00248         17 EDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLI-RVGRHEVVVVLRVDKEKGYIDLSKKRVSPED   95 (319)
T ss_pred             CCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhc-CCCCEEEEEEEEEeCCCCEEEEEeeecccch
Confidence            799999999999999999999   489999999999 88899999886 89999999999999999999999995    5


Q ss_pred             hhh--ccCCCCceEEEEEEEEec-ceEEEE------ECCCceEEEEEeeccccccccCcccccC---CCCEEEEEEEE
Q 010232          368 WAT--LNLREGTLLEGTVKKIYP-YGAQIR------IGDSNRSGLLHISNMSRTRVTSVSDLLN---EGERVKVLVVK  433 (514)
Q Consensus       368 ~~~--~~l~~G~iV~G~V~~I~~-~GaFV~------I~~~gi~GLvh~Sels~~~v~~~~~~~k---vGd~VkvkVi~  433 (514)
                      |..  ..++.|+++.|+|..+.. +|++++      ..+ .+.++.|..+++...+.++.+.|.   +++.++..++.
T Consensus        96 w~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~p-l~~~~gh~y~af~~~v~~~~evl~~l~i~~ev~~~l~~  172 (319)
T PTZ00248         96 IEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWP-LYKKYGHALDALKEALTNPDNVFEGLDIPEEVKESLLQ  172 (319)
T ss_pred             HHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHH-HHHhcCCHHHHHHHHhcCchhhhccCCCCHHHHHHHHH
Confidence            654  479999999999999955 999998      455 689999999999888888887777   67666555543

>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=3.8e-14  Score=116.36  Aligned_cols=70  Identities=24%  Similarity=0.367  Sum_probs=65.0

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCc---ccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSV---SDLLNEGERVKVLVVKSM-FPDKISLS  443 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~---~~~~kvGd~VkvkVi~vd-e~~rI~LS  443 (514)
                      +++|++|.|+|++++++|+||++++ ++.|+||+++++|.++.++   .+.|++||.|+|+|+++| +++||.||
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            5799999999999999999999998 8999999999999997775   588999999999999998 78899886

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.

>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=99.49  E-value=1e-13  Score=113.05  Aligned_cols=71  Identities=24%  Similarity=0.386  Sum_probs=66.8

Q ss_pred             CCCCceEEEEEEEEec-ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 010232          373 LREGTLLEGTVKKIYP-YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA  445 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~-~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK  445 (514)
                      +++|++|.|+|+++.+ +|+||++.+ +..|++|+|+++++++.++.+.|++||.|+|+|++++. +|+.||+|
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            5799999999999986 899999998 89999999999999999999999999999999999865 99999986

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

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

Probab=99.47  E-value=2.7e-13  Score=109.96  Aligned_cols=73  Identities=30%  Similarity=0.562  Sum_probs=69.2

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK  445 (514)
                      .+++|+++.|+|+++.++|+||++++ ++.||||.+++++.+..++...+++||+|+|+|++++ +++++.||+|
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            37899999999999999999999997 8999999999999999999999999999999999998 8889999986

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 ....

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

Probab=99.46  E-value=3.6e-13  Score=109.90  Aligned_cols=71  Identities=34%  Similarity=0.534  Sum_probs=65.1

Q ss_pred             CCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 010232          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI  444 (514)
Q Consensus       374 ~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSl  444 (514)
                      +.|+++.|+|++|++||+||++.+.+.+||+|+|+++|.++.++.+.|++||+|+|+|++++..+|+.||+
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            58999999999999999999996433699999999999999999999999999999999998545999987

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.

>PRK08059 general stress protein 13; Validated

Probab=99.45  E-value=2.5e-13  Score=122.14  Aligned_cols=105  Identities=30%  Similarity=0.446  Sum_probs=90.3

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE  450 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~  450 (514)
                      ++++|+++.|+|++++++|+||++++ ++.||+|.+++++.++.++.+.|++||.|+|+|++++ +++++.||+|.+..+
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 789999999999888


Q ss_pred             CCccccchhhhhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCcc
Q 010232          451 PGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEA  499 (514)
Q Consensus       451 P~~~~~~k~~v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~  499 (514)
                      |.            ..+.+..+.+.+...+          |++||++.-
T Consensus        83 ~~------------~~~~~~~~l~~~~~~~----------g~~~l~~~~  109 (123)
T PRK08059         83 PE------------AKRKKGKILIPNPSEQ----------GFNTLRDKL  109 (123)
T ss_pred             cc------------cccccccccccccccC----------CchhHHHHH
Confidence            73            1122445556666666          888887764

>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=99.43  E-value=9.2e-13  Score=108.27  Aligned_cols=71  Identities=25%  Similarity=0.302  Sum_probs=65.2

Q ss_pred             cCCCCceEEEEEEEEecceEEEEEC-CCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIG-DSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~-~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~  449 (514)
                      +++.|+++.|+|++|+++|+||+++ + |+.||+|.++++|.      +.+++||.+.|+|++++ +++++.||+|++.+
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 DLVEGMVLSGCVSSVEDHGYILDIGIP-GTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV   73 (74)
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEeCCC-CcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            4789999999999999999999997 5 79999999999976      77999999999999998 88999999998764

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

>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.43  E-value=5.3e-13  Score=107.20  Aligned_cols=69  Identities=26%  Similarity=0.352  Sum_probs=65.8

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK  445 (514)
                      |+++.|+|++++++|+||++++ ++.||+|++++++.++.++.+.+++||.|+|+|++++ +++++.||+|
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            7899999999999999999998 7999999999999999999999999999999999998 6889999986

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.43  E-value=3.4e-13  Score=153.48  Aligned_cols=89  Identities=27%  Similarity=0.384  Sum_probs=82.8

Q ss_pred             cCCCCceEE-EEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCC
Q 010232          372 NLREGTLLE-GTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESE  450 (514)
Q Consensus       372 ~l~~G~iV~-G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~  450 (514)
                      ..++|+++. |+|++|++||+||+|.+ |++||||+|+|+|.++.++.+.|++||.|+|+|+++|.++||.||+|++.++
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 69999999999999998 8999999999999999999999999999999999998889999999999999


Q ss_pred             CCccccchhhh
Q 010232          451 PGLFVSDKERV  461 (514)
Q Consensus       451 P~~~~~~k~~v  461 (514)
                      ||+.+.++++-
T Consensus       829 Pw~~~~~~~~~  839 (891)
T PLN00207        829 ANSEKSSQKQQ  839 (891)
T ss_pred             chhhhhhhhhh
Confidence            99988665544

>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=6.4e-13  Score=108.75  Aligned_cols=69  Identities=17%  Similarity=0.162  Sum_probs=65.4

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeecccccc--ccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR--VTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~--v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK  445 (514)
                      |++|.|+|++++++|+||.+++ +++|+||.++++|.+  ..++.+.|++||.|+|+|+.+| +++||.||+|
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 GQEVTGFVNNVSKEFVWLTISP-DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCC-CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            7899999999999999999998 899999999999864  8899999999999999999998 7899999996

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=5.4e-13  Score=111.24  Aligned_cols=73  Identities=27%  Similarity=0.346  Sum_probs=69.4

Q ss_pred             ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (514)
Q Consensus       371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl  444 (514)
                      .++++|+++.|+|++++++|+||++++ ++.||+|.+++++.++.++.+.|++||.|+|+|++++ ++++|.|||
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            368999999999999999999999998 7999999999999999999999999999999999998 789999986

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.

>PRK07252 hypothetical protein; Provisional

Probab=99.42  E-value=9.5e-13  Score=117.98  Aligned_cols=77  Identities=38%  Similarity=0.592  Sum_probs=72.7

Q ss_pred             CCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCCC
Q 010232          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESEP  451 (514)
Q Consensus       374 ~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~P  451 (514)
                      ++|+++.|+|++|+++|+||+|.+ ++.||+|++++++.++.++.+.|++||.|+|+|+++| +.+++.||+|++++++
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            689999999999999999999998 7999999999999999999999999999999999998 6899999999998743

>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=1.6e-12  Score=105.46  Aligned_cols=72  Identities=21%  Similarity=0.309  Sum_probs=67.8

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK  445 (514)
                      +++|+++.|+|++++++|+||++++ +++|++|.+++++++..++.+.|++||.|+|+|++++ +++++.||+|
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            5789999999999999999999998 7999999999999988888999999999999999998 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=99.41  E-value=1.5e-12  Score=107.38  Aligned_cols=75  Identities=32%  Similarity=0.573  Sum_probs=69.4

Q ss_pred             CceEEEEEEEEecceEEEEECCC--ceEEEEEeeccccccc-cCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCCC
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDS--NRSGLLHISNMSRTRV-TSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP  451 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~--gi~GLvh~Sels~~~v-~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~P  451 (514)
                      |+++.|+|+++++||+||+|++.  ++.||+|.+++++.++ .++.+.|++||+|+|+|++++ ++++.||+|++.++.
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  6899999999999986 999999999999999999998 899999999998764

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

>PRK05807 hypothetical protein; Provisional

Probab=99.40  E-value=1.5e-12  Score=119.11  Aligned_cols=75  Identities=39%  Similarity=0.582  Sum_probs=70.9

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCc
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLE  448 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~  448 (514)
                      .+++|++|.|+|++|+++|+||.|.  +..||||++++++.++.++.+.|++||.|+|+|++++++++|.||+|.+.
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            3689999999999999999999994  68999999999999999999999999999999999987799999999987

>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=1.6e-12  Score=104.46  Aligned_cols=68  Identities=22%  Similarity=0.449  Sum_probs=64.8

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl  444 (514)
                      |+++.|+|++|.++|+||++++ +++||+|.+++++.+..++.+.|++||.++|+|+++| +++++.||+
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            7899999999999999999988 7999999999999999999999999999999999998 789999985

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=99.38  E-value=2.4e-12  Score=104.76  Aligned_cols=74  Identities=31%  Similarity=0.395  Sum_probs=68.2

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD  446 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~  446 (514)
                      ++.|+++.|+|.++.++|+||++.+. ++.||+|++++++.++.++.+.|++||.|+|+|++++ +.+++.||+|+
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            36899999999999999999999742 5899999999999999999999999999999999998 67899999974

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

>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=99.37  E-value=2e-12  Score=105.08  Aligned_cols=68  Identities=25%  Similarity=0.403  Sum_probs=64.2

Q ss_pred             CceEE-EEEEEE-ecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232          376 GTLLE-GTVKKI-YPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (514)
Q Consensus       376 G~iV~-G~V~~I-~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl  444 (514)
                      |++++ |+|+++ .++|+||++.+ |++||+|+|++++.++.++.+.|++||.++|+|+.+| .+++|.||+
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            78899 999999 69999999998 8999999999999999999999999999999999998 788999986

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=3.6e-12  Score=103.61  Aligned_cols=74  Identities=35%  Similarity=0.542  Sum_probs=68.5

Q ss_pred             CCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecC
Q 010232          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADL  447 (514)
Q Consensus       374 ~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l  447 (514)
                      ++|+++.|+|++++++|+||++.+.++.|++|.+++++.+..++.+.|++||.|+|+|++++ +.+++.||+|..
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            46999999999999999999998436999999999999999999999999999999999998 689999999864

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=99.37  E-value=3.4e-12  Score=102.87  Aligned_cols=72  Identities=31%  Similarity=0.527  Sum_probs=67.7

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~  448 (514)
                      |+++.|+|+++.++|+||++++ +++|++|.+++++.++.++.+.|++||.|+|+|++++ +++++.||+|.++
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 6689999998753

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=102.66  Aligned_cols=67  Identities=21%  Similarity=0.311  Sum_probs=63.7

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS  443 (514)
                      |+++.|+|+++.++|+||++.+ ++.||+|++++++.+..++.+.|++||.|+|+|+++| ++++|.||
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 68899876

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

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

Probab=99.34  E-value=3.1e-12  Score=102.21  Aligned_cols=67  Identities=31%  Similarity=0.560  Sum_probs=62.4

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeecccc-ccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR-TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~-~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS  443 (514)
                      |+++.|+|++++++|+||++.+ +++||+|.++++| .++.++.+.|++||+|+|+|+++| +++||.||
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            7899999999999999999998 8999999999997 578889999999999999999998 78899875

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=99.33  E-value=6.7e-12  Score=99.16  Aligned_cols=69  Identities=45%  Similarity=0.755  Sum_probs=65.3

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA  445 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK  445 (514)
                      |+++.|+|++++++|+||++++ ++.||+|.+++++.++.++.+.|++||.|+|+|++++.++++.||+|
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            7899999999999999999998 79999999999999999999999999999999999877789999986

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.

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

Probab=99.30  E-value=2.5e-12  Score=127.15  Aligned_cols=96  Identities=24%  Similarity=0.410  Sum_probs=81.6

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCC
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE  450 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~  450 (514)
                      .++|++|-|+|.+|.+||+||.|..+ |++||+|+||++.+|+.++++++++||++-|+|+++| .++-|+||||.+.++
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            58999999999999999999999765 7999999999999999999999999999999999999 789999999999876


Q ss_pred             CCccccchhhhhhHHHHH
Q 010232          451 PGLFVSDKERVFSEAEEM  468 (514)
Q Consensus       451 P~~~~~~k~~v~~~ae~~  468 (514)
                      --..-...++..++|...
T Consensus        89 q~~~k~~~wk~~qka~kl  106 (269)
T COG1093          89 QRRKKIQEWKKEQKADKL  106 (269)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            544433334444444333

>PHA02945 interferon resistance protein; Provisional

Probab=99.28  E-value=1.7e-11  Score=102.79  Aligned_cols=75  Identities=23%  Similarity=0.227  Sum_probs=69.3

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCC-ceEEEEEeecc--ccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNM--SRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sel--s~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~  448 (514)
                      .++|+++.|+|+. .+||+||.+.++ |.+||||+|++  +..++++ ++++ .||+|.|+|+++| .++-|+||||+..
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            4899999999999 999999999876 89999999955  9999999 9999 9999999999998 7899999999886


Q ss_pred             CC
Q 010232          449 SE  450 (514)
Q Consensus       449 ~~  450 (514)
                      ++
T Consensus        86 ~~   87 (88)
T PHA02945         86 RH   87 (88)
T ss_pred             cC
Confidence            53

>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=98.42  Aligned_cols=69  Identities=25%  Similarity=0.379  Sum_probs=65.5

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK  445 (514)
                      |++|.|+|.++.++|+||+++. +.+|++|.+++++.++.++.+.|++||.++|+|++++ +.++|.||+|
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 6789999985

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=99.26  E-value=2.7e-11  Score=97.95  Aligned_cols=70  Identities=31%  Similarity=0.488  Sum_probs=63.0

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccc-cccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~-~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS  443 (514)
                      +.+|+++.|+|++|+++|+||++.+ +++||+|.++++|. +..++.+.|++||.|+|+|++++ +++++.|+
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            4689999999999999999999998 79999999999975 55577888999999999999998 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=99.24  E-value=4.9e-11  Score=96.69  Aligned_cols=71  Identities=23%  Similarity=0.450  Sum_probs=62.9

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                      ++.|+++.|+|++++++|+||+++ |++||||.+++ +.+..++.... .+||++.|+|+++|++++++.+|+|
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            468999999999999999999998 89999999999 44444555543 7999999999999999999999986

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 ....

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

Probab=99.22  E-value=4.9e-11  Score=120.25  Aligned_cols=79  Identities=28%  Similarity=0.507  Sum_probs=73.3

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCC
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE  450 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~  450 (514)
                      .++|++|.|+|++|.++|+||++.++ |+.||||+|+++++++.++.+.+++||.|.|+|+++| ++++|.||+|.+.++
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            57999999999999999999999754 7999999999999999999999999999999999998 778999999988865


Q ss_pred             C
Q 010232          451 P  451 (514)
Q Consensus       451 P  451 (514)
                      .
T Consensus        86 e   86 (262)
T PRK03987         86 Q   86 (262)
T ss_pred             h
Confidence            4

>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=99.22  E-value=2.4e-11  Score=105.61  Aligned_cols=74  Identities=30%  Similarity=0.407  Sum_probs=66.4

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc-------------------cCcccccCCCCEEEEEEEE
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-------------------TSVSDLLNEGERVKVLVVK  433 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v-------------------~~~~~~~kvGd~VkvkVi~  433 (514)
                      |++|++|.|+|++|.++|+||.+.+ |+.|++|+++++|.+.                   .++.+.|++||.|+|+|++
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            5799999999999999999999998 8999999999998763                   3477889999999999999


Q ss_pred             Ee-C---CCeEEEEEecC
Q 010232          434 SM-F---PDKISLSIADL  447 (514)
Q Consensus       434 vd-e---~~rI~LSlK~l  447 (514)
                      ++ +   ++||.||+|..
T Consensus        80 ~d~~~~~~~~i~LSlr~~   97 (100)
T cd05693          80 LDKSKSGKKRIELSLEPE   97 (100)
T ss_pred             ccCCcCCCcEEEEEecHH
Confidence            98 4   68999999753

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

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

Probab=99.22  E-value=3.6e-11  Score=94.85  Aligned_cols=67  Identities=39%  Similarity=0.583  Sum_probs=63.0

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS  443 (514)
                      |+++.|+|++++++|+||++++ +..||+|.+++++.++.++.+.|++||.|+|+|++++ +++++.||
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            7899999999999999999998 7999999999999999999999999999999999998 67898876

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.

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

Probab=99.21  E-value=4.5e-11  Score=100.13  Aligned_cols=74  Identities=18%  Similarity=0.199  Sum_probs=67.3

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccc----ccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR----TRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~----~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l  447 (514)
                      +++|++|.|+|++++++|++|++++ +++|++|.+++++    .+..++.+.+++||.|+|+|+++++++++.||+|..
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            5899999999999999999999998 7999999999996    456778888999999999999998669999999864

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=1.1e-10  Score=93.31  Aligned_cols=66  Identities=41%  Similarity=0.700  Sum_probs=58.9

Q ss_pred             CCEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          297 NEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                      |++++|+|+++.++|++|+++|++||||.+++ +.+..++.+   .+|+.+.|+|+++|++++++.+|+|
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            78999999999999999999889999999999 455555544   4899999999999999999999986

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.

>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=99.19  E-value=7.5e-11  Score=94.62  Aligned_cols=65  Identities=18%  Similarity=0.328  Sum_probs=58.7

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS  443 (514)
                      |++|+|+|+++.++|+||++.+ +++|++|.++++..+..  .+.|++||+|+|+|+.+| +++||.||
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  678999999999999998 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.

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

Probab=99.19  E-value=4.2e-10  Score=112.05  Aligned_cols=144  Identities=18%  Similarity=0.164  Sum_probs=116.1

Q ss_pred             cCCCCCCEEEEEEEEEe-CCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccC
Q 010232          168 YEPKPGDFVIGVVVSGN-ENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~-~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~  246 (514)
                      ..+..|++-.++|+.++ +.|+|||.|-..+.++|.+++...  +++                                 
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            46788999999999999 899999999999999999998532  111                                 


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhhHHHh-hhc--CCCEEEEEEEEEECCeEEEEEC-CEEEE
Q 010232          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQ-IKQ--LNEPIEVKFTEWNTGGLLTRIE-GLRAF  322 (514)
Q Consensus       247 ~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~~l~~-~~k--~GeiV~GkV~~v~~~G~fVdi~-Gi~gF  322 (514)
                             =+++||.+-|.++ .|+.+|+..+++....-   +.+.. +..  .|+.++|+|.+....|.||-++ +..||
T Consensus       114 -------wpq~Gd~l~v~l~-~Dkk~Ri~g~~a~~~~l---~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~Gf  182 (287)
T COG2996         114 -------WPQKGDKLLVYLY-VDKKGRIWGTLAIEKIL---ENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGF  182 (287)
T ss_pred             -------CCCCCCEEEEEEE-EccCCcEEEEecchhHH---HhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEE
Confidence                   1579999999988 89999999887654322   11111 221  5999999999999999999995 69999


Q ss_pred             EeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          323 LPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       323 VP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      ||.||.....        .+|++++++|+.+.+ .++|-||.+.
T Consensus       183 Ih~sEr~~~p--------rlG~~l~~rVi~~re-Dg~lnLSl~p  217 (287)
T COG2996         183 IHKSERFAEP--------RLGERLTARVIGVRE-DGKLNLSLRP  217 (287)
T ss_pred             Ecchhhcccc--------cCCceEEEEEEEEcc-CCeeeccccc
Confidence            9999984332        489999999999976 8999999985

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

Probab=99.18  E-value=1e-10  Score=92.69  Aligned_cols=68  Identities=43%  Similarity=0.605  Sum_probs=63.6

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI  444 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSl  444 (514)
                      |+++.|+|.++.++|+||++++ +..||+|.+++++.++.++.+.|++||.|+|+|++++..+++.||+
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            6899999999999999999998 7999999999999999999999999999999999997777999885

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.

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

Probab=99.16  E-value=1.8e-10  Score=90.74  Aligned_cols=71  Identities=37%  Similarity=0.597  Sum_probs=66.0

Q ss_pred             CCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (514)
Q Consensus       374 ~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK  445 (514)
                      ++|+++.|+|.+++++|+||++++ ++.|++|.+++++.+..++...|++||.|+|+|++++ +++++.||++
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            479999999999999999999998 7999999999999888888889999999999999998 6699999985

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

Probab=99.16  E-value=1.5e-10  Score=92.45  Aligned_cols=66  Identities=21%  Similarity=0.309  Sum_probs=60.4

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEe
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIA  445 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK  445 (514)
                      |+++.|+|+++.++|++|++ + |+.||||.+++++.+..++...  +||.++|+|+++| ++++|.||.|
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-GVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-C-CEEEEEEHHHCCCcccCChHHh--CCCEEEEEEEEEeCCCCEEEEEcC
Confidence            78999999999999999999 5 7999999999999888877663  8999999999998 6889999985

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.

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

Probab=99.15  E-value=7.6e-11  Score=104.66  Aligned_cols=74  Identities=22%  Similarity=0.301  Sum_probs=68.1

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA  369 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~  369 (514)
                      ++.|.+++|+|+.+.++||||.++ |-.||||+|++ ...++++.++. .+||.|.|+|+.+|+ +++|.||.|.+.+
T Consensus         3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L-~vG~eV~vKVl~ide-~GKisLSIr~~~e   78 (129)
T COG1098           3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHL-KVGQEVKVKVLDIDE-NGKISLSIRKLEE   78 (129)
T ss_pred             ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHh-cCCCEEEEEEEeecc-CCCcceehHHhhh
Confidence            579999999999999999999996 58999999999 67888888886 899999999999998 9999999998755

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

Probab=99.15  E-value=1.6e-10  Score=91.37  Aligned_cols=67  Identities=46%  Similarity=0.671  Sum_probs=62.5

Q ss_pred             CCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (514)
Q Consensus       375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS  443 (514)
                      +|+++.|+|.++.++|+||+++  +++|++|.+++++.++.++.+.|++||.|+|+|++++ +++++.||
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            5899999999999999999997  5899999999999999999999999999999999998 67899876

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.

>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=99.14  E-value=1.9e-10  Score=94.51  Aligned_cols=69  Identities=12%  Similarity=0.124  Sum_probs=60.3

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChh---hHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFT---ELKEKVGRRMYVQITRINEDTNDLILS  363 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~---el~~~VGq~V~vkVl~vD~e~~rIiLS  363 (514)
                      ++.|+++.|+|+++.++|+||+++ |++||||.+++ +.++.+++   +. +++|+.+.|+|+++|+++++|.||
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            368999999999999999999996 79999999999 55655553   33 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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.11  E-value=8.6e-11  Score=131.61  Aligned_cols=71  Identities=32%  Similarity=0.456  Sum_probs=66.4

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccc----cccccCcccccCCCCEEEEEEEEEeCCCeEEEE
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS----RTRVTSVSDLLNEGERVKVLVVKSMFPDKISLS  443 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels----~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LS  443 (514)
                      .+++|++|.|+|++|++||+||+|.+ |++||||+|+|+    +.++.++.+++++||+|+|+|+++|+++||.|+
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            47899999999999999999999988 899999999996    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.

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

Probab=99.11  E-value=3e-10  Score=96.48  Aligned_cols=72  Identities=32%  Similarity=0.450  Sum_probs=62.9

Q ss_pred             cCCCCceEEEEEEEEecc--eEEEEECCCceEEEEEeecccc---ccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232          372 NLREGTLLEGTVKKIYPY--GAQIRIGDSNRSGLLHISNMSR---TRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~--GaFV~I~~~gi~GLvh~Sels~---~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl  444 (514)
                      .+++|+++.|+|++|.++  ||||++++ |.+||||+|+++|   .++.++.+.+++||.|.|+|++.. ..+-..||.
T Consensus         4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~   81 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTT   81 (88)
T ss_pred             cCCCCCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEE
Confidence            468999999999999997  99999998 8999999999999   678899999999999999999875 444444444

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

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=99.08  E-value=5.3e-10  Score=126.61  Aligned_cols=75  Identities=36%  Similarity=0.546  Sum_probs=71.6

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l  447 (514)
                      .+++|+++.|+|++|.+||+||+|.+ +.+||+|+|++++.++.++.+.|++||.|+|+|+++|..+||.||+|.+
T Consensus       618 ~~~vG~v~~G~V~~I~~fGafVei~~-~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~~  692 (693)
T PRK11824        618 EPEVGEIYEGKVVRIVDFGAFVEILP-GKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV  692 (693)
T ss_pred             cCcCCeEEEEEEEEEECCeEEEEECC-CCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCCCcEEEEEEec
Confidence            68999999999999999999999998 8999999999999999999999999999999999998559999999976

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

Probab=99.08  E-value=8.1e-10  Score=91.14  Aligned_cols=70  Identities=21%  Similarity=0.422  Sum_probs=61.4

Q ss_pred             CCceEEEEEEEEecceEEEEECCCceEEEEEeecccccccc-----------CcccccCCCCEEEEEEEEEe-CCCeEEE
Q 010232          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FPDKISL  442 (514)
Q Consensus       375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~-----------~~~~~~kvGd~VkvkVi~vd-e~~rI~L  442 (514)
                      +|+++.|+|++|+++|+||++++.+++|++|.+++++.++.           .....|++||.|+|+|+.++ ++++|.+
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            48999999999999999999997569999999999876432           44578999999999999998 6899999


Q ss_pred             EE
Q 010232          443 SI  444 (514)
Q Consensus       443 Sl  444 (514)
                      ++
T Consensus        81 ~l   82 (83)
T cd04471          81 EL   82 (83)
T ss_pred             EE
Confidence            86

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.

>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=99.08  E-value=5.1e-10  Score=89.83  Aligned_cols=68  Identities=21%  Similarity=0.328  Sum_probs=60.6

Q ss_pred             CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                      |+++.|+|+++.++|+||++. ++.||+|.+++ ..+..++.+.. ++||.++|+|+++|++++++.||+|
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 69999999999 45566666643 7999999999999999999999975

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.

>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=99.08  E-value=6.7e-10  Score=90.91  Aligned_cols=68  Identities=12%  Similarity=0.179  Sum_probs=60.5

Q ss_pred             CCEEEEEEEEEECCeEEEEEC-CEEEEEeccccc-c--ccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELL-S--RVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel~-~--~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                      |+++.|+|+++.++|+||.++ +++||||.+++. .  +..++.+.+ ++|+.++|+|+++|+++++|.||.|
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 799999999994 3  256666654 8999999999999999999999986

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.

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=99.05  E-value=2.7e-10  Score=127.19  Aligned_cols=80  Identities=35%  Similarity=0.545  Sum_probs=75.3

Q ss_pred             ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcC
Q 010232          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (514)
Q Consensus       371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~  449 (514)
                      .+|++|+++.|+|+++++||+||+|+- +.+||||+|++++.++.+|.+++++||.|+|+|+++| .++||.|||+....
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 7999999999999999999999999999999999999 88999999997665


Q ss_pred             CC
Q 010232          450 EP  451 (514)
Q Consensus       450 ~P  451 (514)
                      .+
T Consensus       733 ~~  734 (780)
T COG2183         733 EG  734 (780)
T ss_pred             cc
Confidence            43

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=99.04  E-value=7.2e-10  Score=120.01  Aligned_cols=108  Identities=20%  Similarity=0.270  Sum_probs=86.6

Q ss_pred             CcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhh-----HHHhhhc--CCCEEEEEEEEEECCeEEEEECCEEEEEec
Q 010232          253 PVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWH-----RVRQIKQ--LNEPIEVKFTEWNTGGLLTRIEGLRAFLPK  325 (514)
Q Consensus       253 ~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~-----~l~~~~k--~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~  325 (514)
                      +.+++||.+.+.|...+ -||..++..+......|.     .+.+.++  .|++|+|+|.++.++|++|+++|++||||.
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            34789999999987555 566655554444334444     7777776  999999999999999999999999999999


Q ss_pred             cccccccCChhhHhhhcCCEEEEEEEEEeCCCC--ceEeehhhh
Q 010232          326 AELLSRVNNFTELKEKVGRRMYVQITRINEDTN--DLILSEREA  367 (514)
Q Consensus       326 sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~--rIiLS~K~~  367 (514)
                      +++..     .+. +++|++++|+|++||++++  +|+|||+.+
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            99942     222 2699999999999999877  999999864

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

Probab=99.03  E-value=1.1e-09  Score=90.94  Aligned_cols=73  Identities=16%  Similarity=0.145  Sum_probs=68.2

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEec
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIAD  446 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~  446 (514)
                      .++|++|.|+|+++.+.|++|+++. +.+|++|.++++..+..++.+.+++||.|.|+|+++++.+++.||++.
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            4799999999999999999999988 799999999999888889999999999999999999755899999976

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".

>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=99.03  E-value=1.1e-09  Score=90.03  Aligned_cols=67  Identities=21%  Similarity=0.289  Sum_probs=59.1

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC--CEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      ++.|+++.|+|+++.++|+||+++  |+.||+|.+++...    ..+  ++||.+.|+|+++|++++++.||.|+
T Consensus         2 l~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~----~~~--~~Gq~v~~~V~~vd~~~~~v~ls~k~   70 (74)
T cd05694           2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF----SKL--KVGQLLLCVVEKVKDDGRVVSLSADP   70 (74)
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc----ccc--CCCCEEEEEEEEEECCCCEEEEEEee
Confidence            468999999999999999999996  79999999999432    112  69999999999999999999999875

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.

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

Probab=99.02  E-value=1.9e-09  Score=88.95  Aligned_cols=65  Identities=29%  Similarity=0.394  Sum_probs=59.9

Q ss_pred             ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 010232          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI  444 (514)
Q Consensus       371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSl  444 (514)
                      .+++.|+.+.|+|++++++|+||++.+ ++.||+|.+++.        +.+++||+++++|+++.+++|+.||+
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            468999999999999999999999998 799999999975        56999999999999987789999986

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.

>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=99.01  E-value=1.8e-09  Score=86.67  Aligned_cols=67  Identities=12%  Similarity=0.309  Sum_probs=58.9

Q ss_pred             CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~  364 (514)
                      |+++.|+|+++.++|+||+++ |++||+|.+++ +.+..++.+. +++|+.+.|+|+++|++++++.||+
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 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKK-FKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHc-CCCCCEEEEEEEEEECCCCEEEEEC
Confidence            789999999999999999995 79999999999 5555555554 3799999999999999999999884

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.

>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=99.01  E-value=1.6e-09  Score=90.26  Aligned_cols=70  Identities=17%  Similarity=0.200  Sum_probs=63.1

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~  364 (514)
                      ++.|+++.|+|+++.++|+||+++ |++||+|.+++ +.++.++.+.. .+||.++|+|+++|.+++++.+|+
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            579999999999999999999995 79999999999 56666777654 899999999999999999999985

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.

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

Probab=98.97  E-value=1.3e-09  Score=120.01  Aligned_cols=77  Identities=36%  Similarity=0.578  Sum_probs=73.8

Q ss_pred             ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCc
Q 010232          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLE  448 (514)
Q Consensus       371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~  448 (514)
                      .++++|+++.|+|+++.+||+||.+.+ |-.||+|+|++++.|+.+..+++++||.|.|+|+.+|+.+|+.||+|...
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            479999999999999999999999999 89999999999999999999999999999999999999999999998754

>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=98.97  E-value=1.9e-09  Score=87.06  Aligned_cols=63  Identities=21%  Similarity=0.345  Sum_probs=57.8

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeecccccc--ccCcccccCCCCEEEEEEEEEeCCCe
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR--VTSVSDLLNEGERVKVLVVKSMFPDK  439 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~--v~~~~~~~kvGd~VkvkVi~vde~~r  439 (514)
                      |++|.|+|+++.++|++|.+++ +++|++|++++++.+  ..++.+.|++||.|+|+|++++..++
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~-~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~   65 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLAD-NVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT   65 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCC-CcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence            7899999999999999999998 899999999999885  88899999999999999999974443

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=3.4e-09  Score=102.01  Aligned_cols=89  Identities=24%  Similarity=0.368  Sum_probs=75.6

Q ss_pred             EeCCCCceEeehhhhhhh--ccCCCCceEEEEEEEEecceEEEEECC---------CceEEEEEeeccccccccCccccc
Q 010232          353 INEDTNDLILSEREAWAT--LNLREGTLLEGTVKKIYPYGAQIRIGD---------SNRSGLLHISNMSRTRVTSVSDLL  421 (514)
Q Consensus       353 vD~e~~rIiLS~K~~~~~--~~l~~G~iV~G~V~~I~~~GaFV~I~~---------~gi~GLvh~Sels~~~v~~~~~~~  421 (514)
                      +|.++++|.+.   +|..  ..+++|++|.|+|++|.++|+||+|..         .++.|++|.+++++.+..++.+.|
T Consensus        43 id~~~~~Isv~---P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~  119 (189)
T PRK09521         43 IDDINRKISVI---PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAF  119 (189)
T ss_pred             EcCCCCEEEEe---cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhcc
Confidence            46666666664   4433  367899999999999999999999952         157899999999999999999999


Q ss_pred             CCCCEEEEEEEEEeCCCeEEEEEec
Q 010232          422 NEGERVKVLVVKSMFPDKISLSIAD  446 (514)
Q Consensus       422 kvGd~VkvkVi~vde~~rI~LSlK~  446 (514)
                      ++||.|.|+|++++  +++.||+|+
T Consensus       120 ~~GD~V~akV~~i~--~~i~LS~k~  142 (189)
T PRK09521        120 KIGDIVRAKVISYT--DPLQLSTKG  142 (189)
T ss_pred             CCCCEEEEEEEecC--CcEEEEEec
Confidence            99999999999886  899999985

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

Probab=98.94  E-value=4.8e-09  Score=84.25  Aligned_cols=68  Identities=19%  Similarity=0.339  Sum_probs=60.9

Q ss_pred             CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                      |+++.|+|.++.++|++|+++ +.+|++|.+++ +.+..++.+.. ++|+.++|+|+++|++++++.||+|
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 56666776654 7999999999999988899999985

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.

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

Probab=98.94  E-value=3.3e-09  Score=86.26  Aligned_cols=67  Identities=24%  Similarity=0.197  Sum_probs=57.7

Q ss_pred             CCEEE-EEEEEE-ECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232          297 NEPIE-VKFTEW-NTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (514)
Q Consensus       297 GeiV~-GkV~~v-~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~  364 (514)
                      |+++. |+|+++ .++|+||++. |++||+|.+++ +.+..++.+.. ++|+.+.++|+.+|+.++++.||.
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            67888 999999 6999999994 79999999999 55555554433 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.

>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=98.93  E-value=4e-09  Score=84.43  Aligned_cols=66  Identities=18%  Similarity=0.282  Sum_probs=58.5

Q ss_pred             CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS  363 (514)
                      |+++.|+|+++.++|+||++. ++.||+|.+++ +.+..++.+.. .+||.++|+|+++|++++++.||
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 69999999999 55566666644 79999999999999999999886

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.

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

Probab=98.93  E-value=3e-09  Score=82.17  Aligned_cols=64  Identities=33%  Similarity=0.497  Sum_probs=58.9

Q ss_pred             EEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232          379 LEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (514)
Q Consensus       379 V~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS  443 (514)
                      +.|+|.++.++|+||++++ ++.|++|.+++++.++.++.+.|++||.|+|+|++++ +++++.||
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            4799999999999999998 7999999999999888888899999999999999998 67888775

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.

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

Probab=98.92  E-value=5.7e-09  Score=85.10  Aligned_cols=68  Identities=19%  Similarity=0.324  Sum_probs=60.3

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECC--EEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEG--LRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~G--i~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~  364 (514)
                      +.|+++.|+|+++.++|+||++.|  .+||+|.+++ +.++.++.+.. ++||++.|+|+++|.++ ++.||+
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 66777777654 79999999999999876 888886

pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.

>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=98.92  E-value=6.1e-09  Score=84.34  Aligned_cols=70  Identities=10%  Similarity=0.037  Sum_probs=60.8

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                      +.|+++.|+|+++.++|++|+++ +++||+|.+++ +.+..++.+.. ++||.++++|+++|..++++.||.|
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 44444444443 7999999999999999999999974

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.

>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=98.92  E-value=4.6e-09  Score=84.24  Aligned_cols=64  Identities=14%  Similarity=0.188  Sum_probs=54.9

Q ss_pred             CCEEEEEEEEEECCeEEEEE-CCEEEEEecccccc-ccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi-~Gi~gFVP~sel~~-~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS  363 (514)
                      |++++|+|+++.++|++|++ ++++||+|.+|+.. +.. .+.+  ++|++++|+|+.+|+++++|.||
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-KSTY--KEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc-ccCc--CCCCEEEEEEEEEeCCCCEEecC
Confidence            78999999999999999999 57999999999942 322 3333  79999999999999999999887

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.

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

Probab=98.90  E-value=9.1e-09  Score=83.63  Aligned_cols=71  Identities=21%  Similarity=0.353  Sum_probs=62.9

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC---CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~---Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      +.|+++.|+|+++.++|+||++.   |+.||+|.+++ +.++.++.+.. .+||.++++|+++|..++++.+|+|+
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   58999999999 66677776654 79999999999999999999999873

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

>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=98.87  E-value=8.8e-09  Score=83.96  Aligned_cols=68  Identities=21%  Similarity=0.095  Sum_probs=60.3

Q ss_pred             cCCCEEEEEEEEEEC-CeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          295 QLNEPIEVKFTEWNT-GGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       295 k~GeiV~GkV~~v~~-~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                      +.|+++.|+|+++.+ +|+||++. |.+|++|.+++ +.+..++.+.. .+||.++|+|+++|+  +++.||+|
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 89999995 79999999999 67777777754 799999999999985  89999975

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.

>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=98.87  E-value=1.1e-08  Score=83.10  Aligned_cols=71  Identities=17%  Similarity=0.354  Sum_probs=62.1

Q ss_pred             CCCEEEEEEEEEECCeEEEEEC--CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          296 LNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       296 ~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      .|+++.|+|+++.++|+||++.  ++.|++|.+++ +.+..++.+.. .+||.++|+|+++|.+++++.+|+|.+
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            6899999999999999999997  58999999999 55555555543 799999999999999999999998753

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.

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

Probab=98.86  E-value=1.1e-08  Score=88.25  Aligned_cols=79  Identities=27%  Similarity=0.433  Sum_probs=68.5

Q ss_pred             ceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccC-----------cccccCCCCEEEEEEEEEe-CC-----Ce
Q 010232          377 TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTS-----------VSDLLNEGERVKVLVVKSM-FP-----DK  439 (514)
Q Consensus       377 ~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~-----------~~~~~kvGd~VkvkVi~vd-e~-----~r  439 (514)
                      +++.|+|++|.++|+||++.  ++.|++|.++++++++..           ....|++||.|+|+|.+++ +.     .+
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            47899999999999999998  489999999999876653           3578999999999999998 32     58


Q ss_pred             EEEEEecCcCCCCccccc
Q 010232          440 ISLSIADLESEPGLFVSD  457 (514)
Q Consensus       440 I~LSlK~l~~~P~~~~~~  457 (514)
                      +.||+|+....||+.+.+
T Consensus        79 i~ls~k~~~~g~~~~~~~   96 (99)
T cd04460          79 IGLTMRQPGLGKLEWIEE   96 (99)
T ss_pred             EEEEEecCCCCcHHHhhh
Confidence            999999999999987653

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=98.84  E-value=1.6e-08  Score=81.31  Aligned_cols=69  Identities=30%  Similarity=0.422  Sum_probs=61.2

Q ss_pred             CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      |+++.|+|+++.++|++|+++ +++||+|.+++ ..++.++.+.. .+|+.++|+|+++|.+++++.||+|.
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            789999999999999999994 79999999999 55566666654 89999999999999999999999874

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.

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

Probab=98.81  E-value=2.4e-08  Score=78.87  Aligned_cols=67  Identities=18%  Similarity=0.345  Sum_probs=59.0

Q ss_pred             CCCEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (514)
Q Consensus       296 ~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS  363 (514)
                      .|+++.|+|+++.++|++|+++++.||+|.+++ +.+..++.+. +.+||.++|+|+++|.+++++.+|
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 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEV-VNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccccCHhHE-ECCCCEEEEEEEEEECCCCEEecC
Confidence            488999999999999999999889999999999 5555556554 379999999999999999998876

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.80  E-value=1.2e-08  Score=115.43  Aligned_cols=70  Identities=37%  Similarity=0.593  Sum_probs=65.8

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL  442 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~L  442 (514)
                      .+++|+++.|+|++|.+||+||++.+ +++||+|+|+++|.++.++.+.|++||.|+|+|++++.++||.|
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            57999999999999999999999998 89999999999999999999999999999999999987677764

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).

>PRK07252 hypothetical protein; Provisional

Probab=98.80  E-value=2.1e-08  Score=90.05  Aligned_cols=72  Identities=24%  Similarity=0.364  Sum_probs=63.6

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      +.|+++.|+|+++.++|+||+++ ++.||+|.+++ +.++.++.+.. .+||.|.|+|+++|.+++++.+|+|..
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~-~vGD~V~VkI~~iD~~~~ri~lSlk~~   75 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLL-KVGEEVLVQVVDFDEYTGKASLSLRTL   75 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhcc-CCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence            47999999999999999999995 69999999999 56666665543 799999999999999999999999864

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

Probab=98.80  E-value=2.8e-08  Score=78.28  Aligned_cols=67  Identities=18%  Similarity=0.337  Sum_probs=59.0

Q ss_pred             CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                      |+++.|+|+++.++|+||+++ +..||+|.+++ +.+..++.+.. .+|+.+.++|+++|. ++++.+|.|
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 55666665543 799999999999998 899999875

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.

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

Probab=98.80  E-value=2e-08  Score=80.04  Aligned_cols=66  Identities=15%  Similarity=0.318  Sum_probs=57.2

Q ss_pred             CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-c-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-L-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS  363 (514)
                      |+++.|+|+++.++|+||+++ +++||+|.+++ + .+..++.+.. ++||.++|+|+++|.+++++.+|
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 69999999999 3 3455565543 79999999999999999998875

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.

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

Probab=98.79  E-value=3.3e-08  Score=77.74  Aligned_cols=69  Identities=28%  Similarity=0.463  Sum_probs=59.5

Q ss_pred             CCCEEEEEEEEEECCeEEEEEC-CEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          296 LNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       296 ~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                      .|+++.|+|+++++.|++|+++ ++.||+|.+++. .+..++.+. +.+|+.+.|+|+++|..++++.+|++
T Consensus         2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~-~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEV-LKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHe-ecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            6999999999999999999997 799999999994 334444443 37999999999999999899999874

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.79  E-value=3.4e-08  Score=98.32  Aligned_cols=75  Identities=19%  Similarity=0.225  Sum_probs=69.2

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc----cCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----TSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v----~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l  447 (514)
                      ..++|++|.|+|++++++|+||+|+. .+.|+||.+++++.++    .++++.|++||.|.|+|++++..+++.||+|+.
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            46999999999999999999999997 6899999999999987    889999999999999999998767899999864

>PRK08582 hypothetical protein; Provisional

Probab=98.79  E-value=2e-08  Score=92.39  Aligned_cols=72  Identities=18%  Similarity=0.280  Sum_probs=62.9

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      ++.|+++.|+|+.++++|+||+++ ++.||||++++ +.++.++.+.. .+||.|+|+|+++|. .++|.||+|++
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            568999999999999999999996 69999999999 56666665543 799999999999997 48999999865

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

Probab=98.77  E-value=5.1e-08  Score=81.01  Aligned_cols=75  Identities=25%  Similarity=0.325  Sum_probs=62.1

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~  247 (514)
                      |-+++|++|.|+|+++++++++|+++.+.+|++|.+++....           .++.                       
T Consensus         2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~-----------~~~~-----------------------   47 (82)
T cd04454           2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKD-----------KKEI-----------------------   47 (82)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcc-----------hHHH-----------------------
Confidence            567899999999999999999999999999999999985321           0011                       


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 010232          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (514)
Q Consensus       248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk  280 (514)
                          ...+++||.|.|+|++.+.++++.||.+.
T Consensus        48 ----~~~~~~GD~i~~~V~~~~~~~~i~LS~~~   76 (82)
T cd04454          48 ----RKSLQPGDLILAKVISLGDDMNVLLTTAD   76 (82)
T ss_pred             ----HhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence                23479999999999998766899999875

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=98.76  E-value=5e-08  Score=81.63  Aligned_cols=80  Identities=28%  Similarity=0.349  Sum_probs=63.0

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~  247 (514)
                      |.+++|++|.|+|+++.+.|++|+++.+.+|+||.+++....   ..    +...+.                       
T Consensus         2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~---~~----~~~~~~-----------------------   51 (86)
T cd05789           2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPR---TD----EDELNM-----------------------   51 (86)
T ss_pred             CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCC---Cc----cchHHH-----------------------
Confidence            567899999999999999999999999999999999985200   00    000000                       


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 010232          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (514)
Q Consensus       248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~  281 (514)
                          ...+++||.+.|+|++.+.++++.||+++.
T Consensus        52 ----~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~   81 (86)
T cd05789          52 ----RSYLDEGDLIVAEVQSVDSDGSVSLHTRSL   81 (86)
T ss_pred             ----HhhCCCCCEEEEEEEEECCCCCEEEEeCcc
Confidence                234799999999999988779999999875

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".

>TIGR01953 NusA transcription termination factor NusA

Probab=98.74  E-value=4.7e-08  Score=102.19  Aligned_cols=108  Identities=23%  Similarity=0.286  Sum_probs=84.1

Q ss_pred             CcccCCCEEEEEEEEEcCCCcEEEEehHH-----HHHhhhhHHHhhh--cCCCEEEEEEEEEECCe-EEEEECCEEEEEe
Q 010232          253 PVVETGTVLFAEVLGRTLSGRPLLSTRRL-----FRKMAWHRVRQIK--QLNEPIEVKFTEWNTGG-LLTRIEGLRAFLP  324 (514)
Q Consensus       253 ~~~~vGd~V~v~Vl~~d~~grliLS~kk~-----~~~~~w~~l~~~~--k~GeiV~GkV~~v~~~G-~fVdi~Gi~gFVP  324 (514)
                      +.+++||.|.+.+. ...-||..++..+.     ..+..++.+.+.+  +.|++++|+|.++.++| ++|+++|++||||
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 PDVQIGDEVKKEIP-PENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGILP  160 (341)
T ss_pred             cccccCCEEEEEec-ccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEECCeEEEec
Confidence            45789999998875 33456665555444     3356777777777  49999999999999988 6999999999999


Q ss_pred             ccccccccCChhhHhhhcCCEEEEEEEEEeCCC--CceEeehhhh
Q 010232          325 KAELLSRVNNFTELKEKVGRRMYVQITRINEDT--NDLILSEREA  367 (514)
Q Consensus       325 ~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~--~rIiLS~K~~  367 (514)
                      .+++...     +. +.+|++++|+|++++...  ..|+||++.+
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            9999522     11 269999999999999654  5799999864

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.

>PRK05807 hypothetical protein; Provisional

Probab=98.74  E-value=3.6e-08  Score=90.32  Aligned_cols=72  Identities=18%  Similarity=0.253  Sum_probs=63.7

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      ++.|++++|+|+.+.++|+||++++..||||.+++ +.++.++.+.. .+||.|.|+|+++|. +++|.||+|.+
T Consensus         3 ~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~~~~~-kvGd~V~VkV~~id~-~gkI~LSlk~~   75 (136)
T PRK05807          3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHL-KEQDKVKVKVISIDD-NGKISLSIKQA   75 (136)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCccccC-CCCCEEEEEEEEECC-CCcEEEEEEec
Confidence            46899999999999999999999889999999999 56666665543 799999999999998 79999999865

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

Probab=98.73  E-value=1.6e-08  Score=108.67  Aligned_cols=83  Identities=25%  Similarity=0.357  Sum_probs=78.8

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCCC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP  451 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~P  451 (514)
                      ++..|-+++|+|+++.++|+||++.+ +..||+|+|+++..++.+|++.+.+||+|.|+.+..|+.+.+.+|-|.+.++|
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            78999999999999999999999999 99999999999999999999999999999999999999999999999999988


Q ss_pred             Cccc
Q 010232          452 GLFV  455 (514)
Q Consensus       452 ~~~~  455 (514)
                      -...
T Consensus       744 ~~~~  747 (760)
T KOG1067|consen  744 ATKE  747 (760)
T ss_pred             ccCC
Confidence            6553

>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=98.70  E-value=8.1e-08  Score=75.55  Aligned_cols=66  Identities=18%  Similarity=0.206  Sum_probs=57.2

Q ss_pred             CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS  363 (514)
                      |+++.|+|+++.++|+||+++ +..||+|.+++ +.+..++.+.. ++||.+.|+|+++|.+++++.+|
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 58999999999 45555665543 79999999999999999998876

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=98.69  E-value=5.5e-08  Score=84.59  Aligned_cols=72  Identities=14%  Similarity=0.248  Sum_probs=61.4

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccc-------------------cCChhhHhhhcCCEEEEEEEEE
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSR-------------------VNNFTELKEKVGRRMYVQITRI  353 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~-------------------i~~~~el~~~VGq~V~vkVl~v  353 (514)
                      +.|++|.|+|+++.+.|++|.+. |+.||+|++++ +.+                   ..++.+.+ ++||.++|+|+++
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 79999999999 432                   12345554 8999999999999


Q ss_pred             eCC---CCceEeehhhh
Q 010232          354 NED---TNDLILSEREA  367 (514)
Q Consensus       354 D~e---~~rIiLS~K~~  367 (514)
                      |++   +++|.||.|..
T Consensus        81 d~~~~~~~~i~LSlr~~   97 (100)
T cd05693          81 DKSKSGKKRIELSLEPE   97 (100)
T ss_pred             cCCcCCCcEEEEEecHH
Confidence            987   78999999864

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=98.68  E-value=8e-08  Score=79.21  Aligned_cols=67  Identities=18%  Similarity=0.259  Sum_probs=58.8

Q ss_pred             CCEEEEEEEEEECCeEEEEEC----CEEEEEecccc-cccc-CChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE----GLRAFLPKAEL-LSRV-NNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~----Gi~gFVP~sel-~~~i-~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      |+++.|+|+++.++|+||+++    ++.||+|.+++ +.+. .++.+.. ++||.++|+|+++|  ++++.+|+|.
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~-~~Gd~v~v~v~~vd--~~~i~~s~k~   73 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVV-KRGQKVKVKVISIQ--NGKISLSMKD   73 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhhee-CCCCEEEEEEEEEe--CCEEEEEEEe
Confidence            678999999999999999997    68999999999 5554 6666553 89999999999999  7899999875

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.66  E-value=6.8e-08  Score=104.81  Aligned_cols=112  Identities=15%  Similarity=0.207  Sum_probs=85.2

Q ss_pred             EEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh-hhh----hh-------hccCC--CCceEEEEEEE
Q 010232          320 RAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE-REA----WA-------TLNLR--EGTLLEGTVKK  385 (514)
Q Consensus       320 ~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~-K~~----~~-------~~~l~--~G~iV~G~V~~  385 (514)
                      .++||.++....  ++.   ..+|+.+.+.|...+  .+|+.++. |+.    |.       ...++  .|++|.|+|.+
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   259999999998766  44444443 332    22       12454  99999999999


Q ss_pred             EecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCC--eEEEEEec
Q 010232          386 IYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD--KISLSIAD  446 (514)
Q Consensus       386 I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~--rI~LSlK~  446 (514)
                      +.++|+||+++  |++||||.++++      |.+.|++||+|+|+|++++ +++  +|.||.+.
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            99999999997  689999999996      6789999999999999997 444  89999853

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

Probab=98.66  E-value=1e-07  Score=76.96  Aligned_cols=68  Identities=16%  Similarity=0.265  Sum_probs=56.6

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-cc-ccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LS-RVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~-~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS  363 (514)
                      ..|+++.|+|+++.++|+||+++ |+.||+|.+++ +. +..++... +++||+++|+|+++|.+++++.+|
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            58999999999999999999995 69999999999 43 22233333 379999999999999999988764

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.

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

Probab=98.64  E-value=1.5e-07  Score=75.61  Aligned_cols=62  Identities=24%  Similarity=0.396  Sum_probs=53.5

Q ss_pred             CCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CC--CeEEEE
Q 010232          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP--DKISLS  443 (514)
Q Consensus       374 ~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~--~rI~LS  443 (514)
                      +.|++|+|+|.++.++|+||+++  +++|+||.++++.      .+.+++||+|+|+|++++ ++  ..|.||
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            47999999999999999999997  4899999999973      467899999999999997 32  357776

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.64  E-value=2.1e-07  Score=104.87  Aligned_cols=95  Identities=18%  Similarity=0.237  Sum_probs=74.8

Q ss_pred             EEcCCCcEEEEe-hHHHHHhhhhHHHhh-----hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc----c-cccCC
Q 010232          267 GRTLSGRPLLST-RRLFRKMAWHRVRQI-----KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL----L-SRVNN  334 (514)
Q Consensus       267 ~~d~~grliLS~-kk~~~~~~w~~l~~~-----~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel----~-~~i~~  334 (514)
                      .++.+|.+.++. .+.....+.+.+...     .+.|+++.|+|+++.++|+||++. |++||||.|++    | .++.+
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            356788886554 344444444444432     469999999999999999999995 89999999998    2 57788


Q ss_pred             hhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232          335 FTELKEKVGRRMYVQITRINEDTNDLILS  363 (514)
Q Consensus       335 ~~el~~~VGq~V~vkVl~vD~e~~rIiLS  363 (514)
                      +.++. ++||+|+|+|+++|+ ++||.|+
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 7788876

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.

>PRK08059 general stress protein 13; Validated

Probab=98.62  E-value=1.5e-07  Score=84.78  Aligned_cols=73  Identities=16%  Similarity=0.293  Sum_probs=64.2

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      ++.|+++.|+|+++.++|++|+++ ++.||+|.+++ ..++.++.+.. .+|+.+.|+|+++|.+++++.+|+|..
T Consensus         5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~-~vGD~I~vkI~~id~~~~~i~lslk~~   79 (123)
T PRK08059          5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFL-SVGDEVKVKVLSVDEEKGKISLSIRAT   79 (123)
T ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcC-CCCCEEEEEEEEEECCCCeEEEEEEEc
Confidence            568999999999999999999996 69999999999 55565555543 799999999999999999999999865

>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=75.49  Aligned_cols=64  Identities=20%  Similarity=0.342  Sum_probs=54.2

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCC--CceEeeh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDT--NDLILSE  364 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~--~rIiLS~  364 (514)
                      +.|++++|+|.+++++|++|++++.+||||.+++...     +. +++|++++++|+++++++  .+|++|+
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~~-----~~-~~~Gd~v~v~v~~v~~~~~~~~i~lSr   67 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPG-----ES-YRPGDRIKAYVLEVRKTSKGPQIILSR   67 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCCC-----Cc-CCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence            4799999999999999999999889999999999421     11 269999999999998654  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.

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

Probab=98.62  E-value=7.4e-08  Score=95.76  Aligned_cols=71  Identities=17%  Similarity=0.276  Sum_probs=66.4

Q ss_pred             cCCCEEEEEEEEEECCeEEEEE---CCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi---~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      ..|++|-|+|..+.++|+||.+   +|++||||.||+ ..++++.+++. ++||++-|+|++||++++.|-||+|.
T Consensus        10 eeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~v-kegqkvV~kVlrVd~~rg~IDLSlkr   84 (269)
T COG1093          10 EEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYV-KEGQKVVAKVLRVDPKRGHIDLSLKR   84 (269)
T ss_pred             CCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHh-hcCCeEEEEEEEEcCCCCeEeeehhh
Confidence            4899999999999999999999   589999999999 67889999887 89999999999999999999999983

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

Probab=98.61  E-value=2.1e-07  Score=73.58  Aligned_cols=66  Identities=23%  Similarity=0.327  Sum_probs=57.1

Q ss_pred             CCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~  364 (514)
                      |+++.|+|+++.++|+||+++ +..||+|.+++ +.++.++.+.. .+||.+.|+|.++|+ ++++.+|+
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 59999999999 55555555543 799999999999998 88999885

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=98.60  E-value=1.8e-07  Score=107.29  Aligned_cols=99  Identities=17%  Similarity=0.180  Sum_probs=76.1

Q ss_pred             CCCcEE-EEehHHHHHhhhhHHHh---hhcCCCEEE-EEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhc
Q 010232          270 LSGRPL-LSTRRLFRKMAWHRVRQ---IKQLNEPIE-VKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKV  342 (514)
Q Consensus       270 ~~grli-LS~kk~~~~~~w~~l~~---~~k~GeiV~-GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~V  342 (514)
                      ++|.+. ++........+.+.+.+   ..+.|+++. |+|+++.++|+||++. |++||||+|++ +.++.++.+.. ++
T Consensus       723 ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~-kv  801 (891)
T PLN00207        723 DDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAF-KV  801 (891)
T ss_pred             CCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhc-CC
Confidence            455553 33333333334333333   357999996 6999999999999995 79999999999 77788888765 89


Q ss_pred             CCEEEEEEEEEeCCCCceEeehhh----hhhh
Q 010232          343 GRRMYVQITRINEDTNDLILSERE----AWAT  370 (514)
Q Consensus       343 Gq~V~vkVl~vD~e~~rIiLS~K~----~~~~  370 (514)
                      ||.|+|+|+++|+ +++|.||+|.    +|+.
T Consensus       802 GD~V~VkVi~ID~-~grI~LSlK~l~~~Pw~~  832 (891)
T PLN00207        802 GDRIDVKLIEVND-KGQLRLSRRALLPEANSE  832 (891)
T ss_pred             CCEEEEEEEEECC-CCcEEEEEeccccCchhh
Confidence            9999999999997 7899999985    6764

>PHA02945 interferon resistance protein; Provisional

Probab=98.57  E-value=1.7e-07  Score=78.86  Aligned_cols=69  Identities=14%  Similarity=0.176  Sum_probs=60.8

Q ss_pred             cCCCEEEEEEEEEECCeEEEEE---CCEEEEEecccc---ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL---LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi---~Gi~gFVP~sel---~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      +.|+++-|+|.. .++|+||.+   +|++||||.|+.   ..++++ ++..  +||++.|+|+++|+.++.|-||.|+.
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            589999999999 999999999   489999999955   456677 6664  99999999999999999999999853

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.52  E-value=3.9e-07  Score=95.97  Aligned_cols=109  Identities=17%  Similarity=0.238  Sum_probs=78.5

Q ss_pred             CcccCCCEEEEEEEEEcCCCcEEEEehHHHH----HhhhhHHHhhh--cCCCEEEEEEEEEECCeEEEEECCEEEEEecc
Q 010232          253 PVVETGTVLFAEVLGRTLSGRPLLSTRRLFR----KMAWHRVRQIK--QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKA  326 (514)
Q Consensus       253 ~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~----~~~w~~l~~~~--k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~s  326 (514)
                      +..++||.+...+...+.+...+.+.++...    +...+.+.+.+  +.|++++|+|.++.++|++|+++|++||||.+
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            3478999998876533333323333333322    23344455555  79999999999999999999999999999998


Q ss_pred             ccccccCChhhHhhhcCCEEEEEEEEEeCCCC--ceEeehhhh
Q 010232          327 ELLSRVNNFTELKEKVGRRMYVQITRINEDTN--DLILSEREA  367 (514)
Q Consensus       327 el~~~i~~~~el~~~VGq~V~vkVl~vD~e~~--rIiLS~K~~  367 (514)
                      ++...     +. +++|++++|+|++++.+++  .|+||+..+
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 2699999999999996554  699999754

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

Probab=98.49  E-value=4.2e-07  Score=77.87  Aligned_cols=74  Identities=19%  Similarity=0.259  Sum_probs=66.2

Q ss_pred             CCCCceEEEEEEEEecceEEEEE--------CCCceEEEEEeecccccccc--CcccccCCCCEEEEEEEEEeCCCeEEE
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRI--------GDSNRSGLLHISNMSRTRVT--SVSDLLNEGERVKVLVVKSMFPDKISL  442 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I--------~~~gi~GLvh~Sels~~~v~--~~~~~~kvGd~VkvkVi~vde~~rI~L  442 (514)
                      .++|++|.|+|++++...+.|+|        .. ...|++|++++...++.  ++.+.|++||.|+|+|+++.+...+.|
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            48999999999999999999999        66 58999999999887776  788999999999999999877678999


Q ss_pred             EEecC
Q 010232          443 SIADL  447 (514)
Q Consensus       443 SlK~l  447 (514)
                      |+++-
T Consensus        83 st~~~   87 (92)
T cd05791          83 STAEN   87 (92)
T ss_pred             EecCC
Confidence            99753

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=98.48  E-value=8.6e-07  Score=84.71  Aligned_cols=81  Identities=25%  Similarity=0.405  Sum_probs=67.9

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccccc-----------CcccccCCCCEEEEEEEEEe------
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM------  435 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~-----------~~~~~~kvGd~VkvkVi~vd------  435 (514)
                      ..+|+++.|+|++++++|+||+++  .++|++|.+++.+.+..           +....+++||.|+++|++++      
T Consensus        79 p~~gEvv~G~V~~v~~~GifV~lg--~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~  156 (179)
T TIGR00448        79 PELGEIVEGEVIEIVEFGAFVSLG--PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP  156 (179)
T ss_pred             ccCCCEEEEEEEEEEeeEEEEEeC--CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC
Confidence            467999999999999999999996  48999999999866432           23478999999999999996      


Q ss_pred             CCCeEEEEEecCcCCCCccc
Q 010232          436 FPDKISLSIADLESEPGLFV  455 (514)
Q Consensus       436 e~~rI~LSlK~l~~~P~~~~  455 (514)
                      +..+|.||+|+.-.-|++.+
T Consensus       157 ~~~~I~lt~k~~~LG~~~w~  176 (179)
T TIGR00448       157 EGSKIGLTMRQPLLGKLEWI  176 (179)
T ss_pred             CcceEEEEeccCcCCccccc
Confidence            24689999999877777655

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

>TIGR02063 RNase_R ribonuclease R

Probab=98.47  E-value=5.2e-07  Score=102.94  Aligned_cols=73  Identities=26%  Similarity=0.446  Sum_probs=64.0

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc-----------cCcccccCCCCEEEEEEEEEe-CCCe
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDK  439 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v-----------~~~~~~~kvGd~VkvkVi~vd-e~~r  439 (514)
                      .-++|+++.|+|++|++||+||++.+.+++||+|+++++++++           .+....|++||+|+|+|+++| .+++
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            4578999999999999999999998656999999999986643           344567999999999999998 7899


Q ss_pred             EEEEE
Q 010232          440 ISLSI  444 (514)
Q Consensus       440 I~LSl  444 (514)
                      |.+++
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.

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

Probab=98.46  E-value=6e-07  Score=90.84  Aligned_cols=70  Identities=19%  Similarity=0.302  Sum_probs=63.7

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC---CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~---Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                      +.|+++.|+|+++.++|+||++.   |++||||.+++ +.++.++.+.. .+|+.+.|+|+++|.+++++.||.|
T Consensus         7 ~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~-kvGd~V~vkVi~VD~~k~~I~LSlK   80 (262)
T PRK03987          7 EEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHV-KEGQKVVCKVIRVDPRKGHIDLSLK   80 (262)
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhC-CCCCEEEEEEEEEecccCeEEEEEE
Confidence            58999999999999999999994   79999999999 56677776654 8999999999999999999999997

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

Probab=98.45  E-value=5.4e-07  Score=69.42  Aligned_cols=63  Identities=22%  Similarity=0.347  Sum_probs=52.9

Q ss_pred             EEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232          300 IEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (514)
Q Consensus       300 V~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS  363 (514)
                      +.|+|+++.++|++|+++ +..||+|.+++ ..+..++.+. ..+|+.+.|+|+++|++++++.+|
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~-~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEV-FKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhE-eCCCCEEEEEEEEEcCCcCEEecC
Confidence            479999999999999997 79999999999 4434444443 379999999999999988888876

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.

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

Probab=98.42  E-value=1e-06  Score=74.81  Aligned_cols=71  Identities=17%  Similarity=0.232  Sum_probs=58.7

Q ss_pred             hcCCCEEEEEEEEEECC--eEEEEEC-CEEEEEecccc-c---cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          294 KQLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAEL-L---SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~--G~fVdi~-Gi~gFVP~sel-~---~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                      .+.|+++.|+|+++.++  |+||+++ |.+||||.+++ +   .++.++.+.. .+|+.|.|+|++....++-..+|.+
T Consensus         5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~-~~Gd~v~VqV~~~~~~~K~~~lt~~   82 (88)
T cd04453           5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLL-KEGQEILVQVVKEPIGTKGPRLTTN   82 (88)
T ss_pred             CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcC-CCCCEEEEEEEEecCCCCCceEEEE
Confidence            46899999999999996  9999996 79999999999 4   4566666644 7999999999998776666666543

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

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=98.38  E-value=1.5e-06  Score=98.86  Aligned_cols=98  Identities=18%  Similarity=0.202  Sum_probs=76.2

Q ss_pred             EcCCCcEEEEe-hHHHHHhhhhH---HHhhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhh
Q 010232          268 RTLSGRPLLST-RRLFRKMAWHR---VRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEK  341 (514)
Q Consensus       268 ~d~~grliLS~-kk~~~~~~w~~---l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~  341 (514)
                      .+.+|.+.++. .+...+.+...   +....+.|+++.|+|+++.++|+||++. |.+||+|++++ +.++.++.+.. +
T Consensus       589 i~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~-k  667 (693)
T PRK11824        589 IEDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVL-K  667 (693)
T ss_pred             cCCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCcccee-C
Confidence            34578876554 33333333332   2234589999999999999999999995 79999999999 67777777654 8


Q ss_pred             cCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          342 VGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       342 VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      +||.|+|+|+++|.+ +++.||+|..
T Consensus       668 vGD~V~VkV~~iD~~-grI~LS~k~~  692 (693)
T PRK11824        668 EGDEVKVKVLEIDKR-GRIRLSRKAV  692 (693)
T ss_pred             CCCEEEEEEEEECCC-CcEEEEEEec
Confidence            999999999999987 9999999753

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=98.38  E-value=1.4e-06  Score=69.06  Aligned_cols=61  Identities=21%  Similarity=0.115  Sum_probs=38.9

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCCCCCC
Q 010232          172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPG  251 (514)
Q Consensus       172 ~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~~~~~  251 (514)
                      +|++++.+|+++++.|+|++.|...+.+||.+|+.                                             
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            48999999999999999999988889999988872                                             


Q ss_pred             CCcccCCCEEEEEEEEEcCCCcEEEEeh
Q 010232          252 RPVVETGTVLFAEVLGRTLSGRPLLSTR  279 (514)
Q Consensus       252 ~~~~~vGd~V~v~Vl~~d~~grliLS~k  279 (514)
                       ..+++||.|.++|| .|.++|+++|++
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             22689999999999 788999999974

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

Probab=98.33  E-value=2.1e-06  Score=70.64  Aligned_cols=68  Identities=12%  Similarity=0.238  Sum_probs=54.8

Q ss_pred             CCCEEEEEEEEEECCeEEEEEC--CEEEEEeccccc-cccC-----------ChhhHhhhcCCEEEEEEEEEeCCCCceE
Q 010232          296 LNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL-SRVN-----------NFTELKEKVGRRMYVQITRINEDTNDLI  361 (514)
Q Consensus       296 ~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~-~~i~-----------~~~el~~~VGq~V~vkVl~vD~e~~rIi  361 (514)
                      .|+++.|+|++++++|+||+++  |++||+|.+++. .++.           ..... .++|+.++|+|+++|.+++++.
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~-~~~gd~v~v~v~~vd~~~~~i~   79 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKV-FRLGDKVKVRVVRVDLDRRKID   79 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCE-EcCCCEEEEEEEEeccccCEEE
Confidence            3889999999999999999997  699999999983 3211           11122 2689999999999999888988


Q ss_pred             eeh
Q 010232          362 LSE  364 (514)
Q Consensus       362 LS~  364 (514)
                      ++.
T Consensus        80 ~~l   82 (83)
T cd04471          80 FEL   82 (83)
T ss_pred             EEE
Confidence            874

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.

>PRK11642 exoribonuclease R; Provisional

Probab=98.33  E-value=2.2e-06  Score=98.88  Aligned_cols=77  Identities=25%  Similarity=0.366  Sum_probs=65.6

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccccc-----------CcccccCCCCEEEEEEEEEe-CCCeE
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FPDKI  440 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~-----------~~~~~~kvGd~VkvkVi~vd-e~~rI  440 (514)
                      -++|++++|+|++|+++|+||+|.+.+++||||.+++.+++..           +....|++||+|+|+|+.+| ++++|
T Consensus       641 ~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI  720 (813)
T PRK11642        641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKI  720 (813)
T ss_pred             ccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeE
Confidence            3789999999999999999999987469999999999876321           23567999999999999998 88999


Q ss_pred             EEEEecCcC
Q 010232          441 SLSIADLES  449 (514)
Q Consensus       441 ~LSlK~l~~  449 (514)
                      .|++-....
T Consensus       721 ~f~l~~~~~  729 (813)
T PRK11642        721 DFSLISSER  729 (813)
T ss_pred             EEEEecccc
Confidence            999954443

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

Probab=98.31  E-value=1.6e-06  Score=82.55  Aligned_cols=75  Identities=27%  Similarity=0.461  Sum_probs=62.9

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc----------cC-cccccCCCCEEEEEEEEEe--CC--
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----------TS-VSDLLNEGERVKVLVVKSM--FP--  437 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v----------~~-~~~~~kvGd~VkvkVi~vd--e~--  437 (514)
                      ...|++|.|.|.++.++|+||.|++  .+||+|+|++.++++          .+ -..++++||.|++||+.+.  ..  
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            5679999999999999999999997  799999999998843          22 3347999999999999885  32  


Q ss_pred             --CeEEEEEecCcC
Q 010232          438 --DKISLSIADLES  449 (514)
Q Consensus       438 --~rI~LSlK~l~~  449 (514)
                        .+|.|+||+.-.
T Consensus       157 ~~~~I~lTmrq~~L  170 (183)
T COG1095         157 RESKIGLTMRQPGL  170 (183)
T ss_pred             ccceEEEEeccccC
Confidence              689999987654

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

Probab=98.30  E-value=2.5e-06  Score=96.56  Aligned_cols=73  Identities=22%  Similarity=0.386  Sum_probs=63.5

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc-----------cCcccccCCCCEEEEEEEEEe-CCCe
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDK  439 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v-----------~~~~~~~kvGd~VkvkVi~vd-e~~r  439 (514)
                      .-++|++++|+|++|+++|+||+|.+.+++||||++++.+++.           .+....|++||+|+|+|+++| ++++
T Consensus       569 ~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~  648 (654)
T TIGR00358       569 LDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRS  648 (654)
T ss_pred             hhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence            3468999999999999999999998548999999999988641           234577999999999999998 8899


Q ss_pred             EEEEE
Q 010232          440 ISLSI  444 (514)
Q Consensus       440 I~LSl  444 (514)
                      |.+++
T Consensus       649 I~f~l  653 (654)
T TIGR00358       649 IIFEL  653 (654)
T ss_pred             EEEEE
Confidence            99986

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.

>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=98.28  E-value=3.8e-06  Score=67.75  Aligned_cols=61  Identities=10%  Similarity=0.167  Sum_probs=51.7

Q ss_pred             CCEEEEEEEEEECCeEEEEEC-CEEEEEeccccc-c--ccCChhhHhhhcCCEEEEEEEEEeCCCC
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELL-S--RVNNFTELKEKVGRRMYVQITRINEDTN  358 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel~-~--~i~~~~el~~~VGq~V~vkVl~vD~e~~  358 (514)
                      |+++.|+|+++.+.|++|+++ |++|++|.+++. .  ...++.+.. .+||.+.|+|+++|.++.
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 799999999994 4  255565543 799999999999987653

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=98.28  E-value=3.9e-06  Score=80.90  Aligned_cols=103  Identities=15%  Similarity=0.215  Sum_probs=78.4

Q ss_pred             CCcccCCCEEEEEEEEE---cCCC-cEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC----------
Q 010232          252 RPVVETGTVLFAEVLGR---TLSG-RPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE----------  317 (514)
Q Consensus       252 ~~~~~vGd~V~v~Vl~~---d~~g-rliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~----------  317 (514)
                      ...+..+..|.+-+.+.   |.++ ++.+.        .|.......+.|++|.|+|+++.+.|++|++.          
T Consensus        24 ~Gty~~~~~i~as~~G~~~id~~~~~Isv~--------P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~   95 (189)
T PRK09521         24 EGTYEDNGEVYASVVGKVFIDDINRKISVI--------PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELA   95 (189)
T ss_pred             CCEEeeCCEEEEEeeEEEEEcCCCCEEEEe--------cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccC
Confidence            44567788899888883   4433 34442        45543445679999999999999999999994          


Q ss_pred             -CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          318 -GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       318 -Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                       ++.||+|.+++ +.+..+..+.. ++|+.|.|+|++++   +++.||.|.
T Consensus        96 ~~~~G~l~~s~i~~~~~~~~~~~~-~~GD~V~akV~~i~---~~i~LS~k~  142 (189)
T PRK09521         96 TSKLAYIHISQVSDGYVESLTDAF-KIGDIVRAKVISYT---DPLQLSTKG  142 (189)
T ss_pred             CCceeeEEhhHcChhhhhhHHhcc-CCCCEEEEEEEecC---CcEEEEEec
Confidence             47899999999 44444444443 89999999999997   689999874

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

Probab=98.26  E-value=6.3e-06  Score=67.93  Aligned_cols=62  Identities=19%  Similarity=0.334  Sum_probs=54.5

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~  364 (514)
                      ++.|+.+.|+|+++.++|+||+++ +..||+|.+++...+        ++||+++++|.++ .+++++.+|.
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 LEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY--------EVGDEVIVQVTDI-PENGNIDLIP   76 (77)
T ss_pred             CCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhccCcC--------CCCCEEEEEEEEE-CCCCcEEEEE
Confidence            579999999999999999999996 599999999984322        5999999999999 7889988874

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

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=98.24  E-value=1.8e-06  Score=97.08  Aligned_cols=74  Identities=18%  Similarity=0.131  Sum_probs=67.7

Q ss_pred             hhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          293 IKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       293 ~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      .++.|+++.|+|.++.++|+||+|+ ..+|+||+|++ ...+.+|.++. .+|+.|+|+|+++|..++||.||++..
T Consensus       655 dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv-~vGdiV~v~V~~vD~~r~rI~Lsmr~~  730 (780)
T COG2183         655 DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVV-KVGDIVKVKVIEVDTARKRIALSMRLD  730 (780)
T ss_pred             hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhc-ccCCEEEEEEEEEecccCeeeeEeecc
Confidence            5689999999999999999999995 47999999999 56688888876 899999999999999999999999865

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

Probab=98.22  E-value=6.2e-06  Score=79.19  Aligned_cols=77  Identities=27%  Similarity=0.416  Sum_probs=63.9

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccccc-----------CcccccCCCCEEEEEEEEEe-CC---
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FP---  437 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~-----------~~~~~~kvGd~VkvkVi~vd-e~---  437 (514)
                      ..+|+++.|+|++++++|+||+++.  ++|++|.+++.+++..           +....+++||.|+++|++++ ++   
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            4689999999999999999999984  8999999999876432           34677999999999999997 33   


Q ss_pred             --CeEEEEEecCcCCC
Q 010232          438 --DKISLSIADLESEP  451 (514)
Q Consensus       438 --~rI~LSlK~l~~~P  451 (514)
                        .+|.+|+|+--.-+
T Consensus       157 ~~~~I~ls~~~~~LG~  172 (187)
T PRK08563        157 RGSKIGLTMRQPGLGK  172 (187)
T ss_pred             CCCEEEEEecCCCCCc
Confidence              38999998754433

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.19  E-value=8.2e-06  Score=92.80  Aligned_cols=93  Identities=16%  Similarity=0.176  Sum_probs=70.9

Q ss_pred             EcCCCcEEEEe-hHHHHHhhh---hHHHhhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhh
Q 010232          268 RTLSGRPLLST-RRLFRKMAW---HRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEK  341 (514)
Q Consensus       268 ~d~~grliLS~-kk~~~~~~w---~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~  341 (514)
                      ++.+|++.++. .+.....+-   ..+....+.|+++.|+|+++.++|+||++. |++||+|.|++ +.++.++.+.. +
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            45678885443 333333332   233344578999999999999999999994 79999999999 67787777764 8


Q ss_pred             cCCEEEEEEEEEeCCCCceEe
Q 010232          342 VGRRMYVQITRINEDTNDLIL  362 (514)
Q Consensus       342 VGq~V~vkVl~vD~e~~rIiL  362 (514)
                      +||.|.|+|+++|. ++++.|
T Consensus       665 vGD~V~VkVi~id~-~gki~L  684 (684)
T TIGR03591       665 EGDEVKVKVLEIDK-QGRIKL  684 (684)
T ss_pred             CCCEEEEEEEEECC-CCCccC
Confidence            99999999999997 666643

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).

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=98.17  E-value=4.5e-06  Score=69.75  Aligned_cols=71  Identities=13%  Similarity=0.132  Sum_probs=66.3

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEE-eeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLH-ISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh-~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl  444 (514)
                      -.++|+++. .|..+.+.|++|.+-++|++|+|. .++++.+++.++++.+ +|..+.|+|+.+| +++-|+||.
T Consensus        13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEc
Confidence            358899999 899999999999998888999999 9999999999999999 9999999999999 899999985

>TIGR01953 NusA transcription termination factor NusA

Probab=98.15  E-value=6.3e-06  Score=86.36  Aligned_cols=96  Identities=21%  Similarity=0.356  Sum_probs=73.2

Q ss_pred             hcCCEEEEEEEEEeCCCCceEeehh-hhh----h-------hccC--CCCceEEEEEEEEecce-EEEEECCCceEEEEE
Q 010232          341 KVGRRMYVQITRINEDTNDLILSER-EAW----A-------TLNL--REGTLLEGTVKKIYPYG-AQIRIGDSNRSGLLH  405 (514)
Q Consensus       341 ~VGq~V~vkVl~vD~e~~rIiLS~K-~~~----~-------~~~l--~~G~iV~G~V~~I~~~G-aFV~I~~~gi~GLvh  405 (514)
                      .+|+.+.+.|..  .+-+|+.++.. +.+    .       ...+  +.|++|+|+|.++.+.| ++|+++  +++|+||
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 QIGDEVKKEIPP--ENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELG--KTEGILP  160 (341)
T ss_pred             ccCCEEEEEecc--cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEEC--CeEEEec
Confidence            599999998853  23445544443 321    0       0234  69999999999999988 699996  6899999


Q ss_pred             eeccccccccCcccccCCCCEEEEEEEEEe-CC--CeEEEEEec
Q 010232          406 ISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP--DKISLSIAD  446 (514)
Q Consensus       406 ~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~--~rI~LSlK~  446 (514)
                      .+++.      |.+.|++||+|+|+|++++ ..  ..|.||.+.
T Consensus       161 ~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~  198 (341)
T TIGR01953       161 KKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTH  198 (341)
T ss_pred             HHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence            99987      4567999999999999997 32  478999853

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=98.13  E-value=2.4e-05  Score=78.11  Aligned_cols=159  Identities=18%  Similarity=0.269  Sum_probs=100.2

Q ss_pred             CCcccCCCEEEEEEEEE-cCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-
Q 010232          252 RPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-  328 (514)
Q Consensus       252 ~~~~~vGd~V~v~Vl~~-d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-  328 (514)
                      ...+..+..+.+-+.+. ..+++ .++.+.....       -.-+.|++|.|+|+++...|++|+++ ++.|+||.+++ 
T Consensus        26 ~Gty~~~g~i~As~~G~~~~~~~-~i~V~p~~~~-------y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~   97 (235)
T PRK04163         26 RGTYKENGKIYSTVVGLVDIKDD-KVRVIPLEGK-------YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVL   97 (235)
T ss_pred             CceEEeCCEEEEEEeEEEEEECC-EEEEEECCCc-------ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcC
Confidence            33456677788877772 22222 3333322111       11269999999999999999999997 58999999999 


Q ss_pred             cccc----CChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhhhccCCCCceEEEEEEEEecceEEEEECCCceEEEE
Q 010232          329 LSRV----NNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLL  404 (514)
Q Consensus       329 ~~~i----~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~~~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLv  404 (514)
                      +.+.    .+.++.. .+|+.|.|+|+++++++ .+.||.|..      .-|.+..|.+..|.+.-+---|+.   .|.+
T Consensus        98 ~~~~~~d~~~~~~~~-~~GDlV~akV~~i~~~~-~~~LS~k~~------~lG~L~~G~~~~V~~~~i~~lig~---~g~~  166 (235)
T PRK04163         98 GRPVNVEGTDLRKYL-DIGDYIIAKVKDVDRTR-DVVLTLKGK------GLGKIEGGTIVEIKPVKVPRVIGK---KGSM  166 (235)
T ss_pred             CCccccchhhhHhhC-CCCCEEEEEEEEECCCC-cEEEEEcCC------CCCccCCCEEEEECHHHHHhhcCC---CChh
Confidence            4443    4455543 79999999999998654 599998743      235555555555554433222222   0100


Q ss_pred             EeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 010232          405 HISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA  445 (514)
Q Consensus       405 h~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK  445 (514)
                               +.      ..++...+.|. +..+++|.++-.
T Consensus       167 ---------i~------~l~~~~~~~I~-ig~NG~VwI~~~  191 (235)
T PRK04163        167 ---------IN------MLKEETGCDII-VGQNGRIWIKGP  191 (235)
T ss_pred             ---------Hh------hhhhhhCcEEE-EcCCcEEEEeeC
Confidence                     00      12334445553 567899998884

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.11  E-value=5.4e-06  Score=87.41  Aligned_cols=95  Identities=19%  Similarity=0.254  Sum_probs=71.2

Q ss_pred             hcCCEEEEEEEEEeCCCCceEeehhhhhh-----------hccC--CCCceEEEEEEEEecceEEEEECCCceEEEEEee
Q 010232          341 KVGRRMYVQITRINEDTNDLILSEREAWA-----------TLNL--REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHIS  407 (514)
Q Consensus       341 ~VGq~V~vkVl~vD~e~~rIiLS~K~~~~-----------~~~l--~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~S  407 (514)
                      .+|+.+.+.+...+-.+..+.. .|+.+.           ...+  +.|+++.|+|.++.+.|+||+++  +++|+||.+
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 ELGDVIEIEVTPKDFGRIAAQT-AKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLG--KIEAVLPPA  164 (362)
T ss_pred             cCCCEEEEecCcCCCChHHHHH-HHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeC--CeEEEecHH
Confidence            5999999988754433222222 222111           1244  99999999999999999999997  589999998


Q ss_pred             ccccccccCcccccCCCCEEEEEEEEEe-CCC--eEEEEE
Q 010232          408 NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD--KISLSI  444 (514)
Q Consensus       408 els~~~v~~~~~~~kvGd~VkvkVi~vd-e~~--rI~LSl  444 (514)
                      ++.      |.+.|++||+|+|+|++++ +.+  .|.||.
T Consensus       165 E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSR  198 (362)
T PRK12327        165 EQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSR  198 (362)
T ss_pred             HcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEe
Confidence            875      3688999999999999997 333  577777

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

Probab=98.02  E-value=1.4e-05  Score=68.92  Aligned_cols=69  Identities=19%  Similarity=0.213  Sum_probs=55.3

Q ss_pred             CEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccCCh-----------hhHhhhcCCEEEEEEEEEeCCC-----Cce
Q 010232          298 EPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNF-----------TELKEKVGRRMYVQITRINEDT-----NDL  360 (514)
Q Consensus       298 eiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~~~-----------~el~~~VGq~V~vkVl~vD~e~-----~rI  360 (514)
                      +++.|+|++++++|+||+++++.||+|.+++ ..+....           ... +.+|+.+.++|.++|.+.     .++
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 3333211           122 379999999999999764     479


Q ss_pred             Eeehhhh
Q 010232          361 ILSEREA  367 (514)
Q Consensus       361 iLS~K~~  367 (514)
                      .||.|..
T Consensus        80 ~ls~k~~   86 (99)
T cd04460          80 GLTMRQP   86 (99)
T ss_pred             EEEEecC
Confidence            9999863

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.

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

Probab=98.00  E-value=2.3e-05  Score=87.20  Aligned_cols=98  Identities=15%  Similarity=0.177  Sum_probs=76.6

Q ss_pred             EcCCCcEEEEeh-HHHHHh---hhhHHHhhhcCCCEEEEEEEEEECCeEEEEE-CCEEEEEecccc-ccccCChhhHhhh
Q 010232          268 RTLSGRPLLSTR-RLFRKM---AWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEK  341 (514)
Q Consensus       268 ~d~~grliLS~k-k~~~~~---~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi-~Gi~gFVP~sel-~~~i~~~~el~~~  341 (514)
                      ++++|.+..+.. ......   ....+....+.|+++.|+|+++.++|+||.+ +|-+|++|.|++ +.++.+..+.. +
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            457888854433 233333   3344455668999999999999999999999 578999999999 66777666665 8


Q ss_pred             cCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          342 VGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       342 VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      +||.+.|+|+.+|+ .+++.+|++..
T Consensus       666 ~Gd~v~Vkv~~iD~-~Gri~ls~~~~  690 (692)
T COG1185         666 EGDEVKVKVIEIDK-QGRIRLSIKAV  690 (692)
T ss_pred             cCceEEEEEeeecc-cCCccceehhc
Confidence            99999999999985 68899998753

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

Probab=97.92  E-value=1e-05  Score=77.21  Aligned_cols=107  Identities=17%  Similarity=0.173  Sum_probs=70.7

Q ss_pred             EEEEEEEE-c-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccC----
Q 010232          261 LFAEVLGR-T-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVN----  333 (514)
Q Consensus       261 V~v~Vl~~-d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~----  333 (514)
                      +.+.|+.. + .+|+++...-....+..+..|.-.-..|++|.|.|++++++|+||.++-++||+|.+|+ +.++.    
T Consensus        44 ~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~  123 (183)
T COG1095          44 LVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEK  123 (183)
T ss_pred             EEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEeccccEEEEEEEEEeecceEEEeccccccccHhhccCcccccCcc
Confidence            33444542 2 56666633222222222222222235899999999999999999999889999999999 33221    


Q ss_pred             ------ChhhHhhhcCCEEEEEEEEEeCCC-----CceEeehhhh
Q 010232          334 ------NFTELKEKVGRRMYVQITRINEDT-----NDLILSEREA  367 (514)
Q Consensus       334 ------~~~el~~~VGq~V~vkVl~vD~e~-----~rIiLS~K~~  367 (514)
                            .-......+|+.|+++|+.+....     .+|.+++|++
T Consensus       124 ~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~~I~lTmrq~  168 (183)
T COG1095         124 NKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMRQP  168 (183)
T ss_pred             cceeeecccceEEecCCEEEEEEEEEecccCccccceEEEEeccc
Confidence                  111122368999999999987655     4788888875

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.92  E-value=4.3e-05  Score=80.54  Aligned_cols=108  Identities=19%  Similarity=0.180  Sum_probs=74.7

Q ss_pred             CcccCCCEEEEEEEEEcCCCcEE-EEehHHHHH----hhhhHHHhhh--cCCCEEEEEEEEEEC-CeEEEEECCEEEEEe
Q 010232          253 PVVETGTVLFAEVLGRTLSGRPL-LSTRRLFRK----MAWHRVRQIK--QLNEPIEVKFTEWNT-GGLLTRIEGLRAFLP  324 (514)
Q Consensus       253 ~~~~vGd~V~v~Vl~~d~~grli-LS~kk~~~~----~~w~~l~~~~--k~GeiV~GkV~~v~~-~G~fVdi~Gi~gFVP  324 (514)
                      +.+++||.+...+-- ..=||+. -+.++...+    ...+.+.+.+  +.|++++|+|.++.. ++++|++++..|+||
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 PSVEIGDELTYELSL-ENMGRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEIDEIRAVLP  167 (374)
T ss_pred             CCCCCCCEEEEecCh-hhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEcCCeEEEeC
Confidence            457899999876542 2234443 233333211    1112222222  699999999999996 569999999999999


Q ss_pred             ccccccccCChhhHhhhcCCEEEEEEEEEeCCCC---ceEeehhhh
Q 010232          325 KAELLSRVNNFTELKEKVGRRMYVQITRINEDTN---DLILSEREA  367 (514)
Q Consensus       325 ~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~---rIiLS~K~~  367 (514)
                      .+++...-     . +.+|++++|+|.+|+...+   .|+|||..+
T Consensus       168 ~~eqip~E-----~-~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p  207 (374)
T PRK12328        168 MKNRIKGE-----K-FKVGDVVKAVLKRVKIDKNNGILIELSRTSP  207 (374)
T ss_pred             HHHcCCCC-----c-CCCCCEEEEEEEEEecCCCCCCEEEEEcCCH
Confidence            99984221     1 2599999999999988765   899999753

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

Probab=97.81  E-value=8.3e-06  Score=81.20  Aligned_cols=88  Identities=22%  Similarity=0.283  Sum_probs=78.3

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~  449 (514)
                      -.+++++|-+.|.+|...|+||.+-.+ +++|+|-.|+||..|+.++.+..++|..=.|.|+.+| +++-|+||.+.+.+
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            468999999999999999999999443 7999999999999999999999999999999999999 89999999999988


Q ss_pred             CCCccccchh
Q 010232          450 EPGLFVSDKE  459 (514)
Q Consensus       450 ~P~~~~~~k~  459 (514)
                      +.-....+++
T Consensus        93 ed~~kC~Er~  102 (304)
T KOG2916|consen   93 EDKEKCEERF  102 (304)
T ss_pred             HHHHHHHHHH
Confidence            6655544443

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

Probab=97.78  E-value=0.00013  Score=62.45  Aligned_cols=77  Identities=21%  Similarity=0.257  Sum_probs=59.0

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEe--------CCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecc
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNV--------GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD  239 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdI--------G~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~  239 (514)
                      +-+++||+|.|+|+++....+.|+|        .....|++|.+++.+.+-.+                           
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            4578999999999999999999999        66778999988875331000                           


Q ss_pred             ccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 010232          240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (514)
Q Consensus       240 d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk  280 (514)
                        ..+       ...|++||.|.|+|++.+....+.||++.
T Consensus        55 --~~~-------~~~f~~GDiV~AkVis~~~~~~~~Lst~~   86 (92)
T cd05791          55 --VEM-------YKCFRPGDIVRAKVISLGDASSYYLSTAE   86 (92)
T ss_pred             --HHH-------HhhcCCCCEEEEEEEEcCCCCCcEEEecC
Confidence              001       23489999999999987666778899864

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".

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

Probab=97.74  E-value=0.00021  Score=60.82  Aligned_cols=59  Identities=10%  Similarity=0.180  Sum_probs=49.3

Q ss_pred             CCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCc-----------ccccCCCCEEEEEEEEEe
Q 010232          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSV-----------SDLLNEGERVKVLVVKSM  435 (514)
Q Consensus       375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~-----------~~~~kvGd~VkvkVi~vd  435 (514)
                      +|++++|+|++++++|+||.+++  +.+|+|.+.+......++           ...+++|+.|++||+.+.
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            58999999999999999999996  799999988865433332           345889999999999885

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=97.74  E-value=0.00014  Score=57.66  Aligned_cols=61  Identities=20%  Similarity=0.235  Sum_probs=37.9

Q ss_pred             CCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 010232          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA  445 (514)
Q Consensus       375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK  445 (514)
                      +|++...+|.+++++|+|++.+. +-.-|+|.+++.        ..+++||.|.|.|. .|.++|+..|+|
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            58899999999999999999887 689999999986        45899999999997 477789999885

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

Probab=97.73  E-value=8.1e-05  Score=71.18  Aligned_cols=73  Identities=12%  Similarity=0.172  Sum_probs=58.8

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccc-cccC-Chh---------hHhhhcCCEEEEEEEEEe-----CCCC
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL-SRVN-NFT---------ELKEKVGRRMYVQITRIN-----EDTN  358 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~-~~i~-~~~---------el~~~VGq~V~vkVl~vD-----~e~~  358 (514)
                      ..|+++.|+|++++++|+||+++.++|++|.+++. .+.. ++.         .....+|+.|+++|.++|     ++..
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            48999999999999999999997799999999983 3221 111         123479999999999998     5667


Q ss_pred             ceEeehhhh
Q 010232          359 DLILSEREA  367 (514)
Q Consensus       359 rIiLS~K~~  367 (514)
                      +|.+|+|++
T Consensus       160 ~I~lt~k~~  168 (179)
T TIGR00448       160 KIGLTMRQP  168 (179)
T ss_pred             eEEEEeccC
Confidence            899999975

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

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

Probab=97.70  E-value=0.00024  Score=67.97  Aligned_cols=88  Identities=22%  Similarity=0.288  Sum_probs=68.8

Q ss_pred             CCceEeehhhhhh-hccCCCCceEEEEEEEEecceEEEEECCC---------ceEEEEEeeccccccccCcccccCCCCE
Q 010232          357 TNDLILSEREAWA-TLNLREGTLLEGTVKKIYPYGAQIRIGDS---------NRSGLLHISNMSRTRVTSVSDLLNEGER  426 (514)
Q Consensus       357 ~~rIiLS~K~~~~-~~~l~~G~iV~G~V~~I~~~GaFV~I~~~---------gi~GLvh~Sels~~~v~~~~~~~kvGd~  426 (514)
                      .++..+|.+.... ..-++.|++|-|+|+++....+.|+|-..         -..|-+|+|+++..++.+.++.|++||.
T Consensus        45 ~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDi  124 (188)
T COG1096          45 DKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDI  124 (188)
T ss_pred             ccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccE
Confidence            3444555543322 23578999999999999999999988521         1467899999999999999999999999


Q ss_pred             EEEEEEEEeCCCeEEEEEec
Q 010232          427 VKVLVVKSMFPDKISLSIAD  446 (514)
Q Consensus       427 VkvkVi~vde~~rI~LSlK~  446 (514)
                      |+|+|++.-  ..+.||++.
T Consensus       125 vrA~Vis~~--~~~~Lst~~  142 (188)
T COG1096         125 VRARVISTG--DPIQLSTKG  142 (188)
T ss_pred             EEEEEEecC--CCeEEEecC
Confidence            999999753  667888754

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

Probab=97.66  E-value=0.00034  Score=59.44  Aligned_cols=73  Identities=26%  Similarity=0.416  Sum_probs=58.6

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~  247 (514)
                      |.+++||+|-|+|+.+....+.|||+....|+||..++.-.                                       
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            57889999999999999999999999888999887665211                                       


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEeh
Q 010232          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTR  279 (514)
Q Consensus       248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~k  279 (514)
                      ..+.++.+++||.|.|+|...+.+..+.||..
T Consensus        43 tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~   74 (86)
T cd05790          43 TKRNRPNLNVGDLVYARVVKANRDMEPELSCV   74 (86)
T ss_pred             cccccccCCCCCEEEEEEEecCCCCCeEEEEe
Confidence            01114678999999999998887777777764

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=97.65  E-value=0.00017  Score=81.82  Aligned_cols=71  Identities=14%  Similarity=0.173  Sum_probs=58.7

Q ss_pred             CCC--ceEEEEEEEEecceEEEEECCCceEEEEEeeccccc---ccc--C-------cccccCCCCEEEEEEEEEe-CCC
Q 010232          374 REG--TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT---RVT--S-------VSDLLNEGERVKVLVVKSM-FPD  438 (514)
Q Consensus       374 ~~G--~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~---~v~--~-------~~~~~kvGd~VkvkVi~vd-e~~  438 (514)
                      ++|  +.+.|+|++|+++|+||+|.+.+++||||.+.|.+.   +.-  +       -...|++||+|+|+|.++| +++
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            465  599999999999999999987789999999999653   111  1       1246999999999999998 888


Q ss_pred             eEEEEE
Q 010232          439 KISLSI  444 (514)
Q Consensus       439 rI~LSl  444 (514)
                      +|.+++
T Consensus       638 ~i~~~~  643 (644)
T PRK05054        638 SIIARP  643 (644)
T ss_pred             eEEEEE
Confidence            998875

>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=97.55  E-value=0.00026  Score=58.02  Aligned_cols=67  Identities=21%  Similarity=0.356  Sum_probs=56.5

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccC---cccccCCCCEE-EEEEEEEe-CCCeEEEEEe
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTS---VSDLLNEGERV-KVLVVKSM-FPDKISLSIA  445 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~---~~~~~kvGd~V-kvkVi~vd-e~~rI~LSlK  445 (514)
                      |++|+|+|..-++.+++|++.+.|+.|++|..++++ ++.+   .-..+++||++ .+.|+  + ..+.|.||.|
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 4432   33458999999 89998  5 5667788765

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.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.53  E-value=0.00023  Score=76.64  Aligned_cols=62  Identities=35%  Similarity=0.568  Sum_probs=53.8

Q ss_pred             cCCCCceEEEEEEEEecc--eEEEEECCCceEEEEEeeccccc------------cccCcccccCCCCEEEEEEEEE
Q 010232          372 NLREGTLLEGTVKKIYPY--GAQIRIGDSNRSGLLHISNMSRT------------RVTSVSDLLNEGERVKVLVVKS  434 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~--GaFV~I~~~gi~GLvh~Sels~~------------~v~~~~~~~kvGd~VkvkVi~v  434 (514)
                      ...+|+++.|+|.+|.|.  ||||+|+. +..||+|.+++.+.            +..++.+.+++||.|.|.|++-
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            457999999999999999  99999998 89999999998753            2445667899999999999973

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

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

Probab=97.47  E-value=0.00042  Score=68.82  Aligned_cols=76  Identities=24%  Similarity=0.360  Sum_probs=68.0

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc----cCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----TSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v----~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l  447 (514)
                      -.++||+|-|+|..+.+.++.|+|+. -+.+++|.|++.+..+    .+++.+|++||-|.|+|..++..+...|++|+.
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            46899999999999999999999998 5999999999966653    478889999999999999999999999999765


Q ss_pred             c
Q 010232          448 E  448 (514)
Q Consensus       448 ~  448 (514)
                      .
T Consensus       140 ~  140 (239)
T COG1097         140 G  140 (239)
T ss_pred             C
Confidence            4

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

Probab=97.43  E-value=0.00066  Score=65.00  Aligned_cols=73  Identities=10%  Similarity=0.024  Sum_probs=57.2

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccc-----------c-cCcccccCCCCEEEEEEEEEe-C--C
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR-----------V-TSVSDLLNEGERVKVLVVKSM-F--P  437 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~-----------v-~~~~~~~kvGd~VkvkVi~vd-e--~  437 (514)
                      .-.|++++|+|++++++|+||.++.  .++|||.++|.+..           . .+-...++.|+.|++||..+. +  +
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            5789999999999999999999987  67999999997431           1 122456999999999999885 2  2


Q ss_pred             CeEEEEEecC
Q 010232          438 DKISLSIADL  447 (514)
Q Consensus       438 ~rI~LSlK~l  447 (514)
                      .++..|||+-
T Consensus       157 ~~~i~T~~~~  166 (176)
T PTZ00162        157 LFAIATINSD  166 (176)
T ss_pred             cEEEEEecCC
Confidence            3566677653

>TIGR02063 RNase_R ribonuclease R

Probab=97.42  E-value=0.00052  Score=78.64  Aligned_cols=69  Identities=16%  Similarity=0.247  Sum_probs=56.5

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC--CEEEEEeccccc-ccc-----------CChhhHhhhcCCEEEEEEEEEeCCCCce
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL-SRV-----------NNFTELKEKVGRRMYVQITRINEDTNDL  360 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~-~~i-----------~~~~el~~~VGq~V~vkVl~vD~e~~rI  360 (514)
                      +.|+++.|+|++++++|+||++.  |++|+||++++. .++           .+... .+++||+|+|+|.++|..+++|
T Consensus       626 ~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~-~~~lGd~V~Vkv~~vd~~~~~I  704 (709)
T TIGR02063       626 KIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGK-VFRLGDRVKVRVVKADLDTGKI  704 (709)
T ss_pred             cCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCc-EECCCCEEEEEEEEEecccCeE
Confidence            68999999999999999999996  699999999993 221           11111 1369999999999999999999


Q ss_pred             Eeeh
Q 010232          361 ILSE  364 (514)
Q Consensus       361 iLS~  364 (514)
                      .++.
T Consensus       705 ~~~l  708 (709)
T TIGR02063       705 DFEL  708 (709)
T ss_pred             EEEE
Confidence            8874

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.

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

Probab=97.41  E-value=0.00074  Score=67.12  Aligned_cols=80  Identities=21%  Similarity=0.383  Sum_probs=64.7

Q ss_pred             ccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccC
Q 010232          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (514)
Q Consensus       167 ~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~  246 (514)
                      -|.+++||+|-|.|+.+...++.|||++...++||.++++.+.   +                               ..
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            4789999999999999999999999999999999999884321   0                               00


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 010232          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (514)
Q Consensus       247 ~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk  280 (514)
                      ...+-++.+++||.|.|+|...|.++.+.|+.|.
T Consensus       105 ~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~  138 (239)
T COG1097         105 AEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD  138 (239)
T ss_pred             cccccccccccCCEEEEEEEEccCCCceEEEeec
Confidence            0011256789999999999999999999998843

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

Probab=97.40  E-value=0.00094  Score=56.72  Aligned_cols=72  Identities=22%  Similarity=0.128  Sum_probs=62.0

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEec
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIAD  446 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~  446 (514)
                      .++||.|-|+|+.++..+.+|+|+. -..|++|.+.+... .++.+..|++||-|-|+|..++......||+.+
T Consensus         4 P~~gD~VIG~V~~~~~~~~~VdI~s-~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~   75 (86)
T cd05790           4 PAKGDHVIGIVVAKAGDFFKVDIGG-SEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRDMEPELSCVD   75 (86)
T ss_pred             CCCCCEEEEEEEEEcCCeEEEEcCC-CcceEechHHcccc-cccccccCCCCCEEEEEEEecCCCCCeEEEEeC
Confidence            4789999999999999999999998 58999999887533 344567899999999999998877789999976

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=97.39  E-value=0.00068  Score=55.63  Aligned_cols=65  Identities=23%  Similarity=0.390  Sum_probs=53.5

Q ss_pred             CCEEEEEEEEEECCeEEEEEC--CEEEEEeccccccccCC----hhhHhhhcCCEE-EEEEEEEeCCCCceEeehh
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLSRVNN----FTELKEKVGRRM-YVQITRINEDTNDLILSER  365 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~~~i~~----~~el~~~VGq~V-~vkVl~vD~e~~rIiLS~K  365 (514)
                      |..|+|+|...++.+++|+++  |++|++|..|+.+...+    ++.+  .+|+++ .+.|+  |...+.+.+|.|
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            688999999999999999995  69999999999544332    2334  599999 88888  788888888875

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=97.37  E-value=0.00038  Score=66.87  Aligned_cols=72  Identities=19%  Similarity=0.264  Sum_probs=56.7

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccc-cccC-Ch---------hhHhhhcCCEEEEEEEEEeCCCC-----
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL-SRVN-NF---------TELKEKVGRRMYVQITRINEDTN-----  358 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~-~~i~-~~---------~el~~~VGq~V~vkVl~vD~e~~-----  358 (514)
                      ..|+++.|+|+++++.|++|+++.++||++.+++. .+.. ++         ......+|+.++++|.+++....     
T Consensus        80 ~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~~  159 (187)
T PRK08563         80 ELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRGS  159 (187)
T ss_pred             cCCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCCC
Confidence            58999999999999999999998899999999983 3221 00         01123689999999999987543     


Q ss_pred             ceEeehhh
Q 010232          359 DLILSERE  366 (514)
Q Consensus       359 rIiLS~K~  366 (514)
                      +|.+|++.
T Consensus       160 ~I~ls~~~  167 (187)
T PRK08563        160 KIGLTMRQ  167 (187)
T ss_pred             EEEEEecC
Confidence            78889885

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=97.35  E-value=0.00085  Score=72.14  Aligned_cols=109  Identities=15%  Similarity=0.195  Sum_probs=74.0

Q ss_pred             CcccCCCEEEEEEEEE-cCCCcEEE-EehHHHH----HhhhhHHHhhh--cCCCEEEEEEEEEECCeEEEEE----CC--
Q 010232          253 PVVETGTVLFAEVLGR-TLSGRPLL-STRRLFR----KMAWHRVRQIK--QLNEPIEVKFTEWNTGGLLTRI----EG--  318 (514)
Q Consensus       253 ~~~~vGd~V~v~Vl~~-d~~grliL-S~kk~~~----~~~w~~l~~~~--k~GeiV~GkV~~v~~~G~fVdi----~G--  318 (514)
                      +.+++||.|...|.-. ..=||+.+ +.|+...    ....+.+.+.+  +.|+++.|+|.++.+.+++|++    +.  
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            4578999998765321 12355532 2333221    11222233322  6999999999999999999998    42  


Q ss_pred             EEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCC---CceEeehhhh
Q 010232          319 LRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDT---NDLILSEREA  367 (514)
Q Consensus       319 i~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~---~rIiLS~K~~  367 (514)
                      ++|+||.+++...-     . +++|++++|+|.+|+...   -.|+|||..+
T Consensus       181 ~EaiLP~~Eqip~E-----~-y~~Gdrika~i~~V~~~~~kGpqIilSRt~p  226 (449)
T PRK12329        181 VEAELPKREQLPND-----N-YRANATFKVFLKEVSEGPRRGPQLFVSRANA  226 (449)
T ss_pred             eEEEecHHHcCCCC-----c-CCCCCEEEEEEEEeecCCCCCCEEEEEcCCH
Confidence            89999999983221     1 269999999999997753   3799999753

>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=97.28  E-value=0.00076  Score=56.80  Aligned_cols=61  Identities=18%  Similarity=0.310  Sum_probs=41.6

Q ss_pred             CCCceEEEEEEEEecceEEEEECCC-----------------ceEEEEEeeccccccccC--cccccCCCCEEEEEEEEE
Q 010232          374 REGTLLEGTVKKIYPYGAQIRIGDS-----------------NRSGLLHISNMSRTRVTS--VSDLLNEGERVKVLVVKS  434 (514)
Q Consensus       374 ~~G~iV~G~V~~I~~~GaFV~I~~~-----------------gi~GLvh~Sels~~~v~~--~~~~~kvGd~VkvkVi~v  434 (514)
                      ++|++|.|+|+++++.-|+++|-..                 ...|+||.+++.......  +.+.|++||.|+|+|+++
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            6788999999999888887777321                 478999999988765543  578899999999999864

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.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.15  E-value=0.001  Score=70.41  Aligned_cols=94  Identities=16%  Similarity=0.199  Sum_probs=69.0

Q ss_pred             hcCCEEEEEEEEEeCCCCceEee-hhhhh-------------hhccCCCCceEEEEEEEEecc-eEEEEECCCceEEEEE
Q 010232          341 KVGRRMYVQITRINEDTNDLILS-EREAW-------------ATLNLREGTLLEGTVKKIYPY-GAQIRIGDSNRSGLLH  405 (514)
Q Consensus       341 ~VGq~V~vkVl~vD~e~~rIiLS-~K~~~-------------~~~~l~~G~iV~G~V~~I~~~-GaFV~I~~~gi~GLvh  405 (514)
                      .+|+.+...+.--  +-+|+.+. .|+.+             +...-+.|+++.|+|.++... +++|+++  +.+|++|
T Consensus        92 ~vGd~i~~~i~~~--~fgRiaaq~akq~i~Qkir~~er~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdlg--~~ea~LP  167 (374)
T PRK12328         92 EIGDELTYELSLE--NMGRTAANTLFKELEYHIQRLLEESIFEKYKKKVGKIVFGTVVRVDNEENTFIEID--EIRAVLP  167 (374)
T ss_pred             CCCCEEEEecChh--hCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEcC--CeEEEeC
Confidence            5899998766521  22333222 22221             123568999999999999875 5999998  5899999


Q ss_pred             eeccccccccCcccccCCCCEEEEEEEEEe-CCC---eEEEEE
Q 010232          406 ISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD---KISLSI  444 (514)
Q Consensus       406 ~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~---rI~LSl  444 (514)
                      .++..      |.+.|++||+++|+|.+|. ..+   +|.||.
T Consensus       168 ~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSR  204 (374)
T PRK12328        168 MKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIELSR  204 (374)
T ss_pred             HHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEc
Confidence            99976      5688999999999999996 332   677887

>TIGR02062 RNase_B exoribonuclease II

Probab=97.12  E-value=0.0014  Score=74.45  Aligned_cols=68  Identities=12%  Similarity=0.191  Sum_probs=55.0

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeecccc--c-cc--c-----Cc--ccccCCCCEEEEEEEEEe-CCCeEEE
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR--T-RV--T-----SV--SDLLNEGERVKVLVVKSM-FPDKISL  442 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~--~-~v--~-----~~--~~~~kvGd~VkvkVi~vd-e~~rI~L  442 (514)
                      |+.+.|+|++++++|+||++.+.|++||||.+.+..  + +.  .     .+  ...|++||+|+|+|.++| ++++|.+
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            458999999999999999996658999999999965  2 21  1     11  125999999999999998 7888876


Q ss_pred             E
Q 010232          443 S  443 (514)
Q Consensus       443 S  443 (514)
                      .
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.

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

Probab=97.12  E-value=0.0021  Score=73.12  Aligned_cols=69  Identities=16%  Similarity=0.333  Sum_probs=56.1

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC--CEEEEEecccc-cccc-----------CChhhHhhhcCCEEEEEEEEEeCCCCce
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRV-----------NNFTELKEKVGRRMYVQITRINEDTNDL  360 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel-~~~i-----------~~~~el~~~VGq~V~vkVl~vD~e~~rI  360 (514)
                      +.|+.+.|+|++++++|+||++.  |++||||++++ +.+.           ++... .+.+|++|+|+|.++|..+++|
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            68999999999999999999995  69999999999 3321           11111 2369999999999999999998


Q ss_pred             Eeeh
Q 010232          361 ILSE  364 (514)
Q Consensus       361 iLS~  364 (514)
                      .++.
T Consensus       650 ~f~l  653 (654)
T TIGR00358       650 IFEL  653 (654)
T ss_pred             EEEE
Confidence            8763

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.

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=97.08  E-value=0.0015  Score=74.98  Aligned_cols=74  Identities=23%  Similarity=0.363  Sum_probs=63.2

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc-----------cCcccccCCCCEEEEEEEEEe-CCCe
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDK  439 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v-----------~~~~~~~kvGd~VkvkVi~vd-e~~r  439 (514)
                      .-++|+...|+|.+++.+|+||.+.+.+++|++|++.+...+.           ......++.||.|+|+|.+++ ..++
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            5689999999999999999999998867999999999986422           233446999999999999998 7889


Q ss_pred             EEEEEe
Q 010232          440 ISLSIA  445 (514)
Q Consensus       440 I~LSlK  445 (514)
                      |.+++-
T Consensus       699 i~~~~v  704 (706)
T COG0557         699 IDFELV  704 (706)
T ss_pred             eEEEec
Confidence            988873

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

Probab=97.07  E-value=0.0025  Score=54.21  Aligned_cols=33  Identities=18%  Similarity=0.348  Sum_probs=31.1

Q ss_pred             CCCEEEEEEEEEECCeEEEEECCEEEEEecccc
Q 010232          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL  328 (514)
Q Consensus       296 ~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel  328 (514)
                      .|+++.|+|+++++.|++|.++.+++|++.+++
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~i   33 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLI   33 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcCceEEEEeeec
Confidence            489999999999999999999889999998888

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.

>PRK11642 exoribonuclease R; Provisional

Probab=97.03  E-value=0.002  Score=74.83  Aligned_cols=71  Identities=14%  Similarity=0.196  Sum_probs=57.2

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC--CEEEEEecccc-ccccC-Ch---------hhHhhhcCCEEEEEEEEEeCCCCceE
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRVN-NF---------TELKEKVGRRMYVQITRINEDTNDLI  361 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel-~~~i~-~~---------~el~~~VGq~V~vkVl~vD~e~~rIi  361 (514)
                      +.|+++.|+|++++++|+||++.  +++||||.+++ +.++. +.         ..-.+.+|+.|+|+|..+|..+++|.
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            68999999999999999999995  49999999999 33211 00         00123699999999999999999999


Q ss_pred             eehh
Q 010232          362 LSER  365 (514)
Q Consensus       362 LS~K  365 (514)
                      ++.-
T Consensus       722 f~l~  725 (813)
T PRK11642        722 FSLI  725 (813)
T ss_pred             EEEe
Confidence            9863

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=97.02  E-value=0.0022  Score=53.87  Aligned_cols=67  Identities=16%  Similarity=0.255  Sum_probs=57.7

Q ss_pred             cCCCEEEEEEEEEECCeEEEEE--CCEEEEEe-cccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeeh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRI--EGLRAFLP-KAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSE  364 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi--~Gi~gFVP-~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~  364 (514)
                      +.|+.+. .|+.+.+.|++|.+  -|++|+|+ .+++ .+++++..++.  +|....++|+++|+.++-|-||.
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            5788888 89999999999998  25999888 9999 56677777764  99999999999999999888774

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

Probab=96.95  E-value=0.004  Score=68.12  Aligned_cols=72  Identities=17%  Similarity=0.298  Sum_probs=60.5

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAW  368 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~  368 (514)
                      ..|-+.+++|+++.+.|++|.+. +..|++|.+|| ..++.+|.++. .|||.|.++.++.|+.. .+.+|.|+.+
T Consensus       667 ~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~l-evGq~I~vk~ie~d~~g-~~~ls~ralL  740 (760)
T KOG1067|consen  667 EFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLL-EVGQEIQVKYIERDPRG-GIMLSSRALL  740 (760)
T ss_pred             EeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHH-hhcceeEEEEEeecCcc-ceeehhhhhc
Confidence            45778899999999999999995 57999999999 57788998884 89999999999999755 4566666544

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.85  E-value=0.0051  Score=66.31  Aligned_cols=72  Identities=10%  Similarity=0.064  Sum_probs=57.9

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEe----CC-ceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccc
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNV----GA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAI  242 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdI----G~-k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~  242 (514)
                      |.-+.|++|+|+|.+++.++++|++    |. +.+|+||.+|..|.                                  
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            4566899999999999999999998    33 38999999887643                                  


Q ss_pred             cccCCCCCCCCcccCCCEEEEEEEEEcC---C-CcEEEEehHHHH
Q 010232          243 AMSGGSGPGRPVVETGTVLFAEVLGRTL---S-GRPLLSTRRLFR  283 (514)
Q Consensus       243 ~l~~~~~~~~~~~~vGd~V~v~Vl~~d~---~-grliLS~kk~~~  283 (514)
                                ..|++|+.|.|+|..+..   . -+++||+..+..
T Consensus       194 ----------E~y~~Gdrika~i~~V~~~~~kGpqIilSRt~p~l  228 (449)
T PRK12329        194 ----------DNYRANATFKVFLKEVSEGPRRGPQLFVSRANAGL  228 (449)
T ss_pred             ----------CcCCCCCEEEEEEEEeecCCCCCCEEEEEcCCHHH
Confidence                      348999999999999642   2 368899877754

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

Probab=96.84  E-value=0.001  Score=73.03  Aligned_cols=72  Identities=18%  Similarity=0.343  Sum_probs=61.9

Q ss_pred             hccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232          370 TLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (514)
Q Consensus       370 ~~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~  448 (514)
                      +.+++.|.++.|+|.++..||+||+++. .+.||+|.++++..      ..+.+|+.+-|.|..+. +++.|++....+.
T Consensus       117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~-~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~  189 (715)
T COG1107         117 MEDVEAGKYYKGIVSRVEKYGVFVELNS-HVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD  189 (715)
T ss_pred             hhhcccceeeeccccchhhhcceeecCh-hhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence            3479999999999999999999999999 79999999999852      45889999999999987 5578877665544

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

Probab=96.79  E-value=0.0014  Score=76.46  Aligned_cols=76  Identities=21%  Similarity=0.256  Sum_probs=68.2

Q ss_pred             cCCCCceEEEEEEEEecce---EEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecC
Q 010232          372 NLREGTLLEGTVKKIYPYG---AQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADL  447 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~G---aFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l  447 (514)
                      .+..|.+|.++|++|+..-   +-|.+.+ |+.|+||.+++|+..+.+|...+++||+|.++|++++ ++=-+.||+|..
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            5889999999999998765   5678888 9999999999999999999999999999999999998 666788888865


Q ss_pred             c
Q 010232          448 E  448 (514)
Q Consensus       448 ~  448 (514)
                      .
T Consensus      1061 d 1061 (1299)
T KOG1856|consen 1061 D 1061 (1299)
T ss_pred             H
Confidence            4

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

Probab=96.73  E-value=0.0049  Score=59.06  Aligned_cols=35  Identities=20%  Similarity=0.355  Sum_probs=32.7

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccc
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL  329 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~  329 (514)
                      -.|+++.|+|+++++.|++|.+|-+++|||.++|.
T Consensus        80 f~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~  114 (176)
T PTZ00162         80 FKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIP  114 (176)
T ss_pred             CCCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCC
Confidence            38999999999999999999997799999999994

>PRK10811 rne ribonuclease E; Reviewed

Probab=95.83  E-value=0.02  Score=66.62  Aligned_cols=60  Identities=27%  Similarity=0.543  Sum_probs=50.2

Q ss_pred             CCCceEEEEEEEEec--ceEEEEECCCceEEEEEeecccccccc---------CcccccCCCCEEEEEEEEE
Q 010232          374 REGTLLEGTVKKIYP--YGAQIRIGDSNRSGLLHISNMSRTRVT---------SVSDLLNEGERVKVLVVKS  434 (514)
Q Consensus       374 ~~G~iV~G~V~~I~~--~GaFV~I~~~gi~GLvh~Sels~~~v~---------~~~~~~kvGd~VkvkVi~v  434 (514)
                      .+|.||.|+|.+|.+  .++||+|+. |..||+|.+++......         .....+++||.|-|.|.+-
T Consensus        37 ~vGnIYkGkVenIvPGInAAFVDIG~-gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE  107 (1068)
T PRK10811         37 KKANIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE  107 (1068)
T ss_pred             CccceEEEEEecccCCcceeEEEecC-CcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence            589999999999987  689999999 89999999998643321         2345699999999999874

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

Probab=95.80  E-value=0.011  Score=59.41  Aligned_cols=71  Identities=21%  Similarity=0.376  Sum_probs=63.7

Q ss_pred             cCCCEEEEEEEEEECCeEEEEE---CCEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi---~Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      +.+++|-+.|..+..-|++|.+   +.++|+|-+|+|+ +|+++...+- +||..=.|.|++||++++-|-||.|+
T Consensus        15 ev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~kli-rVGr~E~vvVlrVDkekGYIDLSkrr   89 (304)
T KOG2916|consen   15 EVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLI-RVGRNEPVVVLRVDKEKGYIDLSKRR   89 (304)
T ss_pred             CcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHH-hcCCcceEEEEEEcCCCCceechhcc
Confidence            5899999999999999999988   5799999999994 6677777765 89999999999999999999999873

>PRK11712 ribonuclease G; Provisional

Probab=95.58  E-value=0.03  Score=61.69  Aligned_cols=62  Identities=29%  Similarity=0.516  Sum_probs=50.3

Q ss_pred             cCCCCceEEEEEEEEec--ceEEEEECCCceEEEEEeeccccc------------cccCcccccCCCCEEEEEEEEE
Q 010232          372 NLREGTLLEGTVKKIYP--YGAQIRIGDSNRSGLLHISNMSRT------------RVTSVSDLLNEGERVKVLVVKS  434 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~--~GaFV~I~~~gi~GLvh~Sels~~------------~v~~~~~~~kvGd~VkvkVi~v  434 (514)
                      ...+|.++.|+|.+|.|  .+|||+|+. +..||+|.+++...            ....+.+.+++||.|-|.|.+-
T Consensus        35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~-~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke  110 (489)
T PRK11712         35 RGIVGNIYKGRVSRVLPGMQAAFVDIGL-DKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD  110 (489)
T ss_pred             ccccccEEEEEEeecCCCCceeEEeeCC-CccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence            35689999999999988  689999999 89999999997321            1123355699999999999874

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=95.55  E-value=0.035  Score=59.98  Aligned_cols=57  Identities=16%  Similarity=0.202  Sum_probs=45.5

Q ss_pred             cCCCEEEEEEEEEECC--eEEEEEC-CEEEEEecccccc-------------ccCChhhHhhhcCCEEEEEEEE
Q 010232          295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLS-------------RVNNFTELKEKVGRRMYVQITR  352 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~--G~fVdi~-Gi~gFVP~sel~~-------------~i~~~~el~~~VGq~V~vkVl~  352 (514)
                      ..|.++.|+|.++.++  |+||+++ |-.||+|++++..             +..+..+.. .+||.|.|.|.+
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            4899999999999999  9999996 5799999999832             122233333 689999999986

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.

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

Probab=95.36  E-value=0.062  Score=45.33  Aligned_cols=23  Identities=39%  Similarity=0.564  Sum_probs=18.1

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEe
Q 010232          170 PKPGDFVIGVVVSGNENKLDVNV  192 (514)
Q Consensus       170 ik~GdiV~G~Vv~v~~~Gv~VdI  192 (514)
                      +++|++|.|+|+++++..++++|
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            57899999999999999999987

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.

>PRK05054 exoribonuclease II; Provisional

Probab=95.20  E-value=0.071  Score=60.80  Aligned_cols=67  Identities=21%  Similarity=0.346  Sum_probs=51.5

Q ss_pred             CCEEEEEEEEEECCeEEEEEC--CEEEEEecccc-cc--ccC---C------hhhHhhhcCCEEEEEEEEEeCCCCceEe
Q 010232          297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LS--RVN---N------FTELKEKVGRRMYVQITRINEDTNDLIL  362 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel-~~--~i~---~------~~el~~~VGq~V~vkVl~vD~e~~rIiL  362 (514)
                      |+.+.|.|++++++|+||.+.  |+.||||.+.| ..  ...   +      ...-.+.+||+|+|+|.++|..+++|.+
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      0011236899999999999998888866


Q ss_pred             e
Q 010232          363 S  363 (514)
Q Consensus       363 S  363 (514)
                      +
T Consensus       642 ~  642 (644)
T PRK05054        642 R  642 (644)
T ss_pred             E
Confidence            4

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

Probab=95.07  E-value=0.15  Score=49.24  Aligned_cols=105  Identities=15%  Similarity=0.193  Sum_probs=66.3

Q ss_pred             CCCcccCCCEEEEEEEEE-c-CCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEECCE---------
Q 010232          251 GRPVVETGTVLFAEVLGR-T-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGL---------  319 (514)
Q Consensus       251 ~~~~~~vGd~V~v~Vl~~-d-~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~Gi---------  319 (514)
                      +...+..|..|.+-+.+. . ...+.++|.+....      .-...+.|++|.|+|+++....+.|++-++         
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            355677788888877762 2 23344445443322      224457999999999999999999999333         


Q ss_pred             --EEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          320 --RAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       320 --~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                        .|-+|.|+. ....++.++.+ .+|+.|+++|++.-   ..+.||.+
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              456777777 44444444443 66777777776542   34555554

>TIGR02062 RNase_B exoribonuclease II

Probab=94.67  E-value=0.13  Score=58.58  Aligned_cols=67  Identities=27%  Similarity=0.420  Sum_probs=50.6

Q ss_pred             CCEEEEEEEEEECCeEEEEE--CCEEEEEecccccc---cc-CChh--------hHhhhcCCEEEEEEEEEeCCCCceEe
Q 010232          297 NEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAELLS---RV-NNFT--------ELKEKVGRRMYVQITRINEDTNDLIL  362 (514)
Q Consensus       297 GeiV~GkV~~v~~~G~fVdi--~Gi~gFVP~sel~~---~i-~~~~--------el~~~VGq~V~vkVl~vD~e~~rIiL  362 (514)
                      |+...|.|+.++++|+||.+  .|+.||||.+.+..   .. -+..        .-.+.+|++|+|+|.++|..+++|.+
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  37999999998822   11 0100        10246899999999999988888765


Q ss_pred             e
Q 010232          363 S  363 (514)
Q Consensus       363 S  363 (514)
                      .
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.

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

Probab=94.59  E-value=0.18  Score=56.02  Aligned_cols=149  Identities=14%  Similarity=0.181  Sum_probs=95.1

Q ss_pred             cccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccccccc
Q 010232          166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS  245 (514)
Q Consensus       166 ~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~  245 (514)
                      .++++..|.+-.|+|.++...|+||++.....|+|+.+.+..                                      
T Consensus       116 ~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~--------------------------------------  157 (715)
T COG1107         116 TMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGG--------------------------------------  157 (715)
T ss_pred             chhhcccceeeeccccchhhhcceeecChhhhccccccccCC--------------------------------------
Confidence            468999999999999999999999999999999988777631                                      


Q ss_pred             CCCCCCCCcccCCCEEEEEEEEEc-CCCcEEEEehHH------HHHh-----hhhHHHhhhcCCC--EEEEEEEEEEC-C
Q 010232          246 GGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRL------FRKM-----AWHRVRQIKQLNE--PIEVKFTEWNT-G  310 (514)
Q Consensus       246 ~~~~~~~~~~~vGd~V~v~Vl~~d-~~grliLS~kk~------~~~~-----~w~~l~~~~k~Ge--iV~GkV~~v~~-~  310 (514)
                            .+.+.+|+++.+.|..+. ..|.+-+....+      ...+     ....|.+  ..|+  .++|+|+.+.. .
T Consensus       158 ------~~~~~vgdeiiV~v~~vr~~~geidf~~~~~~~Y~~~~~~ke~~r~~i~~id~--~ig~tV~I~GeV~qikqT~  229 (715)
T COG1107         158 ------DPDYAVGDEIIVQVSDVRPEKGEIDFEPVGLDRYREVQVEKELPRTLIDDLDE--MIGKTVRIEGEVTQIKQTS  229 (715)
T ss_pred             ------CCCCCCCCeEEEEeeccCCCCCccceeecCCccchhhhhhhhcccccHHHHHh--hcCceEEEEEEEEEEEEcC
Confidence                  234678999998888754 346653332221      1111     1233433  3555  46788998864 3


Q ss_pred             e-EEEEECCEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEee
Q 010232          311 G-LLTRIEGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILS  363 (514)
Q Consensus       311 G-~fVdi~Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS  363 (514)
                      | -+..+-.=.|++|..-+. .-++-.-++  .+|+.|.+.= .++...+++.+-
T Consensus       230 GPTVFtltDetg~i~aAAFe~aGvRAyP~I--evGdiV~ViG-~V~~r~g~lQiE  281 (715)
T COG1107         230 GPTVFTLTDETGAIWAAAFEEAGVRAYPEI--EVGDIVEVIG-EVTRRDGRLQIE  281 (715)
T ss_pred             CCEEEEEecCCCceehhhhccCCcccCCCC--CCCceEEEEE-EEeecCCcEEEe
Confidence            4 333443346777766552 222222223  4899887643 366677777554

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

Probab=94.50  E-value=0.062  Score=63.27  Aligned_cols=72  Identities=21%  Similarity=0.244  Sum_probs=58.7

Q ss_pred             hcCCCEEEEEEEEEECC--eE-EEEE-CCEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          294 KQLNEPIEVKFTEWNTG--GL-LTRI-EGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~--G~-fVdi-~Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      +..|.+|.++|++++.+  +| -|.+ .|+.||||...++ ..+.+|.... ++|+.|.|+|+++|.++-.+-||.|.
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            46899999999999754  44 3455 4899999999995 4677776665 79999999999999998888888873

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

Probab=93.76  E-value=0.29  Score=46.14  Aligned_cols=61  Identities=15%  Similarity=0.214  Sum_probs=43.8

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccc----cccccC-------cccccCCCCEEEEEEEEEe
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS----RTRVTS-------VSDLLNEGERVKVLVVKSM  435 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels----~~~v~~-------~~~~~kvGd~VkvkVi~vd  435 (514)
                      .-.|++|+|+|+++...|+|+++++  ++-++..-.+.    ...-++       -...+++|.+|+++|+..+
T Consensus        79 pfKGEVvdgvV~~Vnk~G~F~~~GP--l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr  150 (170)
T KOG3298|consen   79 PFKGEVVDGVVTKVNKMGVFARSGP--LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR  150 (170)
T ss_pred             ecCCcEEEEEEEEEeeeeEEEeccc--eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence            4579999999999999999999997  55555332222    111111       1226899999999999875

>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]

Probab=93.61  E-value=0.099  Score=52.60  Aligned_cols=97  Identities=24%  Similarity=0.365  Sum_probs=68.0

Q ss_pred             hhhhhchhc----cccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhcc
Q 010232          157 KVGEDKVSV----EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGK  232 (514)
Q Consensus       157 ~~~~~~~~~----~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~  232 (514)
                      ....|++.+    .-|..+.||+|.|+|+.|....+=||++.+.++.|+.+-+.-                      .|.
T Consensus        66 ~rvNkLi~V~plk~rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNL----------------------PGg  123 (301)
T KOG3013|consen   66 QRVNKLISVKPLKSRYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNL----------------------PGG  123 (301)
T ss_pred             hhhcceEEEeehhhhcCCccCCEEEEEeeeeecceeEEecccccceEEEeecccC----------------------Cch
Confidence            334444443    347899999999999999999999999999999988766521                      011


Q ss_pred             cee-eeccccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHH
Q 010232          233 MGI-VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLF  282 (514)
Q Consensus       233 ~~v-~~~~d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~~  282 (514)
                      +.. -.+.|+..|+.       .++.||.|.+.|-..-.+|-+.|-+|...
T Consensus       124 ~~RRk~~~DEl~MR~-------fl~egDLi~AEVQ~v~~dGs~sLhTRS~K  167 (301)
T KOG3013|consen  124 IQRRKSEEDELQMRS-------FLKEGDLIVAEVQNVFHDGSLSLHTRSLK  167 (301)
T ss_pred             hhhccchhhHHHHHH-------HhhccCeehHHHHHhccCCeEEEEecchh
Confidence            111 12234444543       37899999988876667888887776554

>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=93.56  E-value=0.32  Score=42.63  Aligned_cols=46  Identities=13%  Similarity=0.142  Sum_probs=36.1

Q ss_pred             hhhhhchhccc----cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecc
Q 010232          157 KVGEDKVSVEY----YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTK  203 (514)
Q Consensus       157 ~~~~~~~~~~~----~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~s  203 (514)
                      ..|+.++-.+-    -+ ..|.+|.|+|.++.++-+|||+|.|..++++..
T Consensus         5 ~sFaslLR~S~fi~lG~-~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp   54 (104)
T PF10246_consen    5 ESFASLLRNSPFIQLGD-PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRP   54 (104)
T ss_pred             ccHHHHhcCChhhhcCC-ccCCEEEEEEEEEecCceEEEeCCceeEEEecc
Confidence            45666665542    23 369999999999999999999999999987643

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=93.21  E-value=0.5  Score=45.09  Aligned_cols=73  Identities=19%  Similarity=0.136  Sum_probs=52.8

Q ss_pred             cCCCCceEEEEEEEEecceEEEEEC--------CCceEEEEEeeccccc--cccCcccccCCCCEEEEEEEEEeCCCeEE
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIG--------DSNRSGLLHISNMSRT--RVTSVSDLLNEGERVKVLVVKSMFPDKIS  441 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~--------~~gi~GLvh~Sels~~--~v~~~~~~~kvGd~VkvkVi~vde~~rI~  441 (514)
                      -...|++|.++|..+...=|-|+|-        . ...|+||..++...  .--++-+.|++||.|.|+|++........
T Consensus        65 LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~-~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~  143 (193)
T KOG3409|consen   65 LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKK-SFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYL  143 (193)
T ss_pred             CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhh-hhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEE
Confidence            3467888888888877766666552        3 58999999887542  22345566999999999999866666777


Q ss_pred             EEEe
Q 010232          442 LSIA  445 (514)
Q Consensus       442 LSlK  445 (514)
                      ||.-
T Consensus       144 LTtA  147 (193)
T KOG3409|consen  144 LTTA  147 (193)
T ss_pred             EEEe
Confidence            7773

>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=92.88  E-value=0.3  Score=44.17  Aligned_cols=36  Identities=14%  Similarity=0.079  Sum_probs=31.6

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccc
Q 010232          172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (514)
Q Consensus       172 ~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p  207 (514)
                      +|+++.|+|.+.+..|+.|.+|.=-+.+||...|.+
T Consensus         3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~   38 (122)
T PF08292_consen    3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPE   38 (122)
T ss_dssp             TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-T
T ss_pred             CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCC
Confidence            699999999999999999999988889999988863

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

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=91.20  E-value=0.77  Score=53.03  Aligned_cols=71  Identities=15%  Similarity=0.244  Sum_probs=54.0

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC--CEEEEEecccccc-ccC-Ch---------hhHhhhcCCEEEEEEEEEeCCCCce
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS-RVN-NF---------TELKEKVGRRMYVQITRINEDTNDL  360 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~~-~i~-~~---------~el~~~VGq~V~vkVl~vD~e~~rI  360 (514)
                      ...|+...|.|+++..+|+||.+.  |++|+||.+.+.. ++. +.         ....+.+|+.|+++|.++|...+++
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            369999999999999999999995  4899999999842 211 00         0112368999999999998887777


Q ss_pred             Eeeh
Q 010232          361 ILSE  364 (514)
Q Consensus       361 iLS~  364 (514)
                      .++.
T Consensus       700 ~~~~  703 (706)
T COG0557         700 DFEL  703 (706)
T ss_pred             EEEe
Confidence            6653

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

Probab=90.92  E-value=0.95  Score=43.24  Aligned_cols=75  Identities=23%  Similarity=0.285  Sum_probs=51.5

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEe---CCc-----eeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccc
Q 010232          170 PKPGDFVIGVVVSGNENKLDVNV---GAD-----LLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA  241 (514)
Q Consensus       170 ik~GdiV~G~Vv~v~~~Gv~VdI---G~k-----~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~  241 (514)
                      +..|++|+.+|.+++...+-|+|   |.+     ..|+|+..++-+..            ++                 .
T Consensus        66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tE------------kd-----------------r  116 (193)
T KOG3409|consen   66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATE------------KD-----------------R  116 (193)
T ss_pred             CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccc------------cc-----------------h
Confidence            56899999999999998877765   433     45777776664321            00                 0


Q ss_pred             ccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 010232          242 IAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (514)
Q Consensus       242 ~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk  280 (514)
                      +++       -+-|++||.|.+.|++.......+||+.+
T Consensus       117 v~v-------~ksFrPgDiVlAkVis~~~~~~y~LTtAe  148 (193)
T KOG3409|consen  117 VKV-------YKSFRPGDIVLAKVISLGDGSNYLLTTAE  148 (193)
T ss_pred             hhh-------hhccCCCcEEEEEEeecCCCCcEEEEEec
Confidence            111       23488999999999985555667777654

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

Probab=90.82  E-value=0.36  Score=53.34  Aligned_cols=62  Identities=29%  Similarity=0.453  Sum_probs=52.3

Q ss_pred             cCCCCceEEEEEEEEec--ceEEEEECCCceEEEEEeeccccccccC-----cccccCCCCEEEEEEEEEe
Q 010232          372 NLREGTLLEGTVKKIYP--YGAQIRIGDSNRSGLLHISNMSRTRVTS-----VSDLLNEGERVKVLVVKSM  435 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~--~GaFV~I~~~gi~GLvh~Sels~~~v~~-----~~~~~kvGd~VkvkVi~vd  435 (514)
                      ...+|.++.|+|++|.|  -.+||+|+. +-.||+|.+++.+ +...     +...++.||.+-|.|++-.
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            45689999999999988  578999999 8999999999998 4333     3458999999999998753

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=90.30  E-value=1.6  Score=37.29  Aligned_cols=64  Identities=17%  Similarity=0.160  Sum_probs=50.4

Q ss_pred             eEEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 010232          378 LLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD  446 (514)
Q Consensus       378 iV~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~  446 (514)
                      .++|+|+.+.+.+.| |.+.+ |..-+.|+|-=-.    .-.-.+.+||.|.|.+-..| .++||..-.|.
T Consensus         8 e~~G~V~e~Lp~~~frV~Len-G~~vla~isGKmR----~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~   73 (87)
T PRK12442          8 ELDGIVDEVLPDSRFRVTLEN-GVEVGAYASGRMR----KHRIRILAGDRVTLELSPYDLTKGRINFRHKD   73 (87)
T ss_pred             EEEEEEEEECCCCEEEEEeCC-CCEEEEEecccee----eeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence            589999999999988 68888 8888888875221    11223778999999998777 88999988874

>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=89.68  E-value=1.7  Score=39.41  Aligned_cols=60  Identities=17%  Similarity=0.231  Sum_probs=44.0

Q ss_pred             CCceEEEEEEEEecceEEEEECCCceEEEEEeeccccc-------------cccCcccccCCCCEEEEEEEEEe
Q 010232          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-------------RVTSVSDLLNEGERVKVLVVKSM  435 (514)
Q Consensus       375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~-------------~v~~~~~~~kvGd~VkvkVi~vd  435 (514)
                      +|+++.|+|++-+..|+.|.++= =-+-+||.+.|...             +-.+-.-++..|+.|+.||..+.
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            69999999999999999999975 36778888887522             11344455789999999999764

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

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

Probab=89.67  E-value=1.4  Score=41.67  Aligned_cols=30  Identities=23%  Similarity=0.290  Sum_probs=27.5

Q ss_pred             CCCEEEEEEEEEECCeEEEEECCEEEEEec
Q 010232          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPK  325 (514)
Q Consensus       296 ~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~  325 (514)
                      .|++++|.|+.+++.|+|+++|.++.|+-.
T Consensus        81 KGEVvdgvV~~Vnk~G~F~~~GPl~~f~ss  110 (170)
T KOG3298|consen   81 KGEVVDGVVTKVNKMGVFARSGPLEVFYSS  110 (170)
T ss_pred             CCcEEEEEEEEEeeeeEEEeccceEeeeec
Confidence            899999999999999999999888888763

>PRK10811 rne ribonuclease E; Reviewed

Probab=88.77  E-value=0.82  Score=53.84  Aligned_cols=62  Identities=16%  Similarity=0.233  Sum_probs=45.6

Q ss_pred             CCCEEEEEEEEEECC--eEEEEEC-CEEEEEecccccccc-CC---------hhhHhhhcCCEEEEEEEEEeCCCC
Q 010232          296 LNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLSRV-NN---------FTELKEKVGRRMYVQITRINEDTN  358 (514)
Q Consensus       296 ~GeiV~GkV~~v~~~--G~fVdi~-Gi~gFVP~sel~~~i-~~---------~~el~~~VGq~V~vkVl~vD~e~~  358 (514)
                      .|.|+.|+|.++.++  ++||+|+ |..||+|+++....+ .+         ..... ..||.|.|.|.+-...++
T Consensus        38 vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~L-k~GqeILVQV~KEa~gtK  112 (1068)
T PRK10811         38 KANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVL-REGQEVIVQIDKEERGNK  112 (1068)
T ss_pred             ccceEEEEEecccCCcceeEEEecCCcceEEEhhhcccccccccccccccccccccc-CCCCEEEEEEeecccCCC
Confidence            799999999999985  9999996 579999999883211 11         11111 579999999987443333

>TIGR00008 infA translation initiation factor IF-1

Probab=88.45  E-value=2.5  Score=34.47  Aligned_cols=59  Identities=24%  Similarity=0.266  Sum_probs=44.9

Q ss_pred             eEEEEEEEEecceEE-EEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEE
Q 010232          378 LLEGTVKKIYPYGAQ-IRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKIS  441 (514)
Q Consensus       378 iV~G~V~~I~~~GaF-V~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~  441 (514)
                      .+.|+|+...+.+.| |.+.+ |..-+.|++-=-.    .-.-.+.+||.|.|.+-..+ +++||.
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            588999999999988 68888 8899998876221    11234788999999887666 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).

>PRK11712 ribonuclease G; Provisional

Probab=88.27  E-value=1.3  Score=49.00  Aligned_cols=57  Identities=19%  Similarity=0.364  Sum_probs=43.4

Q ss_pred             cCCCEEEEEEEEEECC--eEEEEEC-CEEEEEeccccccc-------------cCChhhHhhhcCCEEEEEEEE
Q 010232          295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLSR-------------VNNFTELKEKVGRRMYVQITR  352 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~--G~fVdi~-Gi~gFVP~sel~~~-------------i~~~~el~~~VGq~V~vkVl~  352 (514)
                      ..|.++.|+|.++.++  ++||+|| +-.||+|++++...             ..+..++. +.||.+.|.|.+
T Consensus        37 ~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l-~~Gq~iLVQV~K  109 (489)
T PRK11712         37 IVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELV-RQGQDIMVQVVK  109 (489)
T ss_pred             ccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhc-cCCCEEEEEEEe
Confidence            3899999999999986  8999996 58999999987210             11122222 589999998886

>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]

Probab=87.98  E-value=2.7  Score=41.45  Aligned_cols=63  Identities=27%  Similarity=0.513  Sum_probs=47.7

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~  247 (514)
                      |-+.+||.|-|.|+....+...||||....+.||.--+.                                       +.
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            678899999999999999999999998667766543331                                       00


Q ss_pred             CCCCCCcccCCCEEEEEEEEEc
Q 010232          248 SGPGRPVVETGTVLFAEVLGRT  269 (514)
Q Consensus       248 ~~~~~~~~~vGd~V~v~Vl~~d  269 (514)
                      ....++.+++||.|.|+|...+
T Consensus       102 tkrNrPnl~vGdliyakv~~a~  123 (230)
T KOG1004|consen  102 TKRNRPNLQVGDLIYAKVVDAN  123 (230)
T ss_pred             cccCCCccccccEEEEEEEecC
Confidence            1112567899999999998644

>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=86.27  E-value=2.8  Score=36.82  Aligned_cols=54  Identities=15%  Similarity=0.196  Sum_probs=45.8

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEE
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS  434 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~v  434 (514)
                      -..|.+|.|+|.+|...-+||++++ ...+.++......       +.|..|.+|.+++...
T Consensus        21 ~~~gk~V~G~I~hvv~ddLYIDfG~-KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdl   74 (104)
T PF10246_consen   21 DPEGKIVIGKIFHVVDDDLYIDFGG-KFHCVCKRPAVNG-------EKYVRGSRVRLRLKDL   74 (104)
T ss_pred             CccCCEEEEEEEEEecCceEEEeCC-ceeEEEecccccc-------cccccCCEEEEEECCH
Confidence            3589999999999999999999999 7999998777542       4588899999988753

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 [].

>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=83.11  E-value=13  Score=29.26  Aligned_cols=59  Identities=31%  Similarity=0.374  Sum_probs=39.9

Q ss_pred             EEEEEEEEec---ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEE
Q 010232          379 LEGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLS  443 (514)
Q Consensus       379 V~G~V~~I~~---~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LS  443 (514)
                      ..|+|+...+   || |+.-.+.+-+-++|.+++....    -..++.|+.|...+.. .+++-....
T Consensus         1 ~~G~V~~~~~~kgyG-FI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~-~~~g~~A~~   62 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYG-FITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE-GKKGPQAVN   62 (66)
T ss_dssp             EEEEEEEEETTTTEE-EEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE-CTTSEEEEE
T ss_pred             CeEEEEEEECCCCce-EEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE-CCCCCEEEE
Confidence            4799999875   66 5555553558999999998653    2458899999999875 444433333

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 ....

>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=80.41  E-value=5.7  Score=31.71  Aligned_cols=64  Identities=19%  Similarity=0.282  Sum_probs=43.8

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl  444 (514)
                      |+.++-+|..+++.|--+--++ .+.|+.    +...|...-...+.+||++++.|+.|| -+-.+.+||
T Consensus         1 G~~L~LvV~~~~edgsv~fs~g-~v~g~t----v~AtryH~~g~nl~pGqK~kaviLhvD~l~~~VhVSl   65 (65)
T cd05700           1 GDQLKLVVQDVTEDGSVMFSGG-QVSGLT----VLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL   65 (65)
T ss_pred             CceEEEEEeeeccCCcEEEecC-CcCCcE----EEEEEEEecceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence            6778888999888776665555 466662    112222233456889999999999998 566666654

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 Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	514
4aid_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		5e-05
4aim_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		5e-05
4am3_A	717	Crystal Structure Of C. Crescentus Pnpase Bound To		6e-05
2eqs_A	103	Solution Structure Of The S1 Rna Binding Domain Of		1e-04
2cqo_A	119	Solution Structure Of The S1 Rna Binding Domain Of		1e-04
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		2e-04
1sro_A	76	S1 Rna Binding Domain, Nmr, 20 Structures Length =		3e-04
3aev_A	275	Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex		7e-04
1yz6_A	274	Crystal Structure Of Intact Alpha Subunit Of Aif2 F		7e-04

>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E Recognition Peptide Length = 726

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 31/90 (34%), Positives = 49/90 (54%), Gaps = 1/90 (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 FPDKISLSIADLESEPGLFVSDKERVFSEA 465
              K  LS+  ++ E G  +S KE    EA
Sbjct: 697 DRGKTKLSMKVVDQETGEDLSKKEAAAEEA 726

>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E Recognition Peptide Length = 726

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 31/90 (34%), Positives = 49/90 (54%), Gaps = 1/90 (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 FPDKISLSIADLESEPGLFVSDKERVFSEA 465
              K  LS+  ++ E G  +S KE    EA
Sbjct: 697 DRGKTKLSMKVVDQETGEDLSKKEAAAEEA 726

>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna Length = 717

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 31/90 (34%), Positives = 49/90 (54%), Gaps = 1/90 (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 FPDKISLSIADLESEPGLFVSDKERVFSEA 465
              K  LS+  ++ E G  +S KE    EA
Sbjct: 688 DRGKTKLSMKVVDQETGEDLSKKEAAAEEA 717

>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 = 44.7 bits (104), Expect = 1e-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|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|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase Length = 723

Iteration: 1
 Score = 44.3 bits (103), 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|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures Length = 76

Iteration: 1
 Score = 43.5 bits (101), 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|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From Pyrococcus Horikoshii Ot3 Length = 275

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-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

>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 = 7e-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

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	514
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	7e-18
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	1e-15
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	9e-15
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	9e-13
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	2e-12
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	2e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	3e-12
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	7e-12
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	3e-11
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	1e-10
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	2e-10
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	4e-10
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	9e-10
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	1e-08
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	7e-07
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	3e-06
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	6e-06
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	3e-05
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	6e-05

>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 119

 Score = 78.6 bits (194), Expect = 7e-18
 Identities = 24/95 (25%), Positives = 46/95 (48%), Gaps = 3/95 (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---KISLSIADLESEPGLFVSDKERVFSEAEE 467
             +   K+SLS+  +    G  +     +      
Sbjct: 83  MKNDRIKVSLSMKVVNQGTGKDLDPNNVIIESGPS 117

>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 = 71.6 bits (176), Expect = 1e-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 = 70.1 bits (172), Expect = 9e-15
 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

>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

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 68.7 bits (169), Expect = 2e-12
 Identities = 31/91 (34%), Positives = 48/91 (52%), Gaps = 1/91 (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 MFPDKISLSIADLESEPGLFVSDKERVFSEA 465
               K  LS+  ++ E G  +S KE    EA
Sbjct: 696 DDRGKTKLSMKVVDQETGEDLSKKEAAAEEA 726

>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 = 64.8 bits (158), 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

>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 = 68.7 bits (167), Expect = 3e-12
 Identities = 61/447 (13%), Positives = 125/447 (27%), Gaps = 145/447 (32%)

Query: 107 SEVDKKSEK--PDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGEDKVS 164
            E   + +      E+A   F+  F  +D    V++    +    E   +D  +      
Sbjct: 12  GEHQYQYKDILSVFEDA---FVDNFDCKD----VQDMPKSILSKEE---IDHIIMSKDAV 61

Query: 165 VEYYEPKPGDFVIGVVVSGNENKLDVNVGADL------LGTMLTKE------VLPLYDKE 212
                      +   ++S  E  +   V   L      L + +  E      +  +Y ++
Sbjct: 62  SGTL------RLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQ 115

Query: 213 MDFLLCDLKKDAEEFMVRGKMGI--------VKDDDAIAMSGGSGPGRPVVETGTVLFAE 264
            D L  D +  A+  + R +  +        ++    + + G  G G+      T +  +
Sbjct: 116 RDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK------TWVALD 169

Query: 265 VLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE------- 317
           V              ++  K+ W  ++        +E+         LL +I+       
Sbjct: 170 VC------LSYKVQCKMDFKIFWLNLKNCNSPETVLEM---LQK---LLYQIDPNWTSRS 217

Query: 318 --GLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLIL---SEREAWATLN 372
                  L    + + +     LK K                  L+L      +AW   N
Sbjct: 218 DHSSNIKLRIHSIQAELRRL--LKSKPYENCL------------LVLLNVQNAKAWNAFN 263

Query: 373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVV 432
           L    LL  T                             TR   V+D L+      + + 
Sbjct: 264 LSCKILL--T-----------------------------TRFKQVTDFLSAATTTHISLD 292

Query: 433 KSMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLP--AVSVSPK-----S 485
                               L   + + +  +  +      Q LP   ++ +P+     +
Sbjct: 293 ---------------HHSMTLTPDEVKSLLLKYLDCRP---QDLPREVLTTNPRRLSIIA 334

Query: 486 ESLPTDTPPFDSEASMCANWKWFRFEQ 512
           ES+      +D       NWK    ++
Sbjct: 335 ESIRDGLATWD-------NWKHVNCDK 354

>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 = 46.8 bits (110), Expect = 2e-05
 Identities = 77/545 (14%), Positives = 158/545 (28%), Gaps = 171/545 (31%)

Query: 64  KDVFDDLSSAQFPENVENEGLEGNEELE-------LLNKPNLVPISNGVASEVDKKSEKP 116
           KDV D   S    E +++  +  +           LL+K         V   V++   + 
Sbjct: 36  KDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQE-----EMVQKFVEE-VLRI 89

Query: 117 D--------EEEALAPFL---KFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGEDKVSV 165
           +        + E   P +    + + RD      +  ++  VSR          + + ++
Sbjct: 90  NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRL-----QPYLKLRQAL 144

Query: 166 EYYEPKPGDFVI--GVVVSG---------NENKLD---------VNVG----ADLLGTML 201
              E +P   V+  GV+ SG            K+          +N+      + +  ML
Sbjct: 145 --LELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEML 202

Query: 202 TK---EVLPLYDKEMDF-----LLCDLKKDAEEFMVRGKMG----IVKDDDAIAMSGGSG 249
            K   ++ P +    D      L     +     +++ K      +V  +          
Sbjct: 203 QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN---------- 252

Query: 250 PGRPVVETGTVL--FAEVLGRTLSGRPLLSTR--RLFRKMAWHRVRQIKQLNEPIEVKFT 305
                V+       F       LS + LL+TR  ++   ++      I    +   +  T
Sbjct: 253 -----VQNAKAWNAF------NLSCKILLTTRFKQVTDFLSAATTTHISL--DHHSMTLT 299

Query: 306 EWNTGGLLTRIEGLRAF-LPK-------------AELL----SRVNNF------------ 335
                 LL +    R   LP+             AE +    +  +N+            
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTII 359

Query: 336 ----TELKEKVGRRMYVQITRINEDTNDLI-----------LSEREAWATLN-LREGTLL 379
                 L+    R+M+ +++      +  I           + + +    +N L + +L+
Sbjct: 360 ESSLNVLEPAEYRKMFDRLSVFPPSAH--IPTILLSLIWFDVIKSDVMVVVNKLHKYSLV 417

Query: 380 EGTVKK--IYPYGAQIRI-GDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMF 436
           E   K+  I      + +         LH S            +++     K      + 
Sbjct: 418 EKQPKESTISIPSIYLELKVKLENEYALHRS------------IVDHYNIPKTFDSDDLI 465

Query: 437 PDKIS----------LSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSE 486
           P  +           L   +      LF      VF +   + +K R    A + S    
Sbjct: 466 PPYLDQYFYSHIGHHLKNIEHPERMTLF----RMVFLDFRFLEQKIRHDSTAWNASGSIL 521

Query: 487 SLPTD 491
           +    
Sbjct: 522 NTLQQ 526

>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 = 44.1 bits (103), Expect = 1e-04
 Identities = 64/394 (16%), Positives = 129/394 (32%), Gaps = 124/394 (31%)

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-LKFFKPRDSAEEVEEEGSEVGVSRESI 152
                         +D + +  P E     P  L        AE + +     G++    
Sbjct: 308 -----------LKYLDCRPQDLPREVLTTNPRRLSII-----AESIRD-----GLAT--W 344

Query: 153 DVDDKVGEDKV------SVE---------YYEPKPGDFVIGVVVSGNENKL--DVNVGAD 195
           D    V  DK+      S+           ++       +               ++   
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD----RLSV----------FPPSAHIPTI 390

Query: 196 LLGT----MLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI-----VKDDDAIAMSG 246
           LL      ++  +V+ + +K   + L  ++K  +E  +     I     VK ++  A+  
Sbjct: 391 LLSLIWFDVIKSDVMVVVNKLHKYSL--VEKQPKESTIS-IPSIYLELKVKLENEYALH- 446

Query: 247 GSGPGRPVVETGTVL----------------FAEVLGRTLSGRPLLSTRRLFRKM----A 286
                R +V+   +                 F   +G  L          LFR +     
Sbjct: 447 -----RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFR 501

Query: 287 WHRVRQIKQLNEPIEVKFTEWNTGG----LLTRIEGLRAFL----PKAE-LLSRVNNFTE 337
           +        L + I    T WN  G     L +++  + ++    PK E L++ + +F  
Sbjct: 502 F--------LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLP 553

Query: 338 -LKEKVGRRMY---VQITRINEDTNDLILSEREA 367
            ++E +    Y   ++I  + ED      + ++ 
Sbjct: 554 KIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587

>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

>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 = 7e-12
 Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 1/93 (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 MFPDKISLSIADLESEPGLFVSDKERVFSEAEE 467
               +I LSI +   +     + +     + E 
Sbjct: 686 DRQGRIRLSIKEATEQSQPAAAPEAPAAEQGEH 718

>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 = 63.4 bits (154), Expect = 3e-11
 Identities = 26/127 (20%), Positives = 51/127 (40%), Gaps = 4/127 (3%)

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--ISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTD 491
            +  +K  I LS   +  E  +   DK         + +   + L               
Sbjct: 73  -VDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRT 131

Query: 492 TPPFDSE 498
              FD +
Sbjct: 132 AWVFDDK 138

>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 = 61.2 bits (148), Expect = 1e-10
 Identities = 20/125 (16%), Positives = 52/125 (41%), Gaps = 4/125 (3%)

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 SMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTP 493
            +   K ++ ++  +           +   +  +   K  + +       + ++      
Sbjct: 71  -VDRRKGTVDVSLKKVTDDERRKKNLQW--KKIQRLDKILELVSQKLKLSEKDAWEQVAW 127

Query: 494 PFDSE 498
             +++
Sbjct: 128 KLEAK 132

>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 = 60.8 bits (147), Expect = 2e-10
 Identities = 27/104 (25%), Positives = 52/104 (50%), Gaps = 2/104 (1%)

Query: 375 EGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVK 433
           EG  +  TVK+I+ YGA + + +   +   +HIS ++ T V ++ D L EG++V   V++
Sbjct: 11  EGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIR 70

Query: 434 -SMFPDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKL 476
                  I LS+  +  +       + +   +AE + +   +KL
Sbjct: 71  VDPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLRLAAEKL 114

>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 = 4e-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

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80

 Score = 54.2 bits (131), Expect = 9e-10
 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 = 7e-07
 Identities = 31/117 (26%), Positives = 53/117 (45%), Gaps = 3/117 (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-ISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESL 488
           +   P   + LS+  +   PG  V  +           ++ R      S  P + ++
Sbjct: 711 EVDIPRNRVGLSMR-MSDTPGEKVEGQRGGRPTGSGQPRQERGAPRGQSAPPANNAM 766

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

 Score = 49.1 bits (117), Expect = 3e-06
 Identities = 10/110 (9%), Positives = 37/110 (33%), Gaps = 9/110 (8%)

Query: 373  LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-SVSDLLNEGERVKVLV 431
              +G+++   V++ +          S    +++    +  ++    +++   G+      
Sbjct: 903  FFKGSIIPVRVERFWHNDIICTTN-SEVECVVNAQRHAGAQLRRPANEIYEIGKTYPA-K 960

Query: 432  VKSMFPDK--ISLSI--ADLESEPGLFVSDKERVF--SEAEEMAKKYRQK 475
            V  +        +S+   D++ +       K+      + E    +  +K
Sbjct: 961  VIYIDYANITAEVSLLDHDVKQQYVPISYSKDPSIWDLKQELEDAEEERK 1010

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

 Score = 48.3 bits (115), Expect = 6e-06
 Identities = 8/108 (7%), Positives = 38/108 (35%), Gaps = 7/108 (6%)

Query: 373  LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-SVSDLLNEGERVKVLV 431
              +G+++   V++ +          S    +++    +  ++    +++   G+      
Sbjct: 900  FFKGSIIPVRVERFWHNDIICTTN-SEVECVVNAQRHAGAQLRRPANEIYEIGKTYPA-K 957

Query: 432  VKSMFPDK--ISLSI--ADLESEPGLFVSDKERVFSEAEEMAKKYRQK 475
            V  +        +S+   D++ +       K+    + ++  +   ++
Sbjct: 958  VIYIDYANITAEVSLLDHDVKQQYVPISYSKDPSIWDLKQELEDAEEE 1005

>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 = 44.6 bits (105), Expect = 3e-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 = 43.8 bits (103), Expect = 6e-05
 Identities = 23/137 (16%), Positives = 48/137 (35%), Gaps = 16/137 (11%)

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 PGLFVSDKERVFSEAEE 467
                +D + + +  E 
Sbjct: 221 M--LENDAQMILTYLES 235

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	514
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	100.0
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.87
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.71
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.69
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.69
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.64
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.63
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
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.55
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.55
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.54
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.52
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.49
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.39
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.38
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.28
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.26
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.22
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.18
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.18
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.15
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.13
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	99.09
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.08
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	99.08
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.07
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.05
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.05
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.04
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	99.04
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.03
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	99.01
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.0
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.98
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.98
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	98.94
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.93
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.91
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.9
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.85
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.84
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.75
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.67
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.65
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.64
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.62
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.6
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.52
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.45
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.45
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	98.44
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.36
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.36
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.34
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.31
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.28
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.28
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.26
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	98.23
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.18
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	98.17
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.17
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.14
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.14
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	98.13
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	98.11
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.08
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	98.06
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	98.05
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	98.01
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	97.97
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.92
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.85
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.81
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.68
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.56
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.44
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.39
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	97.3
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	97.01
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	96.97
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	96.92
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	96.83
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	96.65
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	96.59
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	96.25
2r7d_A	469	Ribonuclease II family protein; structural genomic	91.13
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	90.26
1jjg_A	102	M156R; beta barrel, S1 motif, OB fold, MYXV156R, N	87.1
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	85.2
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	84.99
4b9x_A	226	TDRD1, tudor domain-containing protein 1; replicat	82.33
1wfq_A	89	UNR protein; beta-barrel, translational regulation	81.45
2k5n_A	74	Putative cold-shock protein; GFT protein structure	81.34

>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=1e-39  Score=329.65  Aligned_cols=243  Identities=14%  Similarity=0.064  Sum_probs=212.1

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCCCCC
Q 010232          171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGP  250 (514)
Q Consensus       171 k~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~~~~  250 (514)
                      .+|++++|+|+++++.|+||+++ +.+|+||.+|+.                                            
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            47999999999999999999997 789999998872                                            


Q ss_pred             CCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEE-CCeEEEEECC--EEEEEeccc
Q 010232          251 GRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN-TGGLLTRIEG--LRAFLPKAE  327 (514)
Q Consensus       251 ~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~-~~G~fVdi~G--i~gFVP~se  327 (514)
                        .  ++||+|+|+|| .|.++|+++|++.+.           ++.|+++.|+|++++ ++|+||+|++  .+||||+++
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-TDMKQKLRLTTLEVT-----------ATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDI  103 (285)
T ss_dssp             --C--CTTSEEEEEEE-ECTTSCEEEECSCCC-----------SCSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGG
T ss_pred             --c--ccCCEEEEEEE-ECCCCCEEEeccccc-----------ccCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHH
Confidence              1  68999999999 688999999987652           469999999999999 7999999974  799999999


Q ss_pred             c-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh-----hhhh--ccCCCCceEEEEEEEEecceEEE-EECCC
Q 010232          328 L-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE-----AWAT--LNLREGTLLEGTVKKIYPYGAQI-RIGDS  398 (514)
Q Consensus       328 l-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~-----~~~~--~~l~~G~iV~G~V~~I~~~GaFV-~I~~~  398 (514)
                      + +.+..     ..++|+++.++ +.+|+ ++||.+|+|.     +|..  ..+++|++|+|+|++++++|+|| .+++ 
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 LPELKEL-----WPKKGDQLYIR-LEVDK-KDRIWGLLAYQEDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYLPEN-  175 (285)
T ss_dssp             SCSSGGG-----SCCTTCEEEEE-EEECT-TSCEEEEECCHHHHHHHCCCCCSCCTTCEEEEEEEEEETTEEEEEETTT-
T ss_pred             CCccccc-----ccCCCCEEEEE-EEECC-CCcEEEEehhhhhcchhhhhhhhCCCCCEEEEEEEEEeCCcEEEEEeCC-
Confidence            9 43221     23699999777 57998 7899999862     4643  47999999999999999999999 9988 


Q ss_pred             ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeC-CCeEEEEEecCcCCCCccccchhhhhhHHHHHHHHHHhhCc
Q 010232          399 NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMF-PDKISLSIADLESEPGLFVSDKERVFSEAEEMAKKYRQKLP  477 (514)
Q Consensus       399 gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde-~~rI~LSlK~l~~~P~~~~~~k~~v~~~ae~~a~~~~~kl~  477 (514)
                      ++.||||+||++        +.+++||+|+|+|+++++ ++||+||+|++...++             ++.|+.+.+.|.
T Consensus       176 g~~Glih~SEl~--------~~l~~Gd~v~~~V~~id~~d~kI~LSlk~~~~~~~-------------~~~a~~il~~L~  234 (285)
T 3go5_A          176 NMLGFIHPSERY--------AEPRLGQVLDARVIGFREVDRTLNLSLKPRSFEML-------------ENDAQMILTYLE  234 (285)
T ss_dssp             TEEEEECGGGCS--------SCCCTTCEEEEEEEEEETTTTEEEEECSCCCCCCC-------------CHHHHHHHHHHH
T ss_pred             CeEEEEEHHHcc--------ccCCCCCEEEEEEEEEECCCCeEEEEeChhhhhcc-------------chHHHHHHHHHH
Confidence            899999999998        469999999999999994 9999999988776554             456788899998


Q ss_pred             cCCCCCcccCCCCCCCCCCCccchhhccceeeeecC
Q 010232          478 AVSVSPKSESLPTDTPPFDSEASMCANWKWFRFEQD  513 (514)
Q Consensus       478 ~~~~g~~~e~~v~~~~pfg~~~~~~~~~~~~~~~~~  513 (514)
                      +.+          |++||+|+|+|++|++.|+|||.
T Consensus       235 ~~~----------G~l~~~DkS~pe~I~~~f~~SK~  260 (285)
T 3go5_A          235 SNG----------GFMTLNDKSSPDDIKATFGISKG  260 (285)
T ss_dssp             HTT----------TEESCCTTSCHHHHHHHHSSCHH
T ss_pred             hcC----------CeeccCCCCCHHHHHHHhCcCHH
Confidence            888          99999999999999999999985

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

Probab=99.87  E-value=5.7e-22  Score=200.11  Aligned_cols=169  Identities=12%  Similarity=0.006  Sum_probs=143.0

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhhhccCC
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLR  374 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~~~~l~  374 (514)
                      ..|++++|+|++++++|+||+++|.+||||.+++..          ++|+++.|.|+ .| ..+|+++|++.+|    ++
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            379999999999999999999999999999999942          39999999998 45 4668899988774    79


Q ss_pred             CCceEEEEEEEEe-cceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC-cCCCC
Q 010232          375 EGTLLEGTVKKIY-PYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL-ESEPG  452 (514)
Q Consensus       375 ~G~iV~G~V~~I~-~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l-~~~P~  452 (514)
                      +|+++.|+|++++ ++||||+++..+++||||.|+++|.+.    ..+++||+|.|+ +.+|.++||.||+|+. ..+||
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 799999997313899999999998654    346899999776 4788778999999876 35666


Q ss_pred             ccccchhhhhhHHHHHHHHHHhhCccCCCCCcccCCCCCCCCCCCcc-chhhc
Q 010232          453 LFVSDKERVFSEAEEMAKKYRQKLPAVSVSPKSESLPTDTPPFDSEA-SMCAN  504 (514)
Q Consensus       453 ~~~~~k~~v~~~ae~~a~~~~~kl~~~~~g~~~e~~v~~~~pfg~~~-~~~~~  504 (514)
                      ....                    ....+|+.++|+|.++.|||+|+ .++..
T Consensus       144 ~~~~--------------------~~~~~G~~V~g~V~~i~~~G~fV~~i~~g  176 (285)
T 3go5_A          144 ARPA--------------------YNNMQNQNWPAIVYRLKLSGTFVYLPENN  176 (285)
T ss_dssp             CCCC--------------------CSCCTTCEEEEEEEEEETTEEEEEETTTT
T ss_pred             hhhh--------------------hhCCCCCEEEEEEEEEeCCcEEEEEeCCC
Confidence            5433                    34567999999999999999999 88654

>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=99.71  E-value=1.2e-17  Score=158.34  Aligned_cols=101  Identities=21%  Similarity=0.266  Sum_probs=80.1

Q ss_pred             CCCCceEEEEEEEEecceEEEEE--CCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcC
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRI--GDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I--~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~  449 (514)
                      +++|+++.|+|++|++||+||+|  .+ |++||||+|+|+|.++.++++.+++||.|+|+|+++| +++||+||+|++.+
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             CCCccccchhhhhhHHHHHHHHHHh
Q 010232          450 EPGLFVSDKERVFSEAEEMAKKYRQ  474 (514)
Q Consensus       450 ~P~~~~~~k~~v~~~ae~~a~~~~~  474 (514)
                      +||..+.++++.++.+......+.+
T Consensus        92 ~p~~~~~~~~~~g~~v~g~v~~i~~  116 (182)
T 1kl9_A           92 EEAIKCEDKFTKSKTVYSILRHVAE  116 (182)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHhccCCCEEEEEEEEchh
Confidence            9999999999887776655554444

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

Probab=99.69  E-value=7.9e-17  Score=141.61  Aligned_cols=92  Identities=28%  Similarity=0.470  Sum_probs=83.4

Q ss_pred             hhhh--ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccc-cccCcccccCCCCEEEEEEEEEe-CCCeEEE
Q 010232          367 AWAT--LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVVKSM-FPDKISL  442 (514)
Q Consensus       367 ~~~~--~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~-~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~L  442 (514)
                      +|..  ..+++|+++.|+|++|++||+||+|++ +++||||+|++++. ++.++.+.|++||.|+|+|++++ +++||.|
T Consensus        20 p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~-~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~rI~l   98 (115)
T 2khi_A           20 HWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEE-GVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRRISL   98 (115)
T ss_dssp             -CCCSSCSSCSSCEEEEEEEEEETTEEEEECST-TCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEETTTTEEEE
T ss_pred             CHHHHhhcCCCCCEEEEEEEEEECCEEEEEECC-CCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEECCCCEEEE
Confidence            4543  378999999999999999999999998 89999999999984 78899999999999999999998 6899999


Q ss_pred             EEecCcCCCCccccchh
Q 010232          443 SIADLESEPGLFVSDKE  459 (514)
Q Consensus       443 SlK~l~~~P~~~~~~k~  459 (514)
                      |+|++.++||+.+.+++
T Consensus        99 slk~~~~~p~~~~~~~~  115 (115)
T 2khi_A           99 GLKQCKANPWQQFAETH  115 (115)
T ss_dssp             CCCCCCSSCCCCCCCCC
T ss_pred             EEEecCcCHHHHHHhhC
Confidence            99999999999987653

>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=99.69  E-value=4.5e-17  Score=153.49  Aligned_cols=98  Identities=21%  Similarity=0.282  Sum_probs=81.4

Q ss_pred             CCCceEEEEEEEEecceEEEEEC--CCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCC
Q 010232          374 REGTLLEGTVKKIYPYGAQIRIG--DSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE  450 (514)
Q Consensus       374 ~~G~iV~G~V~~I~~~GaFV~I~--~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~  450 (514)
                      ++|+++.|+|++|++||+||+|.  + |++||||+|+|+|.++.++++.+++||.|+|+|+++| +++||.||+|++.++
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            59999999999999999999994  5 7999999999999999999999999999999999998 789999999999999


Q ss_pred             CCccccchhhhhhHHHHHHHHH
Q 010232          451 PGLFVSDKERVFSEAEEMAKKY  472 (514)
Q Consensus       451 P~~~~~~k~~v~~~ae~~a~~~  472 (514)
                      ||..+.++++.++.+......+
T Consensus        93 ~~~~~~~~~~~g~~v~g~V~~i  114 (175)
T 2a19_A           93 DIIKCEEKYQKSKTVHSILRYC  114 (175)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHhccCCCcceEEEEEc
Confidence            9999999998877665544333

>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=99.64  E-value=3.7e-16  Score=134.83  Aligned_cols=88  Identities=31%  Similarity=0.483  Sum_probs=79.6

Q ss_pred             hhccCCCCceEEEEEEEEecceEEEEECCC--ceEEEEEeecc-ccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEe
Q 010232          369 ATLNLREGTLLEGTVKKIYPYGAQIRIGDS--NRSGLLHISNM-SRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIA  445 (514)
Q Consensus       369 ~~~~l~~G~iV~G~V~~I~~~GaFV~I~~~--gi~GLvh~Sel-s~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK  445 (514)
                      ....+++|+++.|+|++|++||+||+|++.  +++||||+|++ ++.++.++.+.|++||.|+|+|++++. +||.||+|
T Consensus         6 ~~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~-~~i~LSlk   84 (103)
T 2eqs_A            6 SGEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG-TKTSLSMK   84 (103)
T ss_dssp             CCSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET-TEEEEEST
T ss_pred             ccccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC-CeeEEEEe
Confidence            345789999999999999999999999852  69999999999 677889999999999999999999986 69999999


Q ss_pred             cCcCCCCccccc
Q 010232          446 DLESEPGLFVSD  457 (514)
Q Consensus       446 ~l~~~P~~~~~~  457 (514)
                      ++.++||..+..
T Consensus        85 ~~~~~~~~~~~~   96 (103)
T 2eqs_A           85 DVDQETGEDLNP   96 (103)
T ss_dssp             TBCTTTCCBCCS
T ss_pred             ecccCCchhcCc
Confidence            999999998754

>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=99.63  E-value=4.1e-16  Score=138.12  Aligned_cols=86  Identities=28%  Similarity=0.376  Sum_probs=78.8

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CC--CeEEEEEecCc
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP--DKISLSIADLE  448 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~--~rI~LSlK~l~  448 (514)
                      .+++|+++.|+|++|++||+||+|.+.+++||||+|++++.++.++.+.|++||.|+|+|++++ ++  +||.||+|++.
T Consensus        19 ~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~~~~i~LSlk~~~   98 (119)
T 2cqo_A           19 LPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVN   98 (119)
T ss_dssp             SCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECSSCEEEEEESTTBC
T ss_pred             ccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEeccccCceEEEEEeecc
Confidence            6899999999999999999999996523699999999999999999999999999999999998 33  69999999999


Q ss_pred             CCCCccccc
Q 010232          449 SEPGLFVSD  457 (514)
Q Consensus       449 ~~P~~~~~~  457 (514)
                      ++||+.+..
T Consensus        99 ~~~~~~~~~  107 (119)
T 2cqo_A           99 QGTGKDLDP  107 (119)
T ss_dssp             SSSCCBSCT
T ss_pred             cCCccccCc
Confidence            999998753

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

Probab=99.62  E-value=8.1e-16  Score=138.12  Aligned_cols=81  Identities=30%  Similarity=0.489  Sum_probs=77.8

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcCC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLESE  450 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~~  450 (514)
                      .+++|++|.|+|++|++||+||+|++ ++.||||+|++++.++.++.+.|++||.|+|+|++++ ++++|.||+|++.++
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            68999999999999999999999988 8999999999999999999999999999999999998 589999999999999


Q ss_pred             CCc
Q 010232          451 PGL  453 (514)
Q Consensus       451 P~~  453 (514)
                      |+.
T Consensus        83 p~~   85 (130)
T 2k4k_A           83 PEK   85 (130)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            986

>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=1.2e-15  Score=128.29  Aligned_cols=77  Identities=23%  Similarity=0.235  Sum_probs=71.3

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCC-ceEEEEEee-ccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHIS-NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~S-els~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~  448 (514)
                      ..++|+++.|+|+ |++||+||+|.+. +++||+|+| +++++++.++++.+ +||+|+|+|+++| +++||.||+|++.
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            5689999999999 9999999999742 699999999 99999999999999 9999999999998 6899999999987


Q ss_pred             CC
Q 010232          449 SE  450 (514)
Q Consensus       449 ~~  450 (514)
                      ++
T Consensus        86 ~~   87 (88)
T 1luz_A           86 RH   87 (88)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=1.5e-14  Score=118.96  Aligned_cols=73  Identities=27%  Similarity=0.456  Sum_probs=67.1

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~  449 (514)
                      ++++|+++.|+|+++++||+||+|++ +++||+|+|++++.++    +.|++||.|+|+|++++ +++||.||+|++.+
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~~-~~~Gllh~sel~~~~~----~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~~~~   75 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLNE-QVRGLLRPRDMISLRL----ENLNVGDEIIVQAIDVRPEKREIDFKYIPLEH   75 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEET-TEEEEECGGGCSSCCG----GGCCTTCEEEEEEEEEETTTTEEEEEECSCC-
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECC-CCEEEEEHHHCCcccc----eeeCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            47899999999999999999999998 8999999999998776    78999999999999998 56999999998875

>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=99.55  E-value=4.8e-17  Score=154.15  Aligned_cols=118  Identities=12%  Similarity=0.227  Sum_probs=96.7

Q ss_pred             cCCCEEEEEEEEEECCeEEEEE---CCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----  366 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi---~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----  366 (514)
                      +.|+++.|+|+++.++|+||++   +|++||||.|+| +.++.++.+.. .+||.|.|+|+++|+++++|.||+|.    
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   679999999999 67888887765 89999999999999999999999995    


Q ss_pred             hhhh--ccCCCCceEEEEEEEEec-ceEEEEECCCceEEEEEeeccccc-cccC
Q 010232          367 AWAT--LNLREGTLLEGTVKKIYP-YGAQIRIGDSNRSGLLHISNMSRT-RVTS  416 (514)
Q Consensus       367 ~~~~--~~l~~G~iV~G~V~~I~~-~GaFV~I~~~gi~GLvh~Sels~~-~v~~  416 (514)
                      +|..  ..+..|+.+.|+|+++++ ||  |.|.+ |++||+|+|+++|. ++.+
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            4643  378999999999999998 99  78888 89999999998875 3455

>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=99.55  E-value=6.8e-15  Score=149.74  Aligned_cols=92  Identities=24%  Similarity=0.287  Sum_probs=84.5

Q ss_pred             cCCCCceEEEEEEEEecceEEEEEC--CCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIG--DSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~--~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~  448 (514)
                      .+++|+++.|+|++|++||+||+|+  + +++||||+|+++|.++.++.+.|++||.|+|+|+++| +++||.||+|++.
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            4679999999999999999999997  5 7999999999999999999999999999999999998 6899999999999


Q ss_pred             CCCCccccchhhhhhH
Q 010232          449 SEPGLFVSDKERVFSE  464 (514)
Q Consensus       449 ~~P~~~~~~k~~v~~~  464 (514)
                      ++||..+.++++.++.
T Consensus        89 ~~p~~~~~~~~~~G~~  104 (308)
T 1q8k_A           89 PEEAIKCEDKFTKSKT  104 (308)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             cChHHHHHHHccCCCe
Confidence            9999887777666544

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

Probab=99.54  E-value=1.2e-14  Score=145.83  Aligned_cols=97  Identities=26%  Similarity=0.406  Sum_probs=86.3

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECC-CceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGD-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~-~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~  449 (514)
                      ..++|++|.|+|++|++||+||+|++ .|++||||+|+++++++.++.+.+++||.|.|+|+++| ++++|.||+|++.+
T Consensus         8 ~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~~~   87 (275)
T 3aev_A            8 YPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQ   87 (275)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESTTCCH
T ss_pred             CCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEEeecCc
Confidence            35699999999999999999999983 17999999999999999999999999999999999999 68999999999999


Q ss_pred             CCCccccchhhhhhHHHHH
Q 010232          450 EPGLFVSDKERVFSEAEEM  468 (514)
Q Consensus       450 ~P~~~~~~k~~v~~~ae~~  468 (514)
                      +||....+++..++.+...
T Consensus        88 ~~~~~~~~~~~~g~~v~g~  106 (275)
T 3aev_A           88 QQRKAKLQEFKRAQKAENL  106 (275)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHhccCCCeEEEE
Confidence            9998877777665554333

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

Probab=99.52  E-value=1.4e-14  Score=125.92  Aligned_cols=82  Identities=24%  Similarity=0.356  Sum_probs=75.5

Q ss_pred             hhhh--ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEE
Q 010232          367 AWAT--LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLS  443 (514)
Q Consensus       367 ~~~~--~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LS  443 (514)
                      +|+.  ..+++|++|.|+|++|+++|+||+|++ +++||||++++++.++.++.+.|++||.|+|+|++++ +.+||.||
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            5654  379999999999999999999999998 8999999999999999999999999999999999998 56799999


Q ss_pred             EecCcC
Q 010232          444 IADLES  449 (514)
Q Consensus       444 lK~l~~  449 (514)
                      +|++.+
T Consensus       100 ~k~~~~  105 (109)
T 2khj_A          100 VRAKDE  105 (109)
T ss_dssp             TTSSSS
T ss_pred             EeecCh
Confidence            998764

>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=99.49  E-value=1.2e-14  Score=145.34  Aligned_cols=102  Identities=19%  Similarity=0.287  Sum_probs=90.2

Q ss_pred             ccCCCCceEEEEEEEEecceEEEEEC--CCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecC
Q 010232          371 LNLREGTLLEGTVKKIYPYGAQIRIG--DSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADL  447 (514)
Q Consensus       371 ~~l~~G~iV~G~V~~I~~~GaFV~I~--~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l  447 (514)
                      ..+++|+++.|+|++|++||+||+|+  + ++.||||+|+++++++.++.+.+++||.|.|+|++++ ++++|.||+|++
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             cCCCCccccchhhhhhHHHHHHHHHH
Q 010232          448 ESEPGLFVSDKERVFSEAEEMAKKYR  473 (514)
Q Consensus       448 ~~~P~~~~~~k~~v~~~ae~~a~~~~  473 (514)
                      .++||..+.+++...+.+......+.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~iv~~la  111 (266)
T 3cw2_C           86 TDDERRKKNLQWKKIQRLDKILELVS  111 (266)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhhHHHHHHhccccCccceeeeehh
Confidence            99999998888877665444443333

>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=99.39  E-value=5.5e-15  Score=165.99  Aligned_cols=131  Identities=21%  Similarity=0.231  Sum_probs=50.5

Q ss_pred             EEEEE--EECCeEEEEECCEEEEEeccccc-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhhhccCCCCce
Q 010232          302 VKFTE--WNTGGLLTRIEGLRAFLPKAELL-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTL  378 (514)
Q Consensus       302 GkV~~--v~~~G~fVdi~Gi~gFVP~sel~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~~~~l~~G~i  378 (514)
                      |++++  ..+.|++|++++ +|.++++... ...+...+       .+..           +  .  .+   ..+++|++
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            45555  456899999975 8999988873 22221100       0000           0  0  01   35899999


Q ss_pred             EEEEEEEEecceEEEEECCCceEEEEEeecc----ccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCCCCcc
Q 010232          379 LEGTVKKIYPYGAQIRIGDSNRSGLLHISNM----SRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEPGLF  454 (514)
Q Consensus       379 V~G~V~~I~~~GaFV~I~~~gi~GLvh~Sel----s~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~P~~~  454 (514)
                      +.|+|++|++||+||+|.+ |++||||+|+|    +|+|+.++.+.|++||+|+|+|+++|.++||.||+|++.++||..
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            9999999999999999988 89999999999    999999999999999999999999988899999999999999998


Q ss_pred             ccchh
Q 010232          455 VSDKE  459 (514)
Q Consensus       455 ~~~k~  459 (514)
                      ...++
T Consensus       750 ~~~~~  754 (757)
T 1e3p_A          750 EKKDD  754 (757)
T ss_dssp             -----
T ss_pred             hhhcc
Confidence            76655

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

Probab=99.38  E-value=3.4e-14  Score=158.62  Aligned_cols=90  Identities=32%  Similarity=0.441  Sum_probs=0.0

Q ss_pred             ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCC
Q 010232          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESE  450 (514)
Q Consensus       371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~  450 (514)
                      ..+++|++|.|+|++|++||+||+|.+ |++||||+|+++|+|+.++.+.|++||.|+|+|+++|.++||.||+|++.++
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            378999999999999999999999998 8999999999999999999999999999999999998889999999999999


Q ss_pred             CCccccchhhh
Q 010232          451 PGLFVSDKERV  461 (514)
Q Consensus       451 P~~~~~~k~~v  461 (514)
                      ||..+.++..+
T Consensus       712 ~G~~~~~k~~~  722 (726)
T 4aid_A          712 TGEDLSKKEAA  722 (726)
T ss_dssp             -----------
T ss_pred             cchhhhhhhhh
Confidence            99999877654

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

Probab=99.28  E-value=3.2e-13  Score=151.20  Aligned_cols=91  Identities=29%  Similarity=0.463  Sum_probs=0.0

Q ss_pred             ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCC
Q 010232          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESE  450 (514)
Q Consensus       371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~  450 (514)
                      ..+++|+++.|+|++|++||+||+|.+ |++||||+|+++|+|+.++.+.|++||.|+|+|+++|.++||.||+|++.++
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            368999999999999999999999988 8999999999999999999999999999999999998889999999999999


Q ss_pred             CCccccchhhhh
Q 010232          451 PGLFVSDKERVF  462 (514)
Q Consensus       451 P~~~~~~k~~v~  462 (514)
                      ||..+......+
T Consensus       702 ~g~~~~p~~~~~  713 (723)
T 3cdi_A          702 SQPAAAPEAPAA  713 (723)
T ss_dssp             ------------
T ss_pred             CCcccCccccch
Confidence            999876555443

>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=99.26  E-value=5.7e-13  Score=125.43  Aligned_cols=96  Identities=13%  Similarity=0.284  Sum_probs=80.1

Q ss_pred             cCCCEEEEEEEEEECCeEEEEE---CCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----  366 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi---~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----  366 (514)
                      +.|+++.|+|+++.++|+||++   +|++||||.|+| +.++.++.+.. .+||.|.|+|+++|+++++|.||+|.    
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 67777777764 89999999999999999999999995    


Q ss_pred             hhhh--ccCCCCceEEEEEEEEe-cceE
Q 010232          367 AWAT--LNLREGTLLEGTVKKIY-PYGA  391 (514)
Q Consensus       367 ~~~~--~~l~~G~iV~G~V~~I~-~~Ga  391 (514)
                      +|..  ..+..|+.+.|+|++++ ++|+
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            4553  37899999999999998 7887

>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=1.4e-11  Score=108.62  Aligned_cols=78  Identities=26%  Similarity=0.313  Sum_probs=64.6

Q ss_pred             ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeecc-ccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNM-SRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (514)
Q Consensus       371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sel-s~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~  448 (514)
                      .++++|+++.|+|++|++||+||+|+..++.||+|.++. +|.++.++.+.|++||.|+|+|++++ +++||.||+|+..
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            478999999999999999999999983156666555553 24456688999999999999999998 6789999998654

>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=99.18  E-value=3.4e-11  Score=113.92  Aligned_cols=81  Identities=23%  Similarity=0.354  Sum_probs=70.6

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccccc-----------CcccccCCCCEEEEEEEEEe-CC--
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT-----------SVSDLLNEGERVKVLVVKSM-FP--  437 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~-----------~~~~~~kvGd~VkvkVi~vd-e~--  437 (514)
                      ..++|+++.|+|++++++|+||+|++  ++||+|+|++++.++.           ++.+.|++||.|+|+|++++ ++  
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            46899999999999999999999974  8999999999988875           78899999999999999998 43  


Q ss_pred             ---CeEEEEEecCcCCCCcc
Q 010232          438 ---DKISLSIADLESEPGLF  454 (514)
Q Consensus       438 ---~rI~LSlK~l~~~P~~~  454 (514)
                         +||.||+|+...-|+..
T Consensus       156 p~~~~I~lS~k~~~LG~~~w  175 (187)
T 1go3_E          156 KRGSKIALTMRQPYLGKLEW  175 (187)
T ss_dssp             ---CEEEEECCSTTCEEHHH
T ss_pred             CCccEEEEEEcCCCCCcHHH
Confidence               49999999865544433

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

Probab=99.18  E-value=2.7e-11  Score=105.11  Aligned_cols=88  Identities=17%  Similarity=0.231  Sum_probs=73.2

Q ss_pred             ehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeC
Q 010232          278 TRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINE  355 (514)
Q Consensus       278 ~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~  355 (514)
                      .|+. ....|+.+...++.|+++.|+|+++.++|+||+++ |++||||.+++ +.++.++.+.. .+||.|.|+|+++|+
T Consensus        14 iKq~-~~~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~~-~vGd~V~v~V~~vd~   91 (109)
T 2khj_A           14 LVPR-GSHMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVL-SVGDEVEAKFTGVDR   91 (109)
T ss_dssp             --------CHHHHTTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSSSGGGSC-CTTCEEEEEEEEEET
T ss_pred             hhhc-ccCHHHHHhhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccccChhhcc-CCCCEEEEEEEEEEC
Confidence            3443 35689999888999999999999999999999997 79999999999 56666666653 799999999999999


Q ss_pred             CCCceEeehhhh
Q 010232          356 DTNDLILSEREA  367 (514)
Q Consensus       356 e~~rIiLS~K~~  367 (514)
                      ++++|.||+|..
T Consensus        92 ~~~ki~LS~k~~  103 (109)
T 2khj_A           92 KNRAISLSVRAK  103 (109)
T ss_dssp             TTTEEEEETTSS
T ss_pred             CCCEEEEEEeec
Confidence            999999999864

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

Probab=99.15  E-value=4.3e-11  Score=140.02  Aligned_cols=77  Identities=8%  Similarity=0.119  Sum_probs=73.0

Q ss_pred             ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccc-ccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR-VTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (514)
Q Consensus       371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~-v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~  448 (514)
                      ..+++|++|.|+|++|++||+||+|+. |++||||+|+|++.+ +.+|.+.|++||.|+|+|+++| +++||.||||...
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            478999999999999999999999988 899999999999998 8999999999999999999999 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=99.13  E-value=3.6e-12  Score=129.76  Aligned_cols=99  Identities=13%  Similarity=0.256  Sum_probs=88.1

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC---CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----  366 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~---Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----  366 (514)
                      +.|+++.|+|+++.++|+||+++   |++||||.+++ +.++.++.+.. ++||.|.|+|+++|+++++|.||+|.    
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 67777777765 89999999999999999999999984    


Q ss_pred             hhhh--ccCCCCceEEEEEEEEec-ceEEEE
Q 010232          367 AWAT--LNLREGTLLEGTVKKIYP-YGAQIR  394 (514)
Q Consensus       367 ~~~~--~~l~~G~iV~G~V~~I~~-~GaFV~  394 (514)
                      +|..  ..+++|+++.|+|+++.+ ||+|++
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            5653  378999999999999999 699753

>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=99.09  E-value=3.7e-11  Score=135.47  Aligned_cols=76  Identities=32%  Similarity=0.530  Sum_probs=72.2

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~  448 (514)
                      ++++|+++.|+|++|++||+||+|+. +++||||+|+|++.++.++.+.|++||.|+|+|+++| ++++|.||||...
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 7999999999999999999999999999999999999 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=99.08  E-value=2.2e-10  Score=110.66  Aligned_cols=77  Identities=17%  Similarity=0.127  Sum_probs=69.0

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECC-------CceEEEEEeecccccccc--CcccccCCCCEEEEEEEEEeC-CCeEE
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGD-------SNRSGLLHISNMSRTRVT--SVSDLLNEGERVKVLVVKSMF-PDKIS  441 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~-------~gi~GLvh~Sels~~~v~--~~~~~~kvGd~VkvkVi~vde-~~rI~  441 (514)
                      .+++|++|.|+|++|+++|+||+|.+       .++.|+||+|++++.++.  ++.+.|++||.|+|+|+++++ .+++.
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            58999999999999999999999851       157999999999999988  999999999999999999975 45899


Q ss_pred             EEEecCc
Q 010232          442 LSIADLE  448 (514)
Q Consensus       442 LSlK~l~  448 (514)
                      ||+|+..
T Consensus       158 LS~k~~~  164 (209)
T 2nn6_I          158 LTTAENE  164 (209)
T ss_dssp             EECCSSS
T ss_pred             EEEecCC
Confidence            9998754

>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=99.08  E-value=2e-10  Score=108.04  Aligned_cols=75  Identities=21%  Similarity=0.413  Sum_probs=65.7

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc-----------cCcccccCCCCEEEEEEEEEe-C---
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-F---  436 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v-----------~~~~~~~kvGd~VkvkVi~vd-e---  436 (514)
                      ...+|++++|+|++++++|+||++++  .+||+|+|++.++++           ++..+.+++||.|+|||+.++ +   
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            47899999999999999999999984  799999999999877           577889999999999999997 2   


Q ss_pred             -CCeEEEEEecCc
Q 010232          437 -PDKISLSIADLE  448 (514)
Q Consensus       437 -~~rI~LSlK~l~  448 (514)
                       ..||.||||+.-
T Consensus       156 ~~~rI~ls~k~~g  168 (180)
T 4ayb_E          156 RLPRIALTMRQPY  168 (180)
T ss_dssp             ---CEEEECCSTT
T ss_pred             ccCcEEEEcCCCC
Confidence             348999999743

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

Probab=99.07  E-value=1.9e-10  Score=96.39  Aligned_cols=70  Identities=13%  Similarity=0.225  Sum_probs=63.0

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC---CEEEEEecc-cc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKA-EL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~---Gi~gFVP~s-el-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      +.|+++.|+|+ +.++|+||+++   |++||||.| ++ +.++.++++..  +||+++|+|+++|.++++|.||+|+.
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   699999999 99 56666677765  99999999999999999999999853

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

Probab=99.05  E-value=8.3e-10  Score=98.87  Aligned_cols=76  Identities=20%  Similarity=0.246  Sum_probs=67.4

Q ss_pred             hhcCCCEEEEEEEEEECCeEEEEE-CCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh
Q 010232          293 IKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA  369 (514)
Q Consensus       293 ~~k~GeiV~GkV~~v~~~G~fVdi-~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~  369 (514)
                      .++.|+++.|+|+++.++|+||++ +|++||||.+++ +.++.++.+.. .+||.|.|+|+++|.++++|.||+|....
T Consensus         4 ~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~~~~~~~~-~vGd~V~vkV~~vd~~~~kI~LSlk~~~~   81 (130)
T 2k4k_A            4 KFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHL-SVGDEVQVKVLAVDEEKGKISLSIRATQA   81 (130)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCCSCGGGTC-CTTCEEEEEEEEEETTTTEEEEESHHHHH
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccccCccccC-CCCCEEEEEEEEEeCCCCEEEEEEeeccc
Confidence            357999999999999999999999 579999999999 56677776654 89999999999999999999999997643

>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=99.05  E-value=1.7e-10  Score=101.90  Aligned_cols=81  Identities=15%  Similarity=0.241  Sum_probs=69.9

Q ss_pred             hhhHHHhhhcCCCEEEEEEEEEECCeEEEEECCE--EEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCC--Cce
Q 010232          286 AWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGL--RAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDT--NDL  360 (514)
Q Consensus       286 ~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~Gi--~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~--~rI  360 (514)
                      .|+.+....+.|+++.|+|+++.++|+||+++|+  +||||.+++ +.++.++.+.. .+||.|.|+|+++|..+  ++|
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            4566666678999999999999999999999764  999999999 66777777764 89999999999999764  699


Q ss_pred             Eeehhhh
Q 010232          361 ILSEREA  367 (514)
Q Consensus       361 iLS~K~~  367 (514)
                      .||+|..
T Consensus        91 ~LSlk~~   97 (119)
T 2cqo_A           91 SLSMKVV   97 (119)
T ss_dssp             EEESTTB
T ss_pred             EEEEeec
Confidence            9999964

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

Probab=99.04  E-value=3.1e-10  Score=99.43  Aligned_cols=82  Identities=16%  Similarity=0.276  Sum_probs=69.7

Q ss_pred             HhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-c-cccCChhhHhhhcCCEEEEEEEEEeCCCCce
Q 010232          284 KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-L-SRVNNFTELKEKVGRRMYVQITRINEDTNDL  360 (514)
Q Consensus       284 ~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rI  360 (514)
                      ...|..+...++.|+++.|+|+++.++|+||+++ |++||||.+++ + .+..++.+.. .+||.|.|+|+++|.++++|
T Consensus        18 ~~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~-~vGd~V~vkV~~vd~~~~rI   96 (115)
T 2khi_A           18 GSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVV-NVGDVVEVMVLDIDEERRRI   96 (115)
T ss_dssp             ---CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTTC-CTTCEEEEEEEEEETTTTEE
T ss_pred             cCCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccEE-CCCCEEEEEEEEEECCCCEE
Confidence            4588887778899999999999999999999996 79999999999 3 2555555543 79999999999999999999


Q ss_pred             Eeehhh
Q 010232          361 ILSERE  366 (514)
Q Consensus       361 iLS~K~  366 (514)
                      .||+|.
T Consensus        97 ~lslk~  102 (115)
T 2khi_A           97 SLGLKQ  102 (115)
T ss_dssp             EECCCC
T ss_pred             EEEEEe
Confidence            999985

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

Probab=99.04  E-value=2.2e-11  Score=140.51  Aligned_cols=78  Identities=8%  Similarity=0.113  Sum_probs=0.0

Q ss_pred             ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccc-ccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR-VTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (514)
Q Consensus       371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~-v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~  448 (514)
                      ..+++|++|.|+|++|++||+||+|++ |++||||+|+|++.+ +.+|.+.|++||.|+|+|++|| +++||.||||...
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            378999999999999999999999988 899999999999998 8999999999999999999998 8899999999765


Q ss_pred             C
Q 010232          449 S  449 (514)
Q Consensus       449 ~  449 (514)
                      .
T Consensus       980 l  980 (1030)
T 3psf_A          980 V  980 (1030)
T ss_dssp             -
T ss_pred             h
Confidence            3

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

Probab=99.03  E-value=9.9e-10  Score=90.03  Aligned_cols=69  Identities=13%  Similarity=0.175  Sum_probs=60.6

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      ++.|+++.|+|+++.++|+||+++ +++||||.+++ +.++   +.  ..+||.+.|+|+++|+++++|.||+++.
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 79999999999 4433   22  2699999999999999999999999864

>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=5.3e-10  Score=105.45  Aligned_cols=72  Identities=25%  Similarity=0.359  Sum_probs=65.9

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCC---------ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDS---------NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL  442 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~---------gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~L  442 (514)
                      ..+ |++|.|+|++|+++|+||+|...         ++.|+||+|++++.++.++.+.|++||.|.|+|++    +++.|
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 99999999999999999999751         58999999999999999999999999999999996    89999


Q ss_pred             EEecCc
Q 010232          443 SIADLE  448 (514)
Q Consensus       443 SlK~l~  448 (514)
                      |+|+..
T Consensus       130 S~k~~~  135 (179)
T 3m7n_A          130 STKEEE  135 (179)
T ss_dssp             ECCSTT
T ss_pred             EEecCC
Confidence            998743

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

Probab=99.00  E-value=6.7e-11  Score=118.69  Aligned_cols=99  Identities=16%  Similarity=0.272  Sum_probs=87.2

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC---CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh----
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE----  366 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~---Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~----  366 (514)
                      +.|+++.|+|+++.++|+||+++   |++||||.|++ +.++.++.+.. .+||.|.|+|+++|+++++|.||+|.    
T Consensus        10 ~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~-kvGd~V~vkVi~vD~~~~~I~LSlk~~~~~   88 (275)
T 3aev_A           10 EEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYL-KEGQKVVAKVIRVDPRKGHIDLSLRRVTQQ   88 (275)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTC-CTTCEEEEEEEEEETTTTEEEEESTTCCHH
T ss_pred             CCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhcc-CCCCEEEEEEEEEECCCCEEEEEEeecCcc
Confidence            58999999999999999999995   79999999999 67777777764 89999999999999999999999985    


Q ss_pred             hhhh--ccCCCCceEEEEEEEEe-cceEEEE
Q 010232          367 AWAT--LNLREGTLLEGTVKKIY-PYGAQIR  394 (514)
Q Consensus       367 ~~~~--~~l~~G~iV~G~V~~I~-~~GaFV~  394 (514)
                      +|..  ..+..|+.+.|+|..+. ++|++++
T Consensus        89 ~~~~~~~~~~~g~~v~g~v~~v~~~~G~~~e  119 (275)
T 3aev_A           89 QRKAKLQEFKRAQKAENLLRLAAEKLGKDFE  119 (275)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTCCHH
T ss_pred             hhHHHHHhccCCCeEEEEEEEchhhcCCCHH
Confidence            3542  36889999999999999 8888655

>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=98.98  E-value=6.1e-10  Score=109.33  Aligned_cols=75  Identities=16%  Similarity=0.186  Sum_probs=68.4

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccc----cccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT----RVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~----~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l  447 (514)
                      .+++|++|.|+|++++++|+||+|+. ...|+||++++++.    +..++.+.|++||.|.|+|+++++++++.||+|+.
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            57999999999999999999999997 79999999999873    45788899999999999999998777999999864

>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=98.98  E-value=1e-09  Score=106.45  Aligned_cols=86  Identities=15%  Similarity=0.169  Sum_probs=66.5

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcc----------cccCCCCEEEEEEEEEe-CC---
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVS----------DLLNEGERVKVLVVKSM-FP---  437 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~----------~~~kvGd~VkvkVi~vd-e~---  437 (514)
                      ..++|++++|+|+++++||+||+|+.  .+||||+|+|++.+..++.          +.+++||.|+|+|++++ +.   
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            35899999999999999999999985  8999999999866543333          66999999999999998 54   


Q ss_pred             CeEEEEEecCcCCCCccccchhh
Q 010232          438 DKISLSIADLESEPGLFVSDKER  460 (514)
Q Consensus       438 ~rI~LSlK~l~~~P~~~~~~k~~  460 (514)
                      .+|. |||+.-.-||...+.+.+
T Consensus       158 ~~Ig-Smk~~~LG~~~~~~~~~~  179 (215)
T 2b8k_G          158 HAIG-SIKEDYLGAISHEKRRWK  179 (215)
T ss_dssp             EEEE-ECCSTTCEEC--------
T ss_pred             EEEE-EcCCCCCCCcchhhHHHH
Confidence            3778 999877777776555443

>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=98.94  E-value=3.1e-09  Score=91.36  Aligned_cols=72  Identities=19%  Similarity=0.261  Sum_probs=63.0

Q ss_pred             hhcCCCEEEEEEEEEECCeEEEEEC----CEEEEEecccc-c-cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          293 IKQLNEPIEVKFTEWNTGGLLTRIE----GLRAFLPKAEL-L-SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       293 ~~k~GeiV~GkV~~v~~~G~fVdi~----Gi~gFVP~sel-~-~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      ..+.|+++.|+|+++.++|+||+++    +++||||.+++ + .++.++.+.. .+||.|.|+|+++|.  ++|.||+|.
T Consensus         9 ~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~-~~Gd~V~VkV~~vd~--~~i~LSlk~   85 (103)
T 2eqs_A            9 EPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVV-SKGQRVKVKVLSFTG--TKTSLSMKD   85 (103)
T ss_dssp             SCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHC-CTTCEEEEEEEEEET--TEEEEESTT
T ss_pred             cCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEe-CCCCEEEEEEEEEEC--CeeEEEEee
Confidence            3579999999999999999999997    79999999999 4 4566776654 899999999999997  599999996


Q ss_pred             h
Q 010232          367 A  367 (514)
Q Consensus       367 ~  367 (514)
                      .
T Consensus        86 ~   86 (103)
T 2eqs_A           86 V   86 (103)
T ss_dssp             B
T ss_pred             c
Confidence            4

>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=98.93  E-value=1.3e-09  Score=108.01  Aligned_cols=75  Identities=17%  Similarity=0.162  Sum_probs=70.0

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc---cCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV---TSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v---~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l  447 (514)
                      ..++|++|.|+|++++++|+||+|+. ...|+||++++++.++   .++++.|++||.|.|+|+++++++++.||+|+.
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            47999999999999999999999997 6999999999998887   889999999999999999998778999999865

>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=98.91  E-value=3.2e-09  Score=99.10  Aligned_cols=71  Identities=14%  Similarity=0.242  Sum_probs=58.6

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCc------------ccccCCCCEEEEEEEEEe-CCC-
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSV------------SDLLNEGERVKVLVVKSM-FPD-  438 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~------------~~~~kvGd~VkvkVi~vd-e~~-  438 (514)
                      ..+|++++|+|++++++|+||+++.  .+||||+|+|++.+..++            ...+++||.|+|+|++++ +.+ 
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            4799999999999999999999974  679999999986533222            457999999999999998 544 


Q ss_pred             --eEEEEEec
Q 010232          439 --KISLSIAD  446 (514)
Q Consensus       439 --rI~LSlK~  446 (514)
                        ++. |||+
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

>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=98.90  E-value=4e-09  Score=98.53  Aligned_cols=72  Identities=18%  Similarity=0.279  Sum_probs=58.8

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCc----------ccccCCCCEEEEEEEEEe-CC---
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSV----------SDLLNEGERVKVLVVKSM-FP---  437 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~----------~~~~kvGd~VkvkVi~vd-e~---  437 (514)
                      ...+|++++|+|+++++||+||++++  .+||||+|+|++.+..++          ++.+++||.|+|+|++++ +.   
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            35799999999999999999999985  899999999986543222          267999999999999998 54   


Q ss_pred             CeEEEEEec
Q 010232          438 DKISLSIAD  446 (514)
Q Consensus       438 ~rI~LSlK~  446 (514)
                      .+|. |||+
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            3555 6654

>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=98.85  E-value=6.4e-09  Score=101.72  Aligned_cols=76  Identities=16%  Similarity=0.223  Sum_probs=69.7

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccc-cccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCc
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLE  448 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~-~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~  448 (514)
                      ..++|++|.|+|++++++|+||+|+. ...|+||+++++.. +..++++.|++||.|.|+|+++++++++.||+|+..
T Consensus        54 ~p~~GDiV~G~V~~v~~~~a~V~I~~-~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~~~  130 (229)
T 2ba0_A           54 TPSVGDVVIGIIREVAANGWAVDIYS-PYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRI  130 (229)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSS-SSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCSSS
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCC-CeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECCCCcEEEEEcccc
Confidence            47999999999999999999999997 68999999999974 678899999999999999999987789999998653

>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=98.84  E-value=9e-10  Score=113.47  Aligned_cols=182  Identities=16%  Similarity=0.159  Sum_probs=113.6

Q ss_pred             CcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhh----hHHHhhhc--CCCEEEEEEEEEECCeEEEEECCEEEEEecc
Q 010232          253 PVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAW----HRVRQIKQ--LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKA  326 (514)
Q Consensus       253 ~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w----~~l~~~~k--~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~s  326 (514)
                      +.+.+||.+.+.|...+...+.+.+.|+...++..    +.+.+.++  .|++++|+|.+++++|++|++++++|+||.+
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            34789999999987555443344555655433222    12233333  8999999999999999999999999999999


Q ss_pred             ccccccCChhhHhhhcCCEEEEEEEEEeCCCC--ceEeehhhhhh---hccCC-----------------CCceEEEEEE
Q 010232          327 ELLSRVNNFTELKEKVGRRMYVQITRINEDTN--DLILSEREAWA---TLNLR-----------------EGTLLEGTVK  384 (514)
Q Consensus       327 el~~~i~~~~el~~~VGq~V~vkVl~vD~e~~--rIiLS~K~~~~---~~~l~-----------------~G~iV~G~V~  384 (514)
                      ++..     .+. +.+|++++|+|++++++++  +|.||++.+-.   ...++                 +|..-+--|.
T Consensus       165 E~ip-----~E~-~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p~~lk~LfelEVPEI~dG~VeI~~iaRepG~R~KiAV~  238 (344)
T 1hh2_P          165 EWIP-----GEE-IKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVIGLMKLEIPEVENGIVEIKAIAREPGVRTKVAVA  238 (344)
T ss_dssp             GSCT-----TCC-CCTTCEEEEEEEEEEEETTEEEEEEESSSHHHHHHHHHHHCHHHHHSSEEEEEEEEETTTEEEEEEE
T ss_pred             HcCC-----CcC-CCCCCEEEEEEEEEEcCCCCcEEEEEeeccHHHHHHHHhhcccceeeeEEEEEeecccccccceeEE
Confidence            9942     121 2699999999999997554  89999985410   01233                 3444444444


Q ss_pred             E----EecceEEEEECCCceEEEEEeeccccc------cccCcc----cccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232          385 K----IYPYGAQIRIGDSNRSGLLHISNMSRT------RVTSVS----DLLNEGERVKVLVVKSM-FPDKISLSI  444 (514)
Q Consensus       385 ~----I~~~GaFV~I~~~gi~GLvh~Sels~~------~v~~~~----~~~kvGd~VkvkVi~vd-e~~rI~LSl  444 (514)
                      +    |.|.|+.|-..+.  +.-...++|...      |-.+|.    ..+.+-+.+.+.|.  + +.+.+.+..
T Consensus       239 s~d~~iDpvGacvg~~G~--ri~~i~~el~ge~Idii~~s~d~~~fi~nal~Pa~v~~v~~~--d~~~~~~~v~v  309 (344)
T 1hh2_P          239 SNDPNVDPIGACIGEGGS--RIAAILKELKGEKLDVLKWSDDPKQLIANALAPATVIEVEIL--DKENKAARVLV  309 (344)
T ss_dssp             ESSTTSCHHHHHHCTTST--THHHHHHHTTTCEEEEEECCSSHHHHHHHHTCSSCCSEEEEE--ETTTTEEEEEE
T ss_pred             ccCCCccccceeeccCCc--EeHHHHHHhCCCeeeEEecCCCHHHHHHHhcCccEEEEEEEE--cCCCCEEEEEE
Confidence            3    6678888766543  222222333221      112332    33666666666553  4 445555555

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

Probab=98.75  E-value=4.4e-09  Score=98.42  Aligned_cols=71  Identities=13%  Similarity=0.178  Sum_probs=59.9

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCc----------ccccCCCCEEEEEEEEEe-CC---
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSV----------SDLLNEGERVKVLVVKSM-FP---  437 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~----------~~~~kvGd~VkvkVi~vd-e~---  437 (514)
                      ...+|++++|+|++++++|+||+++.  ++||||+|+|++.+..++          ...+++||+|+|+|++++ +.   
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            46899999999999999999999985  689999999986655444          568999999999999998 54   


Q ss_pred             CeEEEEEe
Q 010232          438 DKISLSIA  445 (514)
Q Consensus       438 ~rI~LSlK  445 (514)
                      .+|. |||
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            3566 665

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

Probab=98.67  E-value=3.7e-08  Score=84.48  Aligned_cols=83  Identities=20%  Similarity=0.247  Sum_probs=64.0

Q ss_pred             cCCCEEEEEEEEEE---CCeEEEEE--CCEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhh
Q 010232          295 QLNEPIEVKFTEWN---TGGLLTRI--EGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWA  369 (514)
Q Consensus       295 k~GeiV~GkV~~v~---~~G~fVdi--~Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~  369 (514)
                      +.++.++|+|+..+   .+| |+.-  +|.++|+|++.+...           |-                        .
T Consensus        12 ~~~~~~~G~Vk~fn~~kGfG-FI~~~~gg~dvfvH~s~l~~~-----------~~------------------------~   55 (101)
T 2bh8_A           12 LQSGKMTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAGSSG-----------AA------------------------V   55 (101)
T ss_dssp             ----CEEEEEEEEEGGGTEE-EEEESSSSCEEEEECCCSCSS-----------SC------------------------C
T ss_pred             cccccceeEEEEEECCCCCE-EEEeCCCCcEEEEEEEEEecC-----------Cc------------------------c
Confidence            35678899999996   368 5544  358999999999311           10                        0


Q ss_pred             hccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc
Q 010232          370 TLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV  414 (514)
Q Consensus       370 ~~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v  414 (514)
                      ...+++|++|++.|..+++||+||+|.+ +++||||+|+|+|.++
T Consensus        56 ~~~l~~Ge~V~g~V~~i~~fG~fv~l~~-~~eGlvhis~i~~~~~   99 (101)
T 2bh8_A           56 RGNPQQGDRVEGKIKSITDFGIFIGLDG-GIDGLVHLSDISWAQA   99 (101)
T ss_dssp             CCCCCTTCEEEEEEEECCSEEEEECTTS-CEEEEEEEEEEEECCC
T ss_pred             ccCCCCCCEEEEEEEEeCCcEEEEEcCC-CceEEEEHHHCccCcC
Confidence            1257999999999999999999999987 7999999999998765

>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=98.65  E-value=6.5e-08  Score=99.64  Aligned_cols=96  Identities=20%  Similarity=0.205  Sum_probs=74.7

Q ss_pred             hcCCEEEEEEEEEeCCCCceEeehhhhhh-------------hccCCCCceEEEEEEEEecceEEEEECCCceEEEEEee
Q 010232          341 KVGRRMYVQITRINEDTNDLILSEREAWA-------------TLNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHIS  407 (514)
Q Consensus       341 ~VGq~V~vkVl~vD~e~~rIiLS~K~~~~-------------~~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~S  407 (514)
                      .+|+.+.+.|...|.. ++.+.+.|+.+.             ....+.|++|+|+|.+++++|+||+++  +.+|+||.+
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            5999999999876643 334444454321             113448999999999999999999997  699999999


Q ss_pred             ccccccccCcccccCCCCEEEEEEEEEe-CCC--eEEEEEe
Q 010232          408 NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD--KISLSIA  445 (514)
Q Consensus       408 els~~~v~~~~~~~kvGd~VkvkVi~vd-e~~--rI~LSlK  445 (514)
                      +++      |.+.|++||+|+|+|++++ +++  +|.||.+
T Consensus       165 E~i------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt  199 (344)
T 1hh2_P          165 EWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRR  199 (344)
T ss_dssp             GSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESS
T ss_pred             HcC------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEee
Confidence            997      5688999999999999997 444  5556553

>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=98.64  E-value=1.8e-08  Score=88.50  Aligned_cols=74  Identities=22%  Similarity=0.245  Sum_probs=60.6

Q ss_pred             hhcCCCEEEEEEEEEECCeEEEEEC--CEEEEEeccccc--cccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          293 IKQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL--SRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       293 ~~k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~--~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      .++.|+++.|+|+++.++|+||+++  +..||+|.+++.  .++.++.+.. .+||.|+|+|+++|.++++|.||+|+.
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  588888887762  2222333332 799999999999999999999999853

>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=98.62  E-value=2e-08  Score=100.33  Aligned_cols=72  Identities=22%  Similarity=0.334  Sum_probs=65.8

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEE---CCEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi---~Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      .+.|+++.|+|+++.++|+||++   +|++||||.|++ +.++.++.+.. .+||.|.|+|+++|+++++|.||+|.
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            46899999999999999999999   479999999999 67788887765 89999999999999999999999984

>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=98.60  E-value=1.8e-08  Score=95.08  Aligned_cols=73  Identities=16%  Similarity=0.242  Sum_probs=60.8

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccC-----------ChhhHhhhcCCEEEEEEEEEeCCCC---
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVN-----------NFTELKEKVGRRMYVQITRINEDTN---  358 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~-----------~~~el~~~VGq~V~vkVl~vD~e~~---  358 (514)
                      ...|+++.|+|++++++|+||++++++||+|.+++ +.++.           ++.+. ..+|+.|+|+|+++|...+   
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            46999999999999999999999889999999999 44432           33333 3799999999999998755   


Q ss_pred             --ceEeehhhh
Q 010232          359 --DLILSEREA  367 (514)
Q Consensus       359 --rIiLS~K~~  367 (514)
                        +|.||+|.+
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=98.52  E-value=1.2e-08  Score=114.13  Aligned_cols=99  Identities=11%  Similarity=0.038  Sum_probs=3.5

Q ss_pred             EcCCCcEEEE-ehHHHH---HhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhh
Q 010232          268 RTLSGRPLLS-TRRLFR---KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEK  341 (514)
Q Consensus       268 ~d~~grliLS-~kk~~~---~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~  341 (514)
                      ++.+|++.++ ..+...   ...|+.+...++.|+++.|+|+++.++|+||++. |++||||+|++ +.++.++.+.. +
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            4467777443 323222   2457777777899999999999999999999995 79999999999 67888887765 8


Q ss_pred             cCCEEEEEEEEEeCCCCceEeehhhhh
Q 010232          342 VGRRMYVQITRINEDTNDLILSEREAW  368 (514)
Q Consensus       342 VGq~V~vkVl~vD~e~~rIiLS~K~~~  368 (514)
                      +||.|+|+|+++|+ +++|.||+|...
T Consensus       684 vGD~V~VkVi~iD~-~grI~LS~K~~~  709 (726)
T 4aid_A          684 EGQMVKVKLLGFDD-RGKTKLSMKVVD  709 (726)
T ss_dssp             ---------------------------
T ss_pred             CCCEEEEEEEEECC-CCcEEEEEeecc
Confidence            99999999999998 789999999754

>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=98.45  E-value=7.4e-08  Score=90.41  Aligned_cols=73  Identities=8%  Similarity=0.213  Sum_probs=58.9

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEECCEEEEEecccc-cccc-----------CChhhHhhhcCCEEEEEEEEEeCC----C
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRV-----------NNFTELKEKVGRRMYVQITRINED----T  357 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i-----------~~~~el~~~VGq~V~vkVl~vD~e----~  357 (514)
                      ...|+++.|+|++++++|+||++++++||+|.+++ +.++           ++.... ..+|+.|+|+|+++|.+    .
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            46999999999999999999999889999999999 4433           122222 37999999999999864    3


Q ss_pred             CceEeehhhh
Q 010232          358 NDLILSEREA  367 (514)
Q Consensus       358 ~rIiLS~K~~  367 (514)
                      .+|.||+|++
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

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

Probab=98.45  E-value=2.2e-08  Score=112.26  Aligned_cols=98  Identities=15%  Similarity=0.158  Sum_probs=0.0

Q ss_pred             EcCCCcEEEEehHHH----HHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhh
Q 010232          268 RTLSGRPLLSTRRLF----RKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEK  341 (514)
Q Consensus       268 ~d~~grliLS~kk~~----~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~  341 (514)
                      ++.+|.+.++.....    ....++.+....+.|+++.|+|+++.++|+||++. |++||||.|++ +.++.++.+.. +
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            445777766543322    12345566667789999999999999999999995 79999999999 67787777764 8


Q ss_pred             cCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          342 VGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       342 VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      +||+|+|+|+++|+ +++|.||+|..
T Consensus       674 vGd~V~VkVi~vd~-~grI~LS~k~~  698 (723)
T 3cdi_A          674 MGQEVPVKVLEVDR-QGRIRLSIKEA  698 (723)
T ss_dssp             --------------------------
T ss_pred             CCCEEEEEEEEECC-CCcEEEEEEec
Confidence            99999999999998 89999999964

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

Probab=98.44  E-value=2.2e-07  Score=109.07  Aligned_cols=74  Identities=8%  Similarity=0.076  Sum_probs=66.5

Q ss_pred             hhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccc-cCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          292 QIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSR-VNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       292 ~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~-i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      +.++.|+++.|+|+++.++|+||+++ |++|+||+|+| +.+ +.++.+.. .+||.|+|+|++||.++++|.||+|.
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            44689999999999999999999996 79999999999 555 57777765 89999999999999999999999984

>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=98.36  E-value=4.8e-07  Score=87.25  Aligned_cols=73  Identities=11%  Similarity=0.210  Sum_probs=63.3

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC---------CEEEEEecccc-ccccC--ChhhHhhhcCCEEEEEEEEEeCCCCceE
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE---------GLRAFLPKAEL-LSRVN--NFTELKEKVGRRMYVQITRINEDTNDLI  361 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~---------Gi~gFVP~sel-~~~i~--~~~el~~~VGq~V~vkVl~vD~e~~rIi  361 (514)
                      .+.|++|.|+|+++.++|+||+|.         +++|+||.+++ +.+..  ++.+.+ .+|+.|.|+|+++++.++++.
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            479999999999999999999984         56899999999 45555  666664 899999999999998878999


Q ss_pred             eehhhh
Q 010232          362 LSEREA  367 (514)
Q Consensus       362 LS~K~~  367 (514)
                      ||.|..
T Consensus       158 LS~k~~  163 (209)
T 2nn6_I          158 LTTAEN  163 (209)
T ss_dssp             EECCSS
T ss_pred             EEEecC
Confidence            999864

>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=98.36  E-value=8.8e-07  Score=98.50  Aligned_cols=73  Identities=11%  Similarity=0.136  Sum_probs=62.3

Q ss_pred             cCCCCc--eEEEEEEEEecceEEEEECCCceEEEEEeecccc--ccc----------cCcccccCCCCEEEEEEEEEe-C
Q 010232          372 NLREGT--LLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSR--TRV----------TSVSDLLNEGERVKVLVVKSM-F  436 (514)
Q Consensus       372 ~l~~G~--iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~--~~v----------~~~~~~~kvGd~VkvkVi~vd-e  436 (514)
                      .-++|+  +++|+|++|+++|+||.|.+.|++||||+|+|++  ++.          .+....|++||+|+|+|+++| +
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  9999999999999999995448999999999973  221          144577999999999999998 7


Q ss_pred             CCeEEEEE
Q 010232          437 PDKISLSI  444 (514)
Q Consensus       437 ~~rI~LSl  444 (514)
                      +++|.+++
T Consensus       635 ~~~I~~~l  642 (644)
T 2id0_A          635 TRSIIARP  642 (644)
T ss_dssp             TTEEEEEE
T ss_pred             CCEEEEEE
Confidence            89999997

>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=98.34  E-value=2.3e-07  Score=104.87  Aligned_cols=72  Identities=19%  Similarity=0.129  Sum_probs=65.7

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      ++.|+++.|+|+++.++|+||+++ +++||||+|+| +.++.++.+.. .+||.|+|+|+++|.++++|.||+|.
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 58999999999 66677787765 89999999999999999999999983

>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=98.31  E-value=2.2e-06  Score=83.69  Aligned_cols=76  Identities=22%  Similarity=0.323  Sum_probs=63.0

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~  247 (514)
                      |.+++||+|.|+|+.+.+++++|+|+....|+||.+++....         + .++                        
T Consensus        53 y~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~~---------~-~~~------------------------   98 (229)
T 2ba0_A           53 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMK---------P-NKK------------------------   98 (229)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCC---------T-TSC------------------------
T ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHccccc---------c-ccc------------------------
Confidence            678999999999999999999999999899999999985210         0 000                        


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 010232          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (514)
Q Consensus       248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk  280 (514)
                         -.+.+++||.|.|+|++.+.++++.||++.
T Consensus        99 ---~~~~l~~GD~V~arVi~v~~~~~i~LS~r~  128 (229)
T 2ba0_A           99 ---PNEVLDIGDAIIAKVLNIDPKMKVTLTMKD  128 (229)
T ss_dssp             ---GGGTCCTTCEEEEEEEEECTTCCEEEECCS
T ss_pred             ---hhcccCCCCEEEEEEEEECCCCcEEEEEcc
Confidence               134589999999999999888999999864

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

Probab=98.28  E-value=1.6e-06  Score=83.20  Aligned_cols=61  Identities=11%  Similarity=0.135  Sum_probs=54.3

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc-------------------cCcccccCCCCEEEEEEEE
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-------------------TSVSDLLNEGERVKVLVVK  433 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v-------------------~~~~~~~kvGd~VkvkVi~  433 (514)
                      ..+|++++|+|++++++|+||+++  .++|++|++++.+++.                   ++....+++||.|++||++
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            589999999999999999999995  4899999999987654                   4556789999999999999


Q ss_pred             Ee
Q 010232          434 SM  435 (514)
Q Consensus       434 vd  435 (514)
                      ++
T Consensus       157 v~  158 (203)
T 3ayh_B          157 ED  158 (203)
T ss_dssp             EE
T ss_pred             EE
Confidence            87

>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=98.28  E-value=2e-06  Score=84.21  Aligned_cols=78  Identities=21%  Similarity=0.333  Sum_probs=62.9

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~  247 (514)
                      |.+++||+|.|+|+++.+++++|+||.+.+|+||.+++....            ..+               +.      
T Consensus        62 y~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~~------------~~~---------------~~------  108 (235)
T 2z0s_A           62 YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRP------------FNP---------------AV------  108 (235)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSC------------CCT---------------TT------
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCc------------ccc---------------ch------
Confidence            689999999999999999999999999999999999984210            000               00      


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEeh
Q 010232          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTR  279 (514)
Q Consensus       248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~k  279 (514)
                       .+-...+++||.|.|+|++.+.++++.||++
T Consensus       109 -~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k  139 (235)
T 2z0s_A          109 -DDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQ  139 (235)
T ss_dssp             -TCCTTSSCTTCEEEEEEEEECTTSCEEEECC
T ss_pred             -hhHhhcCCCCCEEEEEEEEECCCCcEEEEEe
Confidence             0113568999999999999888889999976

>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=98.26  E-value=1.5e-06  Score=86.07  Aligned_cols=79  Identities=23%  Similarity=0.262  Sum_probs=63.7

Q ss_pred             ccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccC
Q 010232          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (514)
Q Consensus       167 ~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~  246 (514)
                      -|.+++||+|.|+|+++.+++++|+++...+|+||.+++....            .++               +      
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            4789999999999999999999999999999999999984210            000               0      


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 010232          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (514)
Q Consensus       247 ~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk  280 (514)
                        .+-...+++||.|.|+|++.+.++++.||++.
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              01135689999999999998888899999864

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

Probab=98.23  E-value=1.4e-07  Score=109.19  Aligned_cols=75  Identities=8%  Similarity=0.071  Sum_probs=0.0

Q ss_pred             hhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccc-cCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          292 QIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSR-VNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       292 ~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~-i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      +.++.|+++.|+|+++.++|+||+++ |++|+||.|+| +.+ +.++.+.. .+||.|+|+|++||.++++|.||+|..
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            34679999999999999999999996 79999999999 555 57777765 899999999999999999999999853

>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=3.2e-06  Score=91.41  Aligned_cols=74  Identities=23%  Similarity=0.398  Sum_probs=62.1

Q ss_pred             cCCCCceEEEEEEEEecc--eEEEEECCCceEEEEEeeccccccc---------cCcccccCCCCEEEEEEEEEe-CCCe
Q 010232          372 NLREGTLLEGTVKKIYPY--GAQIRIGDSNRSGLLHISNMSRTRV---------TSVSDLLNEGERVKVLVVKSM-FPDK  439 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~--GaFV~I~~~gi~GLvh~Sels~~~v---------~~~~~~~kvGd~VkvkVi~vd-e~~r  439 (514)
                      ...+|.++.|+|++|.|+  ||||+|+. |..||+|++++++.++         .++.+.+++||.|.|+|++.. ..+.
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            467999999999999999  99999998 8999999999988764         346688999999999999865 4455


Q ss_pred             EEEEEec
Q 010232          440 ISLSIAD  446 (514)
Q Consensus       440 I~LSlK~  446 (514)
                      -.||..-
T Consensus       121 a~lTt~i  127 (517)
T 2bx2_L          121 AALTTFI  127 (517)
T ss_dssp             CEEESSC
T ss_pred             ceEEeeE
Confidence            5555543

>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=98.17  E-value=5.6e-06  Score=81.60  Aligned_cols=76  Identities=22%  Similarity=0.215  Sum_probs=63.0

Q ss_pred             CCCCCCEEEEEEEE----EeCCeEEEEeCC---ceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccc
Q 010232          169 EPKPGDFVIGVVVS----GNENKLDVNVGA---DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA  241 (514)
Q Consensus       169 ~ik~GdiV~G~Vv~----v~~~Gv~VdIG~---k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~  241 (514)
                      .=+.|++|+|+|.+    ++++.++||+|.   +.+|+||.+|+.|.                                 
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   69999999998642                                 


Q ss_pred             ccccCCCCCCCCcccCCCEEEEEEEEEcC---CCcEEEEehHHHHHhhhh
Q 010232          242 IAMSGGSGPGRPVVETGTVLFAEVLGRTL---SGRPLLSTRRLFRKMAWH  288 (514)
Q Consensus       242 ~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~---~grliLS~kk~~~~~~w~  288 (514)
                                 ..|++||.|+|+|++++.   .++++||+..+.....|-
T Consensus        51 -----------E~~~~GDrIkayV~~V~~~~~gpqIiLSRt~p~lvk~Lf   89 (251)
T 2asb_A           51 -----------ESYEHGNRLRCYVVGVTRGAREPLITLSRTHPNLVRKLF   89 (251)
T ss_dssp             -----------CCCCTTCEEEEEEEEEECCSSSCEEEEESSCHHHHHHHH
T ss_pred             -----------ccCCCCCEEEEEEEEEEcCCCCCEEEEEeccHHHHHHHH
Confidence                       348999999999999643   478999999887655543

>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=98.17  E-value=2.7e-06  Score=79.15  Aligned_cols=72  Identities=21%  Similarity=0.220  Sum_probs=55.0

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccccc-----cCCh-------hhHhhhcCCEEEEEEEEEeCCCC--ce
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR-----VNNF-------TELKEKVGRRMYVQITRINEDTN--DL  360 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~~~-----i~~~-------~el~~~VGq~V~vkVl~vD~e~~--rI  360 (514)
                      ..|++++|+|++++++|+||+++..+||||.++|...     ..++       ......+|+.|+|+|+++|.+.+  ..
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            5899999999999999999999888999999998422     1110       01123699999999999997755  23


Q ss_pred             Eeehhh
Q 010232          361 ILSERE  366 (514)
Q Consensus       361 iLS~K~  366 (514)
                      +.|+|.
T Consensus       160 igsm~~  165 (172)
T 2c35_B          160 IGSLMD  165 (172)
T ss_dssp             EEECCS
T ss_pred             EEEecC
Confidence            446664

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

Probab=98.14  E-value=4.8e-06  Score=78.30  Aligned_cols=66  Identities=12%  Similarity=0.118  Sum_probs=58.2

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC-----------CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEe
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE-----------GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLIL  362 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~-----------Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiL  362 (514)
                      + |++|.|+|+++.++|+||+|.           +++|+||.+++ +.+..++.+.+ .+||.|.|+|++     +++.|
T Consensus        57 ~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~-~~GD~V~akVi~-----~~i~L  129 (179)
T 3m7n_A           57 K-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAV-GYLDILKARVIG-----DNLRL  129 (179)
T ss_dssp             T-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTC-CTTCEEEEEEEE-----TTTEE
T ss_pred             C-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcC-CCCCEEEEEEEC-----CeEEE
Confidence            6 999999999999999999994           68999999999 56666777765 899999999996     78999


Q ss_pred             ehhhh
Q 010232          363 SEREA  367 (514)
Q Consensus       363 S~K~~  367 (514)
                      |.|..
T Consensus       130 S~k~~  134 (179)
T 3m7n_A          130 STKEE  134 (179)
T ss_dssp             ECCST
T ss_pred             EEecC
Confidence            99864

>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=98.14  E-value=4.8e-06  Score=77.55  Aligned_cols=71  Identities=15%  Similarity=0.186  Sum_probs=54.6

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccccc-cCCh----------hhHhhhcCCEEEEEEEEEeCCCC--ceE
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR-VNNF----------TELKEKVGRRMYVQITRINEDTN--DLI  361 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~~~-i~~~----------~el~~~VGq~V~vkVl~vD~e~~--rIi  361 (514)
                      ..|++++|+|++++++|+||+++..+||||.|+|..+ .-++          ++. ..+|+.|+|+|+++|.+.+  ..+
T Consensus        82 ~~Gev~~G~V~~v~~fG~FV~l~~~dglvhis~l~~~~~~d~~~~~~~~~~~~~~-~~~Gd~V~vkV~~vd~~~~~~~~i  160 (171)
T 1y14_B           82 FKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDV-ITIKSRIRVKIEGCISQVSSIHAI  160 (171)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTCEECC-----CEECSSCE-ECTTCEEEEEEEEEEEETTEEEEE
T ss_pred             CCCCEEEEEEEEEecCEEEEEecCeEEEEEHHHCCCCceECcccCceEEeccceE-ECCCCEEEEEEEEEEcCCCCcEEE
Confidence            5999999999999999999999779999999999422 1111          122 3789999999999997664  233


Q ss_pred             eehhh
Q 010232          362 LSERE  366 (514)
Q Consensus       362 LS~K~  366 (514)
                      .|++.
T Consensus       161 gsm~~  165 (171)
T 1y14_B          161 GSIKE  165 (171)
T ss_dssp             EECCS
T ss_pred             EEcCC
Confidence            35554

>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=98.13  E-value=6.6e-08  Score=108.88  Aligned_cols=98  Identities=17%  Similarity=0.188  Sum_probs=41.4

Q ss_pred             EcCCCcEEEEehHHHH-Hh---hhhHHH--hhhcCCCEEEEEEEEEECCeEEEEE-CCEEEEEecccc-----ccccCCh
Q 010232          268 RTLSGRPLLSTRRLFR-KM---AWHRVR--QIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-----LSRVNNF  335 (514)
Q Consensus       268 ~d~~grliLS~kk~~~-~~---~w~~l~--~~~k~GeiV~GkV~~v~~~G~fVdi-~Gi~gFVP~sel-----~~~i~~~  335 (514)
                      ++.+|.+.+|...... ..   ..+.+.  ...+.|+++.|+|+++.++|+||++ +|++||||+|++     +.++.++
T Consensus       633 I~~dG~v~Is~~~~~~~~~a~~~i~~i~~p~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s~~rv~~~  712 (757)
T 1e3p_A          633 IEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENV  712 (757)
T ss_dssp             -------CCCBSSHHHHCC---------------------CBEEECC-CSCEECCC---CCCCC----------------
T ss_pred             ecCCceEEEecCCHHHHHHHHHHHHHhcchhhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccCCCcccCc
Confidence            3456777776543321 11   223343  4568999999999999999999999 579999999999     4677777


Q ss_pred             hhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          336 TELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       336 ~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      .+.. ++||+|+|+|+++|+ +++|.||+|..
T Consensus       713 ~~~~-~vGd~V~VkVi~vd~-~grI~LS~k~~  742 (757)
T 1e3p_A          713 EDVL-GVGQKVQVEIAEIDS-RGKLSLIPVIE  742 (757)
T ss_dssp             ---C-CSSCBCCCCCCCCCS-SCC--------
T ss_pred             cccc-CCCCEEEEEEEEECC-CCCEEEEEecC
Confidence            7764 899999999999998 89999999863

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

Probab=98.11  E-value=4.6e-06  Score=80.89  Aligned_cols=63  Identities=11%  Similarity=0.147  Sum_probs=53.8

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc--------------cCcccccCCCCEEEEEEEEEe
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV--------------TSVSDLLNEGERVKVLVVKSM  435 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v--------------~~~~~~~kvGd~VkvkVi~vd  435 (514)
                      .-.+|++++|+|++++++|+||++.+ .++||+|++++..++.              ++-...|++||.|++||++++
T Consensus        78 ~p~vGEv~~G~Is~Vt~fGifVeL~g-~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~  154 (218)
T 2ckz_B           78 KPFLGEIVTGWISKCTAEGIKVSLLG-IFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREV  154 (218)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECTT-SCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEE
T ss_pred             cCCCCCEEEEEEEEEccCcEEEEccC-ccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEE
Confidence            35889999999999999999999965 4899999999976543              344677999999999999987

>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=98.08  E-value=4.6e-06  Score=80.74  Aligned_cols=71  Identities=15%  Similarity=0.186  Sum_probs=54.4

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccccc-cCCh----------hhHhhhcCCEEEEEEEEEeCCCC--ceE
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR-VNNF----------TELKEKVGRRMYVQITRINEDTN--DLI  361 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~~~-i~~~----------~el~~~VGq~V~vkVl~vD~e~~--rIi  361 (514)
                      +.|++++|+|++++++|+||+++.++||||.++|..+ ..++          ++. ..+|+.|+|+|+++|.+.+  ..+
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            6999999999999999999999779999999999432 1111          122 3799999999999997654  222


Q ss_pred             eehhh
Q 010232          362 LSERE  366 (514)
Q Consensus       362 LS~K~  366 (514)
                      .|+|.
T Consensus       161 gSmk~  165 (215)
T 2b8k_G          161 GSIKE  165 (215)
T ss_dssp             EECCS
T ss_pred             EEcCC
Confidence            26554

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

Probab=98.06  E-value=4.5e-06  Score=94.44  Aligned_cols=69  Identities=19%  Similarity=0.230  Sum_probs=53.6

Q ss_pred             ceEEEEEEEEecceEEEEECCCceEEEEEeeccc--cccc-----------cC----cccccCCCCEEEEEEEEEe-C--
Q 010232          377 TLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS--RTRV-----------TS----VSDLLNEGERVKVLVVKSM-F--  436 (514)
Q Consensus       377 ~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels--~~~v-----------~~----~~~~~kvGd~VkvkVi~vd-e--  436 (514)
                      +++.|+|++|+++|+||.|.+.|++||||+|+|+  .++.           .+    ....|++||+|+|+|+.++ +  
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           23    2578999999999999998 5  


Q ss_pred             -CCeEEEEEe
Q 010232          437 -PDKISLSIA  445 (514)
Q Consensus       437 -~~rI~LSlK  445 (514)
                       ++||.||||
T Consensus       751 ~~~kI~lslk  760 (760)
T 2vnu_D          751 SKRKAELLLK  760 (760)
T ss_dssp             -CCEEEC---
T ss_pred             cCCcEEEEeC
Confidence             589999986

>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=98.05  E-value=4e-06  Score=85.28  Aligned_cols=74  Identities=16%  Similarity=0.235  Sum_probs=62.7

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccc----cc------cCcccccCCCCEEEEEEEEEeCCCeEE
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT----RV------TSVSDLLNEGERVKVLVVKSMFPDKIS  441 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~----~v------~~~~~~~kvGd~VkvkVi~vde~~rI~  441 (514)
                      ..++|++|.|+|++++++|+||+|+. ...|++|+|+++..    |.      .++++.|++||.|.|+|++++++.++.
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            47999999999999999999999996 47899999998752    22      245578999999999999998888999


Q ss_pred             EEEec
Q 010232          442 LSIAD  446 (514)
Q Consensus       442 LSlK~  446 (514)
                      ||+|+
T Consensus       171 LStr~  175 (308)
T 2nn6_H          171 LHTRS  175 (308)
T ss_dssp             EECCS
T ss_pred             EEecC
Confidence            99985

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

Probab=98.01  E-value=5.3e-06  Score=96.05  Aligned_cols=70  Identities=19%  Similarity=0.219  Sum_probs=60.2

Q ss_pred             CceEEEEEEEEecceEEEEECCCceEEEEEeeccc--cccc-----------cC----cccccCCCCEEEEEEEEEeC--
Q 010232          376 GTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMS--RTRV-----------TS----VSDLLNEGERVKVLVVKSMF--  436 (514)
Q Consensus       376 G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels--~~~v-----------~~----~~~~~kvGd~VkvkVi~vde--  436 (514)
                      |+++.|+|++|+++|+||.|.+.|++||||+++|+  .++.           .+    ....|++||+|+|+|+.++.  
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    45789999999999998874  


Q ss_pred             --CCeEEEEEe
Q 010232          437 --PDKISLSIA  445 (514)
Q Consensus       437 --~~rI~LSlK  445 (514)
                        ++||.||||
T Consensus       967 ~~~~kI~Lslk  977 (977)
T 2wp8_J          967 TSKRKAELLLK  977 (977)
T ss_dssp             SCCCCCCEEEC
T ss_pred             cCCCceEEEeC
Confidence              379999997

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

Probab=97.97  E-value=2.3e-06  Score=79.90  Aligned_cols=73  Identities=18%  Similarity=0.224  Sum_probs=55.7

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccccc-cCChh---------hHhhhcCCEEEEEEEEEeCCCCce--Ee
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR-VNNFT---------ELKEKVGRRMYVQITRINEDTNDL--IL  362 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~~~-i~~~~---------el~~~VGq~V~vkVl~vD~e~~rI--iL  362 (514)
                      ..|++++|+|++++++|+||+++.++||||.++|... .-++.         +....+|+.|+|+|+++|.+.+++  +.
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            5899999999999999999999889999999999422 11111         112379999999999999876432  22


Q ss_pred             ehhhh
Q 010232          363 SEREA  367 (514)
Q Consensus       363 S~K~~  367 (514)
                      |+|++
T Consensus       163 tm~~~  167 (172)
T 3h0g_G          163 TMKED  167 (172)
T ss_dssp             ECCST
T ss_pred             EcCCC
Confidence            66654

>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=97.92  E-value=2.9e-05  Score=80.41  Aligned_cols=72  Identities=24%  Similarity=0.240  Sum_probs=60.2

Q ss_pred             CCCCCCEEEEEEEE----EeCCeEEEEeCC---ceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccc
Q 010232          169 EPKPGDFVIGVVVS----GNENKLDVNVGA---DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA  241 (514)
Q Consensus       169 ~ik~GdiV~G~Vv~----v~~~Gv~VdIG~---k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~  241 (514)
                      .-+.|++|+|+|.+    ++++++|||+|.   +.+|+||.+|+.|.                                 
T Consensus       127 ~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~EqiP~---------------------------------  173 (366)
T 1k0r_A          127 STREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPG---------------------------------  173 (366)
T ss_dssp             CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSCTT---------------------------------
T ss_pred             HhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcCCC---------------------------------
Confidence            35599999999999    999999999997   69999999998642                                 


Q ss_pred             ccccCCCCCCCCcccCCCEEEEEEEEEcC---CCcEEEEehHHHHH
Q 010232          242 IAMSGGSGPGRPVVETGTVLFAEVLGRTL---SGRPLLSTRRLFRK  284 (514)
Q Consensus       242 ~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~---~grliLS~kk~~~~  284 (514)
                                 ..|++||.|+|+|++++.   ..+++||+..+...
T Consensus       174 -----------E~~~~GDrVkvyV~~V~~~~kgpqI~LSRT~p~lv  208 (366)
T 1k0r_A          174 -----------ESYEHGNRLRCYVVGVTRGAREPLITLSRTHPNLV  208 (366)
T ss_dssp             -----------CCCCTTCEEEEEEEEEECCSSSCEEEEESSCHHHH
T ss_pred             -----------ccCCCCCEEEEEEEEEecCCCccEEEEEeCChHHH
Confidence                       347999999999999653   35789999877543

>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=97.85  E-value=3.3e-05  Score=72.45  Aligned_cols=72  Identities=10%  Similarity=0.043  Sum_probs=62.7

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI  444 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSl  444 (514)
                      ..++||+|.|+|+.+...+++|+|+..-..|++|.+++. ...++.+..|++||.|.|+|..++.+.++.||+
T Consensus         4 ~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~-g~~k~~r~~l~~GDlV~ArV~~~~~~~~~~Ltc   75 (175)
T 2ja9_A            4 IPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFP-NASKKNRPTLQVGDLVYARVCTAEKELEAEIEC   75 (175)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSST-TCCSSSCCCCCTTCEEEEEEEECCTTSCCEEES
T ss_pred             cCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCC-chhhhhhccCCCCCEEEEEEEEecCCCceEEEe
Confidence            368999999999999999999999961289999999886 345678889999999999999988778999993

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

Probab=97.81  E-value=2.5e-05  Score=80.94  Aligned_cols=70  Identities=17%  Similarity=0.306  Sum_probs=57.0

Q ss_pred             cCCCCceEEEEEEE----EecceEEEEECC--CceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232          372 NLREGTLLEGTVKK----IYPYGAQIRIGD--SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (514)
Q Consensus       372 ~l~~G~iV~G~V~~----I~~~GaFV~I~~--~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl  444 (514)
                      .-++|++|+|+|.+    +.+.++||+|+.  .+++|+||.+|+.      |.+.|++||+|+|+|++++ +.+...+.|
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            45699999999999    999999999984  0289999999986      4689999999999999997 444444444


Q ss_pred             ecC
Q 010232          445 ADL  447 (514)
Q Consensus       445 K~l  447 (514)
                      ...
T Consensus       201 SRT  203 (366)
T 1k0r_A          201 SRT  203 (366)
T ss_dssp             ESS
T ss_pred             EeC
Confidence            333

>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=97.68  E-value=0.00018  Score=67.43  Aligned_cols=71  Identities=20%  Similarity=0.301  Sum_probs=59.5

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCC-ceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccC
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~-k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~  246 (514)
                      |.+++||+|.|+|+.+...+++||||. ...|+||.+.+....                                     
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            678999999999999999999999998 799999988763110                                     


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEE
Q 010232          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLS  277 (514)
Q Consensus       247 ~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS  277 (514)
                        .+-.+.+++||.|.|+|...+.++.+.||
T Consensus        46 --k~~r~~l~~GDlV~ArV~~~~~~~~~~Lt   74 (175)
T 2ja9_A           46 --KKNRPTLQVGDLVYARVCTAEKELEAEIE   74 (175)
T ss_dssp             --SSSCCCCCTTCEEEEEEEECCTTSCCEEE
T ss_pred             --hhhhccCCCCCEEEEEEEEecCCCceEEE
Confidence              01146689999999999988888888888

>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=0.00013  Score=71.78  Aligned_cols=67  Identities=18%  Similarity=0.214  Sum_probs=56.9

Q ss_pred             cCCCEEEEEEEE----EECCeEEEEECC----EEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCC--CceEeeh
Q 010232          295 QLNEPIEVKFTE----WNTGGLLTRIEG----LRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDT--NDLILSE  364 (514)
Q Consensus       295 k~GeiV~GkV~~----v~~~G~fVdi~G----i~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~--~rIiLS~  364 (514)
                      +.|++|+|+|.+    +.+..++|+++.    .+|+||.+|+...     +. +.+|++|+++|+++++..  .+|+||+
T Consensus         6 r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqip~-----E~-~~~GDrIkayV~~V~~~~~gpqIiLSR   79 (251)
T 2asb_A            6 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPG-----ES-YEHGNRLRCYVVGVTRGAREPLITLSR   79 (251)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSCTT-----CC-CCTTCEEEEEEEEEECCSSSCEEEEES
T ss_pred             cCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcCCC-----cc-CCCCCEEEEEEEEEEcCCCCCEEEEEe
Confidence            589999999999    899999999975    9999999999421     21 269999999999998764  6899999


Q ss_pred             hhh
Q 010232          365 REA  367 (514)
Q Consensus       365 K~~  367 (514)
                      ..+
T Consensus        80 t~p   82 (251)
T 2asb_A           80 THP   82 (251)
T ss_dssp             SCH
T ss_pred             ccH
Confidence            854

>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=97.44  E-value=5.1e-05  Score=77.12  Aligned_cols=85  Identities=25%  Similarity=0.282  Sum_probs=60.8

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~  247 (514)
                      |.+++||+|.|+|+++...+++|+|+....|+++.+++....     .+.                ......|...+   
T Consensus        91 Y~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~g-----g~i----------------R~~~~~D~~~m---  146 (308)
T 2nn6_H           91 YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPG-----GEL----------------RRRSAEDELAM---  146 (308)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC----------------------------------CHHH---
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhcccc-----cee----------------ecccchhhhhh---
Confidence            689999999999999999999999998788999888873100     000                00000000001   


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 010232          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (514)
Q Consensus       248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk  280 (514)
                          .+.+++||.|.|+|+..+.++.+.||++.
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                24589999999999998888889999874

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

Probab=97.39  E-value=0.00032  Score=59.87  Aligned_cols=39  Identities=13%  Similarity=0.298  Sum_probs=34.2

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEE-CCEEEEEecccc-cccc
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRV  332 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi-~Gi~gFVP~sel-~~~i  332 (514)
                      ++.|+.++++|..+.++|+||++ ++++||||.|++ +.++
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            35899999999999999999999 579999999999 5443

>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=97.30  E-value=0.00068  Score=75.35  Aligned_cols=70  Identities=20%  Similarity=0.303  Sum_probs=56.6

Q ss_pred             hcCCC--EEEEEEEEEECCeEEEEE--CCEEEEEeccccc---cccC----------ChhhHhhhcCCEEEEEEEEEeCC
Q 010232          294 KQLNE--PIEVKFTEWNTGGLLTRI--EGLRAFLPKAELL---SRVN----------NFTELKEKVGRRMYVQITRINED  356 (514)
Q Consensus       294 ~k~Ge--iV~GkV~~v~~~G~fVdi--~Gi~gFVP~sel~---~~i~----------~~~el~~~VGq~V~vkVl~vD~e  356 (514)
                      .+.|+  .++|+|++++++|+||.+  .|++||||.+++.   .++.          +... ...+|++|+|+|.++|..
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            36899  999999999999999999  4799999999984   2210          1111 136999999999999999


Q ss_pred             CCceEeeh
Q 010232          357 TNDLILSE  364 (514)
Q Consensus       357 ~~rIiLS~  364 (514)
                      +++|.++.
T Consensus       635 ~~~I~~~l  642 (644)
T 2id0_A          635 TRSIIARP  642 (644)
T ss_dssp             TTEEEEEE
T ss_pred             CCEEEEEE
Confidence            99998874

>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=97.01  E-value=0.0011  Score=71.65  Aligned_cols=70  Identities=17%  Similarity=0.227  Sum_probs=55.6

Q ss_pred             cCCCEEEEEEEEEECC--eEEEEEC-CEEEEEecccc-cccc---------CChhhHhhhcCCEEEEEEEEEeCCCCceE
Q 010232          295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAEL-LSRV---------NNFTELKEKVGRRMYVQITRINEDTNDLI  361 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~--G~fVdi~-Gi~gFVP~sel-~~~i---------~~~~el~~~VGq~V~vkVl~vD~e~~rIi  361 (514)
                      ..|.++.|+|+++.++  |+||+++ |..||+|++++ +.++         .+..+.. ++||.|.|.|++....++...
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 68999999999 4332         2233433 689999999998776666666


Q ss_pred             eehh
Q 010232          362 LSER  365 (514)
Q Consensus       362 LS~K  365 (514)
                      ||..
T Consensus       123 lTt~  126 (517)
T 2bx2_L          123 LTTF  126 (517)
T ss_dssp             EESS
T ss_pred             EEee
Confidence            6664

>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=96.97  E-value=0.0013  Score=66.32  Aligned_cols=71  Identities=10%  Similarity=-0.000  Sum_probs=63.3

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI  444 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSl  444 (514)
                      -.++|++|-|+|+++....+.|+|.. -..|+||.+++. ...++.+..|++||-|.|+|++++.+..+.||+
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            46999999999999999999999998 588999999876 345678889999999999999987777899998

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

Probab=96.92  E-value=0.001  Score=63.51  Aligned_cols=61  Identities=13%  Similarity=0.091  Sum_probs=45.0

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEecccc-cccc-------------------CChhhHhhhcCCEEEEEEEEEe
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRV-------------------NNFTELKEKVGRRMYVQITRIN  354 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i-------------------~~~~el~~~VGq~V~vkVl~vD  354 (514)
                      ..|+++.|+|++++++|+||.++.++|+++.+++ ..+.                   ++. .....+|+.|+++|.++|
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            5899999999999999999999778999999988 3321                   111 112256777777777766


Q ss_pred             CC
Q 010232          355 ED  356 (514)
Q Consensus       355 ~e  356 (514)
                      ..
T Consensus       159 ~~  160 (203)
T 3ayh_B          159 FV  160 (203)
T ss_dssp             EC
T ss_pred             cc
Confidence            43

>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=96.83  E-value=0.0037  Score=62.95  Aligned_cols=72  Identities=22%  Similarity=0.374  Sum_probs=59.4

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~  247 (514)
                      |-+++||+|.|+|+++....+.|||+....|+||.+.+....                                      
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            689999999999999999999999998888998877753110                                      


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEe
Q 010232          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLST  278 (514)
Q Consensus       248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~  278 (514)
                       .+-.+.|++||.|.|+|+..+.++.+.||.
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             011456899999999999888888888886

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

Probab=96.65  E-value=0.0021  Score=62.18  Aligned_cols=65  Identities=12%  Similarity=0.078  Sum_probs=49.4

Q ss_pred             cCCCEEEEEEEEEECCeEEEEE-CCEEEEEecccc-ccccC-------------ChhhHhhhcCCEEEEEEEEEeCCCCc
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAEL-LSRVN-------------NFTELKEKVGRRMYVQITRINEDTND  359 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi-~Gi~gFVP~sel-~~~i~-------------~~~el~~~VGq~V~vkVl~vD~e~~r  359 (514)
                      ..|+++.|+|++++++|+||.+ +.++|+++.+++ ..+..             .-......+|+.|+++|.++|...+.
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 557999999988 32210             00112236899999999999876543

>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=96.59  E-value=0.0035  Score=70.94  Aligned_cols=71  Identities=10%  Similarity=0.059  Sum_probs=48.8

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC--CEEEEEeccccc---ccc-----------CCh---hhHhhhcCCEEEEEEEEEeC
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL---SRV-----------NNF---TELKEKVGRRMYVQITRINE  355 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~---~~i-----------~~~---~el~~~VGq~V~vkVl~vD~  355 (514)
                      ...+.+.|+|+++.++|+||.+.  |++|+||++++.   .++           .+.   ......+|++|+|+|+.+|.
T Consensus       668 ~~~~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV~~vd~  747 (760)
T 2vnu_D          668 NNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMD  747 (760)
T ss_dssp             TCCSEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC----
T ss_pred             cCceEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcEEecCCEEEEEEEEEEC
Confidence            34489999999999999999994  799999999983   210           111   01123799999999999998


Q ss_pred             C---CCceEeehh
Q 010232          356 D---TNDLILSER  365 (514)
Q Consensus       356 e---~~rIiLS~K  365 (514)
                      +   +++|.+|+|
T Consensus       748 ~~~~~~kI~lslk  760 (760)
T 2vnu_D          748 PITSKRKAELLLK  760 (760)
T ss_dssp             ----CCEEEC---
T ss_pred             ccccCCcEEEEeC
Confidence            7   689999875

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

Probab=96.25  E-value=0.0044  Score=71.89  Aligned_cols=70  Identities=10%  Similarity=0.075  Sum_probs=54.8

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC--CEEEEEeccccc--c-c---------c--CC----hhhHhhhcCCEEEEEEEEEe
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL--S-R---------V--NN----FTELKEKVGRRMYVQITRIN  354 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~--~-~---------i--~~----~~el~~~VGq~V~vkVl~vD  354 (514)
                      ..|+...|+|+++.++|+||.+.  |++|+||+++|.  . +         +  .+    ... ...+|++|+|+|..+|
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  1 1         0  11    112 2379999999999998


Q ss_pred             CC---CCceEeehh
Q 010232          355 ED---TNDLILSER  365 (514)
Q Consensus       355 ~e---~~rIiLS~K  365 (514)
                      ..   +++|.||+|
T Consensus       964 ~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          964 DPITSKRKAELLLK  977 (977)
T ss_dssp             CSSSCCCCCCEEEC
T ss_pred             CcccCCCceEEEeC
Confidence            74   378988875

>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=91.13  E-value=0.38  Score=51.33  Aligned_cols=59  Identities=10%  Similarity=0.074  Sum_probs=45.8

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEE
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSI  444 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSl  444 (514)
                      -++|+.++|.|..         +.+  ..|+||++++...  ......|++||+|+|+|.++| .+++|.+..
T Consensus       401 ~~~g~~f~g~vv~---------l~~--~~glV~v~~l~~d--~~~~~~~~lGd~V~V~v~~vd~~~~~i~f~~  460 (469)
T 2r7d_A          401 AQPERVWDAVVVD---------RRG--AQATLLIPDLAFD--VQVNTPAAPGTALQVQFADIDLPQMRVRARS  460 (469)
T ss_dssp             TCTTCCEEEEEEE---------EET--TEEEEEEGGGTEE--EEEECCCCTTCEEEEEEEEEETTTTEEEEEE
T ss_pred             hCCCCEEEEEEEE---------EeC--cEEEEEECCCCeE--EecCCcCCCCCEEEEEEEEEccCCCEEEEEE
Confidence            4689999998754         333  3788888888754  223457999999999999999 888998776

>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=90.26  E-value=0.71  Score=38.98  Aligned_cols=57  Identities=9%  Similarity=0.051  Sum_probs=48.6

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc-----cC-cccccCCCCEEEEE
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----TS-VSDLLNEGERVKVL  430 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v-----~~-~~~~~kvGd~Vkvk  430 (514)
                      ...|+.+.+.|.++.+.++-|.+.+ |..+.|+.+.|.|.+-     .. +++.+++||.|.|+
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            4458899999999999999999977 6788899999999852     34 66789999999987

>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=87.10  E-value=1.5  Score=36.53  Aligned_cols=62  Identities=21%  Similarity=0.236  Sum_probs=47.5

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCC-ceEEEEEee-ccccccccCcccccCCCCEEEEEEEEEe
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHIS-NMSRTRVTSVSDLLNEGERVKVLVVKSM  435 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~S-els~~~v~~~~~~~kvGd~VkvkVi~vd  435 (514)
                      ++.+|++.+|+|. +.++-.+|.+.++ |.++++-.. ++-.++..++++.+ +|.+|+|+|+.+|
T Consensus        29 ~~~~g~VtkGiVy-~kd~~fyV~L~dY~glEaii~dYvnv~~dr~~klkkkL-VGKtIkVqVIRvD   92 (102)
T 1jjg_A           29 DLSPGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRAD   92 (102)
T ss_dssp             CCCSSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEEC
T ss_pred             ccCCCceEeeEEE-EeCCEEEEEecCCCCceeeeehhhhhhHHHHHHHHHHh-cCceEEEEEEEec
Confidence            6899999999887 5677778999876 788887432 23344566666666 7999999999876

>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=85.20  E-value=1.7  Score=41.52  Aligned_cols=62  Identities=11%  Similarity=0.168  Sum_probs=42.9

Q ss_pred             cCCCEEEEEEEEEECCeEEEEE-CCEEEEEeccccccc---cCC--------h---hhHhhhcCCEEEEEEEEEeCCCC
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR---VNN--------F---TELKEKVGRRMYVQITRINEDTN  358 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi-~Gi~gFVP~sel~~~---i~~--------~---~el~~~VGq~V~vkVl~vD~e~~  358 (514)
                      ..|+++.|+|..+++.|+-+-+ +-+.+|||...+...   ..+        +   .+.  .+|++|+++|..++..++
T Consensus       128 f~GevL~G~V~~~s~~~Ig~~~~G~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~--~ig~~IRFrV~~~~~~~~  204 (214)
T 2rf4_A          128 QVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGE--PIDGKLRFTVRNVHTTGR  204 (214)
T ss_dssp             CTTCEEEEEECCCCSSCEEEEETTTEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCC--BCCSEEEEEEEEEECCSS
T ss_pred             CCCCEEEEEEEEECCCcEEEEEeCCEEEEEcHHHCCCcccccccccccCCCceEcCCCC--CCCCEEEEEEEEEEecCC
Confidence            4899999999999998777644 447899999988211   110        0   111  368888888888775443

>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=84.99  E-value=2.2  Score=40.70  Aligned_cols=67  Identities=12%  Similarity=0.051  Sum_probs=47.6

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcc------------cccCCCCEEEEEEEEEeCCCe
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVS------------DLLNEGERVKVLVVKSMFPDK  439 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~------------~~~kvGd~VkvkVi~vde~~r  439 (514)
                      ...+|+++.|+|+.+++.|+.+.+.+ =...+|+...|...+.-++.            +--++|+.|+++|..++.++.
T Consensus       126 rPf~GevL~G~V~~~s~~~Ig~~~~G-~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~~~~~~~~  204 (214)
T 2rf4_A          126 QPQVGDVLEGYIFIQSASHIGLLIHD-AFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGR  204 (214)
T ss_dssp             CCCTTCEEEEEECCCCSSCEEEEETT-TEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEEEEECCSS
T ss_pred             ecCCCCEEEEEEEEECCCcEEEEEeC-CEEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEEEEEecCC
Confidence            46899999999999999777765544 36789999888533211111            112469999999999875443

>4b9x_A TDRD1, tudor domain-containing protein 1; replication; 2.80A {Mus musculus}

Probab=82.33  E-value=28  Score=32.85  Aligned_cols=171  Identities=13%  Similarity=0.074  Sum_probs=99.5

Q ss_pred             hchhccccCCCCCCEEEEEEEEE-eCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecc
Q 010232          161 DKVSVEYYEPKPGDFVIGVVVSG-NENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD  239 (514)
Q Consensus       161 ~~~~~~~~~ik~GdiV~G~Vv~v-~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~  239 (514)
                      ..++.++-.+.+|+.+...|+.+ +++.+||.+-... .      +     ..+..+..    ...++.           
T Consensus         4 ~~l~~~~~~l~~~~~~~V~Vt~v~sP~~Fyvq~~~~~-~------~-----~~L~~L~~----~l~~~~-----------   56 (226)
T 4b9x_A            4 EALEWTWVEFTVDETVDVVVCMMYSPGEFYCHFLKDD-A------L-----EKLDDLNQ----SLADYC-----------   56 (226)
T ss_dssp             --CCCCBCCCCTTCEEEEEEEEEEETTEEEEEECCTT-H------H-----HHHHHHHH----HHHHHT-----------
T ss_pred             cceeeEEEEcCCCCEEEEEEEEEeCCCEEEEEEcCCc-h------H-----HHHHHHHH----HHHHHH-----------
Confidence            45666778899999999999999 4567889863210 0      0     01111111    111110           


Q ss_pred             ccccccCCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHHHHHhhhhHHHhhhcCCCEEEEEEEEEECCe-EEEEE--
Q 010232          240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGG-LLTRI--  316 (514)
Q Consensus       240 d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G-~fVdi--  316 (514)
                            .........+++|+..-|+.   .                         ..|....|+|.++...| +-|.+  
T Consensus        57 ------~~~~~~~~~~~~G~~c~a~~---~-------------------------~d~~WyRa~V~~~~~~~~~~V~~vD  102 (226)
T 4b9x_A           57 ------AQKPPNGFKAEIGRPCCAFF---S-------------------------GDGNWYRALVKEILPSGNVKVHFVD  102 (226)
T ss_dssp             ------SSSCC--CCCCTTCEEEEEE---T-------------------------TTTEEEEEEEEEECSSSEEEEECTT
T ss_pred             ------hcCCCCCCCCCCCCEEEEEE---C-------------------------CCCeEEEEEEEEECCCCeEEEEEEe
Confidence                  00000122356777654431   0                         24678889999987665 44544  


Q ss_pred             CCEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhhhccCCCCceEEEEEEEEecceEEEEEC
Q 010232          317 EGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTLLEGTVKKIYPYGAQIRIG  396 (514)
Q Consensus       317 ~Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~~~~l~~G~iV~G~V~~I~~~GaFV~I~  396 (514)
                      -|....+|.+++.. +  +.++.....+-++|++..+.+.++.  -|........++-.|..+.++|.++...++.|++.
T Consensus       103 yGn~~~v~~~~l~~-l--~~~f~~lP~qA~~c~L~~v~p~~~~--w~~ea~~~f~~l~~~k~l~~~V~~~~~~~~~V~L~  177 (226)
T 4b9x_A          103 YGNVEEVTTDQLQA-I--LPQFLLLPFQGMQCWLVDIQPPNKH--WTKEATARFQACVVGLKLQARVVEITANGVGVELT  177 (226)
T ss_dssp             TCCEEEEEGGGEEC-C--CGGGSSSCBCCEEEEESSEECSSSS--CCHHHHHHHHHHHTTCCEEEEEEEECSSCEEEEEE
T ss_pred             cCCEEEEEHHHhcc-C--hHHHcccccceEEEEEecEECCCCC--CCHHHHHHHHHHHCCCeEEEEEEEEeCCeEEEEEE
Confidence            37788899998831 1  1223335788899999887664432  11111111234567888999999999988888875


Q ss_pred             C
Q 010232          397 D  397 (514)
Q Consensus       397 ~  397 (514)
                      +
T Consensus       178 d  178 (226)
T 4b9x_A          178 D  178 (226)
T ss_dssp             E
T ss_pred             E
Confidence            3

>1wfq_A UNR protein; beta-barrel, translational regulation, RNA chaperone, RNA/DN binding, QB fold, greek-KEY topology, structur genomics; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=81.45  E-value=15  Score=30.12  Aligned_cols=68  Identities=16%  Similarity=0.191  Sum_probs=46.9

Q ss_pred             CCCCceEEEEEEEEecceE-EEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCC-Ce-EEEEEecC
Q 010232          373 LREGTLLEGTVKKIYPYGA-QIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFP-DK-ISLSIADL  447 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~Ga-FV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~-~r-I~LSlK~l  447 (514)
                      +...+...|+|+... .|. ||.-.+.+-+-|+|++.|...     ...++.||+|...+.. .++ +| -...++.+
T Consensus        13 ~s~~~~~~G~Vkwf~-KGfGFI~~ddgg~DVFvH~s~i~~~-----~~~L~~G~~V~F~v~~-~~k~Gk~~A~~V~~~   83 (89)
T 1wfq_A           13 TSAALRETGVIEKLL-TSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSS-DRRTGKPIAVKLVKI   83 (89)
T ss_dssp             SSCCCEEEEEEEEEC-SSEEEEEETTTTEEEEEETTTCSSC-----TTTCCTTCCEEEEEEE-CSSSCCEEEEEEEES
T ss_pred             CCcccccceEEEEEe-CCeeEEecCCCCccEEEEhHHhhCc-----cCCCCCCCEEEEEEEE-CCCCCCcEEEEEEEC
Confidence            344567899999985 443 666655248999999999743     2568899999998864 344 53 44445444

>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, cold shock structural genomics; NMR {Pectobacterium atrosepticum}

Probab=81.34  E-value=13  Score=29.39  Aligned_cols=61  Identities=11%  Similarity=0.265  Sum_probs=41.6

Q ss_pred             eEEEEEEEEec---ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232          378 LLEGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (514)
Q Consensus       378 iV~G~V~~I~~---~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l  447 (514)
                      ...|+|+...+   || |+.-.+.+-. |+|+|.|....      .++.||+|...+.. .+++.-...++.+
T Consensus         2 ~~~G~Vkwfn~~KGfG-FI~~~dg~~d-FvH~s~i~~~g------~l~~G~~V~F~~~~-g~kG~~A~~V~~~   65 (74)
T 2k5n_A            2 AMNGTITTWFKDKGFG-FIKDENGDNR-YFHVIKVANPD------LIKKDAAVTFEPTT-NNKGLSAYAVKVV   65 (74)
T ss_dssp             CEEEEEEEEETTTTEE-EEEESSSCEE-EEEGGGBSSGG------GCCTTCEEEEEEEE-CSSSEEEEEEEEC
T ss_pred             CcceEEEEEECCCCeE-EEecCCCCce-EEEHhHcccCC------CCCCCCEEEEEEEe-CCCCceeEEEEeC
Confidence            36799998854   66 5555442456 99999997432      68999999998863 4566555555443

---

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	514
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	4e-09
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	6e-09
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	4e-08
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	0.001
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	4e-06
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	4e-06
d1kl9a2	86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	8e-06
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
d1wi5a_	119	b.40.4.5 (A:) S1-domain of RRP5 protein homolog (P	2e-05
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	9e-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 = 57.9 bits (140), 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 = 50.9 bits (122), Expect = 4e-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 = 51.0 bits (122), Expect = 6e-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 = 48.7 bits (116), Expect = 4e-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 = 35.6 bits (82), Expect = 0.001
 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 = 43.1 bits (101), Expect = 4e-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 = 43.0 bits (101), Expect = 4e-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 = 41.9 bits (98), Expect = 8e-06
 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

>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 = 41.5 bits (97), 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 = 41.2 bits (96), 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

>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 = 42.0 bits (98), Expect = 2e-05
 Identities = 20/95 (21%), Positives = 34/95 (35%), Gaps = 2/95 (2%)

Query: 372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT-RVTSVSDLLNEGERVKVL 430
            L+ G LL GTV  +  +G  + IG       L +       R  +    L  G+ +  +
Sbjct: 18  ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCI 77

Query: 431 VVK-SMFPDKISLSIADLESEPGLFVSDKERVFSE 464
           V K       +SLS+   E    +    +    + 
Sbjct: 78  VEKVKGNGGVVSLSVGHSEVSTAIATEQQSWNLNN 112

>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 = 9e-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	514
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.72
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.65
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	99.58
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.54
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.49
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.48
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.42
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.36
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.33
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.32
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.32
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.25
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.24
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.13
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.11
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.05
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	99.02
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.01
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	98.68
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.6
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.52
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	98.52
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.42
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.42
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.38
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.36
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.34
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.29
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	98.09
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.92
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.87
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.3
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.0
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	95.62
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	93.24
d3d31a1	119	Sulfate/molybdate ABC transporter, ATP-binding pro	92.64
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	92.02
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	88.32
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	87.77
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	83.56
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	82.15
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	81.32
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	80.79

>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=2.4e-18  Score=138.82  Aligned_cols=75  Identities=35%  Similarity=0.588  Sum_probs=71.9

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l  447 (514)
                      ++++|+++.|+|++|++||+||+|++ +++||||.|+|+|.++.+|++.|++||+|+|+|+++|+++||.||||++
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            68999999999999999999999998 8999999999999999999999999999999999998778999999974

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

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

Probab=99.65  E-value=1.3e-16  Score=133.59  Aligned_cols=80  Identities=33%  Similarity=0.544  Sum_probs=76.2

Q ss_pred             ccCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCcC
Q 010232          371 LNLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLES  449 (514)
Q Consensus       371 ~~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~~  449 (514)
                      .++++|+++.|+|++|+++|+||+|++ ++.||||.++++|.++.++++.|++||.|+|+|+++| +++||.||+|+. +
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            479999999999999999999999998 8999999999999999999999999999999999998 899999999975 7


Q ss_pred             CCC
Q 010232          450 EPG  452 (514)
Q Consensus       450 ~P~  452 (514)
                      +|+
T Consensus        92 ~P~   94 (94)
T d3bzka4          92 TPG   94 (94)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            775

>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=4.2e-16  Score=128.15  Aligned_cols=74  Identities=24%  Similarity=0.322  Sum_probs=57.7

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD  446 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~  446 (514)
                      .++|++|.|+|++|+++|+||+|... |++||||.++++|.++.++.+.|++||.|+|+|+++| +++||.||+|+
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            47899999999999999999999632 7999999999999999999999999999999999998 89999999985

>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=3.9e-16  Score=127.68  Aligned_cols=74  Identities=26%  Similarity=0.444  Sum_probs=64.7

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCC-ceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEec
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIAD  446 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~  446 (514)
                      .++|+++.|+|++|+++|+||+|... |++||||.++++|.++.++.+.|++||+|+|+|+++| +++||.||+|+
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            46899999999999999999999732 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=99.58  E-value=1.8e-15  Score=123.37  Aligned_cols=78  Identities=17%  Similarity=0.265  Sum_probs=72.0

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccc-ccCcccccCCCCEEEEEEEEEeCCCeEEEEEecCcCCC
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTR-VTSVSDLLNEGERVKVLVVKSMFPDKISLSIADLESEP  451 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~-v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l~~~P  451 (514)
                      .++|++|.|+|++++++|+||+|++ ++.||||+++++|.+ ..++++.|++||.|.|+|+++++++||.||||+....|
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 899999999999875 78999999999999999999987789999999876544

>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=99.54  E-value=3.8e-15  Score=127.22  Aligned_cols=83  Identities=22%  Similarity=0.395  Sum_probs=73.3

Q ss_pred             CCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc-----------cCcccccCCCCEEEEEEEEEe-CCCe--
Q 010232          374 REGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV-----------TSVSDLLNEGERVKVLVVKSM-FPDK--  439 (514)
Q Consensus       374 ~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v-----------~~~~~~~kvGd~VkvkVi~vd-e~~r--  439 (514)
                      ++|++++|+|++|++||+||+|+  +++||||+++|+++++           .++.+.|++||.|+|+|++|| +++|  
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  5999999999999887           478899999999999999998 5554  


Q ss_pred             ---EEEEEecCcCCCCccccch
Q 010232          440 ---ISLSIADLESEPGLFVSDK  458 (514)
Q Consensus       440 ---I~LSlK~l~~~P~~~~~~k  458 (514)
                         |.||+|+...+||+.+.++
T Consensus        80 ~~~i~ls~K~~~~~~~e~~~~~  101 (106)
T d1go3e1          80 GSKIALTMRQPYLGKLEWIEEE  101 (106)
T ss_dssp             -CEEEEECCSTTCEEHHHHHHH
T ss_pred             CceeecccccCCCCcchhhhhH
Confidence               8899999999998776543

>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=99.49  E-value=2e-14  Score=118.21  Aligned_cols=74  Identities=18%  Similarity=0.173  Sum_probs=68.3

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccccc---CcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT---SVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~---~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l  447 (514)
                      .++|++|.|+|++++++|+||+|++ ++.||||.++++|.++.   ++++.|++||.|.|+|+++|+++++.||||+.
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            5789999999999999999999998 79999999999998664   67789999999999999999778999999865

>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=99.48  E-value=2.8e-14  Score=117.50  Aligned_cols=74  Identities=15%  Similarity=0.184  Sum_probs=68.5

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeecccccccc----CcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT----SVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~----~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l  447 (514)
                      .++|++|.|+|++++++|+||+|++ ++.||||.+++++.++.    ++++.|++||.|+|+|+++++++++.||||+.
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            5799999999999999999999998 79999999999998764    67889999999999999999778999999864

>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=120.56  Aligned_cols=80  Identities=25%  Similarity=0.307  Sum_probs=72.7

Q ss_pred             ccCCCCceEEEEEEEEecceEEEEEC-CCceEEEEEeecccccc-ccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecC
Q 010232          371 LNLREGTLLEGTVKKIYPYGAQIRIG-DSNRSGLLHISNMSRTR-VTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADL  447 (514)
Q Consensus       371 ~~l~~G~iV~G~V~~I~~~GaFV~I~-~~gi~GLvh~Sels~~~-v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l  447 (514)
                      ..|++|+++.|+|++|+++|+||+|+ + ++.||||++++++.+ ..+|.+.|++||.|+|+|++++ ++++|.||+|+.
T Consensus        17 ~~l~~G~iv~G~V~~i~~~G~~V~lg~~-~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~k~~   95 (119)
T d1wi5a_          17 EALKPGMLLTGTVSSLEDHGYLVDIGVD-GTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHS   95 (119)
T ss_dssp             TTCCTTCEEEEEEEEECSSEEEEECCCS-SCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCC
T ss_pred             hhcCCCCEEEEEEEEEeccEEEEEEecc-ccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEEecHH
Confidence            47999999999999999999999996 5 799999999999874 7889999999999999999998 788999999977


Q ss_pred             cCCC
Q 010232          448 ESEP  451 (514)
Q Consensus       448 ~~~P  451 (514)
                      ....
T Consensus        96 ~~~~   99 (119)
T d1wi5a_          96 EVST   99 (119)
T ss_dssp             CSCC
T ss_pred             Hhhh
Confidence            6533

>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=99.36  E-value=1.2e-12  Score=107.18  Aligned_cols=71  Identities=18%  Similarity=0.361  Sum_probs=57.2

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC---CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~---Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      +.|+++.|+|+++.++|+||++.   |++||||.+++ +.+..++.+.. .+||.+.|+|+++|+++++|.||+|+
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            57999999999999999999994   79999999999 77788888775 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=99.33  E-value=4.6e-13  Score=107.34  Aligned_cols=72  Identities=19%  Similarity=0.278  Sum_probs=65.7

Q ss_pred             hcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       294 ~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      ++.|+++.|+|+++.++|+||+++ |++||||.+++ +.+..++++.. .+||++.|+|+++|+ ++||.||+|++
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            579999999999999999999996 79999999999 78888998875 899999999999996 57899999864

>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=2.1e-12  Score=107.46  Aligned_cols=85  Identities=16%  Similarity=0.065  Sum_probs=73.6

Q ss_pred             HHHHHhhhhHHHhhhcCCCEEEEEEEEEECCeEEEEEC-CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCC
Q 010232          280 RLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDT  357 (514)
Q Consensus       280 k~~~~~~w~~l~~~~k~GeiV~GkV~~v~~~G~fVdi~-Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~  357 (514)
                      .+.....++.+ +.++.|++++|+|+++.++|+||+++ |+.||||.+++ +.++.++.+.+ ++||.|.|+|+++|.++
T Consensus         3 ~a~~~~~ie~~-~~~k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~-~vGq~v~~~V~~id~~~   80 (94)
T d3bzka4           3 TAEFQEGVESL-KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVV-KAGDIVKVKVMEVDIPR   80 (94)
T ss_dssp             HHHHHHTCCCG-GGCCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSCHHHHC-CTTCEEEEEEEEEETTT
T ss_pred             hhHHHhhhhHH-hcCCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccChhhhh-ccCcEEEEEEEEEECCC
Confidence            34444455554 34689999999999999999999995 79999999999 67788888875 89999999999999999


Q ss_pred             CceEeehhh
Q 010232          358 NDLILSERE  366 (514)
Q Consensus       358 ~rIiLS~K~  366 (514)
                      ++|.||+|.
T Consensus        81 ~~i~LS~K~   89 (94)
T d3bzka4          81 NRVGLSMRM   89 (94)
T ss_dssp             TEEEEESCT
T ss_pred             CEEEEEEec
Confidence            999999985

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.32  E-value=1.7e-12  Score=105.59  Aligned_cols=71  Identities=23%  Similarity=0.358  Sum_probs=61.7

Q ss_pred             cCCCEEEEEEEEEECCeEEEEEC---CEEEEEecccc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAEL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSERE  366 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~---Gi~gFVP~sel-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~  366 (514)
                      +.|++++|+|++++++|+||+++   |++||||.+++ +.+..++.+.. .+||.+.|+|+++|+++++|.||+|+
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            48999999999999999999994   79999999999 67788888875 89999999999999999999999984

>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=99.25  E-value=6.5e-14  Score=108.36  Aligned_cols=58  Identities=34%  Similarity=0.553  Sum_probs=36.2

Q ss_pred             EEEEEEecceEEEEECCCceEEEEEeecccc----ccccCcccccCCCCEEEEEEEEEeCCCe
Q 010232          381 GTVKKIYPYGAQIRIGDSNRSGLLHISNMSR----TRVTSVSDLLNEGERVKVLVVKSMFPDK  439 (514)
Q Consensus       381 G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~----~~v~~~~~~~kvGd~VkvkVi~vde~~r  439 (514)
                      |+|++|++|||||+|++ |++||||+|+|++    .++.+|++.|++||+|+|+|+++|+++|
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 8999999999985    4789999999999999999999986554

>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=99.24  E-value=2.6e-12  Score=107.29  Aligned_cols=74  Identities=16%  Similarity=0.243  Sum_probs=65.2

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccc----------cccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRT----------RVTSVSDLLNEGERVKVLVVKSMFPDKISL  442 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~----------~v~~~~~~~kvGd~VkvkVi~vde~~rI~L  442 (514)
                      .++|++|.|+|++++++|+||+|+. +..|+||+|+++|.          ++.++++.|++||.|.|+|++++.++++.|
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            5789999999999999999999998 79999999999753          445677889999999999999998899999


Q ss_pred             EEecC
Q 010232          443 SIADL  447 (514)
Q Consensus       443 SlK~l  447 (514)
                      |+|..
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=99.13  E-value=1.1e-10  Score=94.49  Aligned_cols=77  Identities=22%  Similarity=0.310  Sum_probs=64.1

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~  247 (514)
                      |.+++||+|.|+|.+++++|+||+++.+..|+||.+|+....          ...++                       
T Consensus         1 Y~Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~----------~~~~~-----------------------   47 (83)
T d2ba0a1           1 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMK----------PNKKP-----------------------   47 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCC----------TTSCG-----------------------
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccccc----------cccCh-----------------------
Confidence            568999999999999999999999999999999999985320          00111                       


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 010232          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (514)
Q Consensus       248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~  281 (514)
                          ...|++||.|.|+|+++|.++++.||+|..
T Consensus        48 ----~~~~~vGd~V~~kV~~vd~~~~i~LS~k~~   77 (83)
T d2ba0a1          48 ----NEVLDIGDAIIAKVLNIDPKMKVTLTMKDR   77 (83)
T ss_dssp             ----GGTCCTTCEEEEEEEEECTTCCEEEECCSS
T ss_pred             ----hhhcccccEEEEEEEEECCCCCEEEEecCC
Confidence                245899999999999999889999999864

>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=99.11  E-value=1.1e-10  Score=95.45  Aligned_cols=81  Identities=22%  Similarity=0.232  Sum_probs=65.8

Q ss_pred             cccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccccccc
Q 010232          166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS  245 (514)
Q Consensus       166 ~~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~  245 (514)
                      +.|.+++||+|.|+|++++++|+||+++.+.+|+||.+++....           ..+.                     
T Consensus         1 s~Y~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~-----------~~~~---------------------   48 (87)
T d2je6i1           1 SFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRS-----------INVG---------------------   48 (87)
T ss_dssp             SCCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSC-----------CCTT---------------------
T ss_pred             CcccCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCce-----------eccc---------------------
Confidence            46789999999999999999999999999999999999985320           0000                     


Q ss_pred             CCCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 010232          246 GGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (514)
Q Consensus       246 ~~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~  281 (514)
                         .+....+++||.|.|+|+..|.++++.||+|..
T Consensus        49 ---~~~~~~~~~Gd~v~~kV~~vd~~~~i~LS~k~~   81 (87)
T d2je6i1          49 ---EDLRRYLDVGDYVIARIENFDRSIDPVLSVKGK   81 (87)
T ss_dssp             ---CCCSSSCCTTCEEEEEEEEEETTEEEEEECCST
T ss_pred             ---cccchhhcccceEEEEEEEECCCCCEEEEEecC
Confidence               011356899999999999999889999998754

>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=99.05  E-value=3e-10  Score=92.90  Aligned_cols=81  Identities=21%  Similarity=0.299  Sum_probs=65.6

Q ss_pred             ccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccC
Q 010232          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (514)
Q Consensus       167 ~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~  246 (514)
                      .|.+++||+|.|+|++++++|+||+|+....|+||.+|+....           .+.+                      
T Consensus         2 ~Y~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~-----------~~~~----------------------   48 (88)
T d2z0sa1           2 IYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRP-----------FNPA----------------------   48 (88)
T ss_dssp             CCCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSC-----------CCTT----------------------
T ss_pred             CcCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCccc-----------cccc----------------------
Confidence            4778999999999999999999999999999999999985321           0000                      


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 010232          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (514)
Q Consensus       247 ~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~  281 (514)
                       ..+....+++||.|.|+|+++|.++++.||+|..
T Consensus        49 -~~~~~~~~~vGd~V~~kV~~vd~~~~i~Ls~k~~   82 (88)
T d2z0sa1          49 -VDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGE   82 (88)
T ss_dssp             -TTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSS
T ss_pred             -ccchhhhcccCcEEEEEEEEECCCCCEEEEEecC
Confidence             0112456899999999999999889999998764

>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=5e-10  Score=91.78  Aligned_cols=68  Identities=12%  Similarity=0.131  Sum_probs=58.4

Q ss_pred             CCceEEEEEEEEecceEEEEECCCceEEEEEeecccccccc------------CcccccCCCCEEEEEEEEEe-CCCeEE
Q 010232          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVT------------SVSDLLNEGERVKVLVVKSM-FPDKIS  441 (514)
Q Consensus       375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~------------~~~~~~kvGd~VkvkVi~vd-e~~rI~  441 (514)
                      .|+.++|+|++|+++|+||+|.+.+++||||+|+|.+++..            +....|++||+|+|+|+++| +++||.
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            47889999999999999999976579999999999987532            23457999999999999999 788886


Q ss_pred             E
Q 010232          442 L  442 (514)
Q Consensus       442 L  442 (514)
                      +
T Consensus        83 ~   83 (87)
T d2ix0a3          83 A   83 (87)
T ss_dssp             E
T ss_pred             E
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=99.01  E-value=3.1e-10  Score=96.20  Aligned_cols=72  Identities=17%  Similarity=0.244  Sum_probs=58.6

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEecccc-cccc-----------CChhhHhhhcCCEEEEEEEEEeCCCCc---
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRV-----------NNFTELKEKVGRRMYVQITRINEDTND---  359 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i-----------~~~~el~~~VGq~V~vkVl~vD~e~~r---  359 (514)
                      +.|+++.|+|++++++|+||++++++||||.++| +.++           .++... +.+||.|+|+|++||.++++   
T Consensus         2 ~~gei~~g~V~~v~~~G~FVel~~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~-~~~Gd~v~vkV~~vd~~~~~~~~   80 (106)
T d1go3e1           2 EMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKV-LEIGDYVRARIVAISLKAERKRG   80 (106)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC--CEEETTTCCE-ECTTCEEEEEEEEEECCC-----
T ss_pred             CCCCEEEEEEEEEeeeEEEEEeeCeEEEEEeecccCceeeeccceeEEeecccccc-eeecceEEEEEEEEchhhccccC
Confidence            4799999999999999999999999999999999 4443           233333 37999999999999988876   


Q ss_pred             --eEeehhhh
Q 010232          360 --LILSEREA  367 (514)
Q Consensus       360 --IiLS~K~~  367 (514)
                        +.||+|+.
T Consensus        81 ~~i~ls~K~~   90 (106)
T d1go3e1          81 SKIALTMRQP   90 (106)
T ss_dssp             CEEEEECCST
T ss_pred             ceeecccccC
Confidence              67788753

>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=1e-10  Score=101.27  Aligned_cols=74  Identities=22%  Similarity=0.245  Sum_probs=63.1

Q ss_pred             hhcCCCEEEEEEEEEECCeEEEEEC--CEEEEEeccccc-c-ccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhh
Q 010232          293 IKQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL-S-RVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREA  367 (514)
Q Consensus       293 ~~k~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel~-~-~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~  367 (514)
                      .++.|+++.|+|+++.++|+||+++  +++||||.+++. . +..++.+.+ ++||.|.|+|+++|+++++|.||+|+.
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            4579999999999999999999994  699999999993 2 344454432 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=1.3e-09  Score=89.58  Aligned_cols=66  Identities=18%  Similarity=0.291  Sum_probs=58.4

Q ss_pred             CCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc----------cCcccccCCCCEEEEEEEEEe-CCCeEEE
Q 010232          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV----------TSVSDLLNEGERVKVLVVKSM-FPDKISL  442 (514)
Q Consensus       375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v----------~~~~~~~kvGd~VkvkVi~vd-e~~rI~L  442 (514)
                      +|++++|+|++++++|+||+++.  ++||||+++|.+++.          .+..+.+++||.|+|+|++++ ++++|..
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  799999999987755          344567999999999999998 8888865

>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=7e-09  Score=85.62  Aligned_cols=66  Identities=12%  Similarity=0.232  Sum_probs=57.7

Q ss_pred             CCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccc------------cCcccccCCCCEEEEEEEEEe-CCCeEE
Q 010232          375 EGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRV------------TSVSDLLNEGERVKVLVVKSM-FPDKIS  441 (514)
Q Consensus       375 ~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v------------~~~~~~~kvGd~VkvkVi~vd-e~~rI~  441 (514)
                      .|++++|+|++++++|+||+++.  ++||+|.++|.+++.            .+....+++||.|++||+.++ +.++|.
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            69999999999999999999974  799999999998753            344567999999999999998 888886


Q ss_pred             E
Q 010232          442 L  442 (514)
Q Consensus       442 L  442 (514)
                      .
T Consensus        82 ~   82 (94)
T d2c35b1          82 A   82 (94)
T ss_dssp             E
T ss_pred             E
Confidence            4

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.80  E-value=4.7e-09  Score=86.07  Aligned_cols=73  Identities=11%  Similarity=0.018  Sum_probs=67.6

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l  447 (514)
                      .++|++|-|+|++++.+|+||+|+. ...|+||++++. .++++.+..+++||.|.|+|.+++.++++.||+.+.
T Consensus         4 P~~GD~ViG~V~~~~~~~~~VdI~s-~~~a~L~~~~f~-g~~k~~r~~l~~GD~V~arV~~v~~~~~~~Lscvd~   76 (88)
T d2nn6g1           4 PVKGDHVIGIVTAKSGDIFKVDVGG-SEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDS   76 (88)
T ss_dssp             CCSSEEEEEEEEEEETTEEEEECSS-SSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCTTSCCEEECSBT
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEcCC-CeeEEEeHHHcC-ccccccCcccCCCCEEEEEEEEeCCCCCEEEEEEcc
Confidence            5799999999999999999999998 799999999995 578889999999999999999999889999999764

>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=98.68  E-value=1.4e-08  Score=84.16  Aligned_cols=87  Identities=24%  Similarity=0.306  Sum_probs=63.6

Q ss_pred             ccCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccC
Q 010232          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (514)
Q Consensus       167 ~~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~  246 (514)
                      -|.+++||+|.|+|+++.++|++|+|+...+|+||.+++....   ..    +. ...             ..+...+  
T Consensus         3 ~Y~P~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~---~~----~r-r~~-------------~~~~~~~--   59 (95)
T d2nn6h1           3 RYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPG---GE----LR-RRS-------------AEDELAM--   59 (95)
T ss_dssp             CCCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC----------------------------------CHHH--
T ss_pred             cccCCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccc---cc----cc-ccc-------------chhhhhh--
Confidence            4678999999999999999999999999899999999985210   00    00 000             0000000  


Q ss_pred             CCCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 010232          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (514)
Q Consensus       247 ~~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~  281 (514)
                           ...+++||.|.|+|+.++.+|++.||+|.+
T Consensus        60 -----~~~~~~Gd~V~~kV~~v~~dg~i~Ls~r~~   89 (95)
T d2nn6h1          60 -----RGFLQEGDLISAEVQAVFSDGAVSLHTRSL   89 (95)
T ss_dssp             -----HHHSCSSCEECCEEEEEETTTEEEEECCSS
T ss_pred             -----hhhcccccEEEEEEEEECCCCCEEEEeccc
Confidence                 234899999999999999999999998754

>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=98.60  E-value=4.1e-08  Score=80.61  Aligned_cols=74  Identities=9%  Similarity=0.005  Sum_probs=68.6

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEEecC
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSIADL  447 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSlK~l  447 (514)
                      .++|++|-|+|+++...|+||+|+. ...|++|.+........+.+..|++||.|.|+|.+++.++++.||+++.
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            4799999999999999999999997 6899999999998999999999999999999999999889999998643

>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=98.52  E-value=1.9e-07  Score=76.29  Aligned_cols=74  Identities=22%  Similarity=0.352  Sum_probs=62.6

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~  247 (514)
                      |.+++||+|.|+|+++..++++|||+....|+||.+++....                                      
T Consensus         2 Y~P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~g~~--------------------------------------   43 (88)
T d2nn6g1           2 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGAT--------------------------------------   43 (88)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCS--------------------------------------
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcCccc--------------------------------------
Confidence            578999999999999999999999999999999998873210                                      


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehH
Q 010232          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (514)
Q Consensus       248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk  280 (514)
                       .+-++.+++||.|.|+|...+.++++.||...
T Consensus        44 -k~~r~~l~~GD~V~arV~~v~~~~~~~Lscvd   75 (88)
T d2nn6g1          44 -KRNRPNVQVGDLIYGQFVVANKDMEPEMVCID   75 (88)
T ss_dssp             -SCSSSSSCTTCEEEEEEEECCTTSCCEEECSB
T ss_pred             -cccCcccCCCCEEEEEEEEeCCCCCEEEEEEc
Confidence             01146689999999999999999999998753

>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=98.52  E-value=9.4e-10  Score=84.50  Aligned_cols=55  Identities=22%  Similarity=0.328  Sum_probs=35.0

Q ss_pred             EEEEEEECCeEEEEEC-CEEEEEeccccc-----cccCChhhHhhhcCCEEEEEEEEEeCCC
Q 010232          302 VKFTEWNTGGLLTRIE-GLRAFLPKAELL-----SRVNNFTELKEKVGRRMYVQITRINEDT  357 (514)
Q Consensus       302 GkV~~v~~~G~fVdi~-Gi~gFVP~sel~-----~~i~~~~el~~~VGq~V~vkVl~vD~e~  357 (514)
                      |+|+++.++|+||++. |++||||.|+|.     .++.++++.. .+||+|+|+|+++|+++
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 799999999993     3567787765 89999999999999764

>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=98.42  E-value=3.4e-07  Score=74.64  Aligned_cols=66  Identities=12%  Similarity=0.136  Sum_probs=52.1

Q ss_pred             CCCEEEEEEEEEECCeEEEEECCEEEEEecccc-ccccCChhh---------HhhhcCCEEEEEEEEEeCCCCceE
Q 010232          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTE---------LKEKVGRRMYVQITRINEDTNDLI  361 (514)
Q Consensus       296 ~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel-~~~i~~~~e---------l~~~VGq~V~vkVl~vD~e~~rIi  361 (514)
                      .|+++.|+|++++++|+||+++.++||||.++| +...-+...         ....+|+.|+++|+.+|.+++++.
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            699999999999999999999889999999999 332111110         123689999999999998887763

>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=98.42  E-value=3.1e-07  Score=74.80  Aligned_cols=66  Identities=23%  Similarity=0.319  Sum_probs=53.9

Q ss_pred             CCCEEEEEEEEEECCeEEEEEC--CEEEEEecccc-ccccC------------ChhhHhhhcCCEEEEEEEEEeCCCCce
Q 010232          296 LNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL-LSRVN------------NFTELKEKVGRRMYVQITRINEDTNDL  360 (514)
Q Consensus       296 ~GeiV~GkV~~v~~~G~fVdi~--Gi~gFVP~sel-~~~i~------------~~~el~~~VGq~V~vkVl~vD~e~~rI  360 (514)
                      .|+..+|+|++++++|+||++.  +++||||.+.| +.+..            +.+. .+++||+|+|+|+++|+++++|
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            4788999999999999999994  68999999999 43321            1111 2379999999999999999998


Q ss_pred             Ee
Q 010232          361 IL  362 (514)
Q Consensus       361 iL  362 (514)
                      .+
T Consensus        82 ~~   83 (87)
T d2ix0a3          82 IA   83 (87)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>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=98.38  E-value=9.9e-07  Score=69.28  Aligned_cols=64  Identities=25%  Similarity=0.297  Sum_probs=55.1

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CCC--eEEEE
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FPD--KISLS  443 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~~--rI~LS  443 (514)
                      .-++|+++.|+|.++.+..++|+|+  +.+|+||.++..      |.+.|++||+|+|.|.+|+ ..+  +|.||
T Consensus         5 ~~~~geiv~G~V~r~~~~~~~Vdlg--~~eaiLp~~eqi------p~E~~~~Gdrik~~i~~V~~~~kgpqI~lS   71 (72)
T d1hh2p1           5 SELKGTVTTAEVIRVMGEWADIRIG--KLETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVS   71 (72)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEEET--TEEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEE
T ss_pred             hhccCcEEEEEEEEEcCCCEEEEEC--CcEEECCHHHcC------CCCCCCCCCEEEEEEEEEEEcCCCCeEEEe
Confidence            3478999999999999999999998  589999999976      5689999999999999996 333  55555

>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=98.36  E-value=9.6e-07  Score=69.35  Aligned_cols=64  Identities=22%  Similarity=0.172  Sum_probs=53.9

Q ss_pred             cCCCEEEEEEEEEECCeEEEEECCEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCC--ceEeeh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTN--DLILSE  364 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~--rIiLS~  364 (514)
                      +.|++++|+|.++.++.++|++++++|+||.+++...     +. +.+|++|+|.|.+|+...+  +|+||+
T Consensus         7 ~~geiv~G~V~r~~~~~~~Vdlg~~eaiLp~~eqip~-----E~-~~~Gdrik~~i~~V~~~~kgpqI~lSR   72 (72)
T d1hh2p1           7 LKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWIPG-----EE-IKAGDLVKVYIIDVVKTTKGPKILVSR   72 (72)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTEEEEEEGGGSCTT-----CC-CCTTCEEEEEEEEEEEETTEEEEEEES
T ss_pred             ccCcEEEEEEEEEcCCCEEEEECCcEEECCHHHcCCC-----CC-CCCCCEEEEEEEEEEEcCCCCeEEEeC
Confidence            5899999999999999999999999999999998321     11 2699999999999976554  678875

>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=1e-06  Score=72.04  Aligned_cols=76  Identities=22%  Similarity=0.310  Sum_probs=62.0

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeeccccccccCC
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~l~~~  247 (514)
                      |.+++||+|.|+|+.+..++++||||....|+||.++..+..                                      
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            568999999999999999999999999889988866654320                                      


Q ss_pred             CCCCCCcccCCCEEEEEEEEEcCCCcEEEEehHH
Q 010232          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (514)
Q Consensus       248 ~~~~~~~~~vGd~V~v~Vl~~d~~grliLS~kk~  281 (514)
                      ..+-++.+.+||.|.|+|...+.++.+.||.+-+
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            0011466899999999999999999999997543

>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=9.6e-07  Score=72.43  Aligned_cols=71  Identities=20%  Similarity=0.271  Sum_probs=54.8

Q ss_pred             CCCEEEEEEEEEECCeEEEEECCEEEEEeccccc-cc-c-CCh---------hhHhhhcCCEEEEEEEEEeCCCCceE--
Q 010232          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL-SR-V-NNF---------TELKEKVGRRMYVQITRINEDTNDLI--  361 (514)
Q Consensus       296 ~GeiV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~-~~-i-~~~---------~el~~~VGq~V~vkVl~vD~e~~rIi--  361 (514)
                      .|++++|+|++++++|+||+++.++||||.++|. .. . .+.         ......+|+.|+++|+.+|.+.+++.  
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            6999999999999999999998899999999993 32 1 110         11123689999999999988887764  


Q ss_pred             eehhh
Q 010232          362 LSERE  366 (514)
Q Consensus       362 LS~K~  366 (514)
                      .++++
T Consensus        84 gt~~~   88 (94)
T d2c35b1          84 GSLMD   88 (94)
T ss_dssp             EECCS
T ss_pred             EEccC
Confidence            44544

>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=98.09  E-value=4.5e-06  Score=72.15  Aligned_cols=74  Identities=15%  Similarity=0.127  Sum_probs=62.1

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCC-------ceEEEEEeeccc--cccccCcccccCCCCEEEEEEEEEeCC-CeEEE
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDS-------NRSGLLHISNMS--RTRVTSVSDLLNEGERVKVLVVKSMFP-DKISL  442 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~-------gi~GLvh~Sels--~~~v~~~~~~~kvGd~VkvkVi~vde~-~rI~L  442 (514)
                      .++|++|.|+|+++.+..++|+|...       .+.|++|.+++.  .....++.+.|++||.|+|+|+++.+. ..+.|
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            47899999999999999999999321       477999999984  345567889999999999999998654 46999


Q ss_pred             EEec
Q 010232          443 SIAD  446 (514)
Q Consensus       443 SlK~  446 (514)
                      |+++
T Consensus        85 st~~   88 (125)
T d2nn6i1          85 TTAE   88 (125)
T ss_dssp             ECCS
T ss_pred             EecC
Confidence            9965

>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=97.92  E-value=1.2e-05  Score=63.49  Aligned_cols=64  Identities=23%  Similarity=0.399  Sum_probs=52.0

Q ss_pred             CCCceEEEEEEEEecce----EEEEECC--CceEEEEEeeccccccccCcccccCCCCEEEEEEEEEe-CC--CeEEEE
Q 010232          374 REGTLLEGTVKKIYPYG----AQIRIGD--SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSM-FP--DKISLS  443 (514)
Q Consensus       374 ~~G~iV~G~V~~I~~~G----aFV~I~~--~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vd-e~--~rI~LS  443 (514)
                      ++|+++.|+|.++....    ++|+|+.  .+++|+||.+|.-      |.+.|++||.|+|.|.+|+ ..  -.|.||
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            68999999999997543    7999972  1699999999975      5689999999999999996 22  256665

>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=97.87  E-value=1.4e-05  Score=63.25  Aligned_cols=64  Identities=27%  Similarity=0.310  Sum_probs=50.9

Q ss_pred             CCCCEEEEEEEEEeCC----eEEEEeC---CceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecccccc
Q 010232          171 KPGDFVIGVVVSGNEN----KLDVNVG---ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA  243 (514)
Q Consensus       171 k~GdiV~G~Vv~v~~~----Gv~VdIG---~k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~d~~~  243 (514)
                      +.|++|+|+|.+++..    .++||+|   .+.+|+||.+|..|.                                   
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   368999999998653                                   


Q ss_pred             ccCCCCCCCCcccCCCEEEEEEEEEcC---CCcEEEEe
Q 010232          244 MSGGSGPGRPVVETGTVLFAEVLGRTL---SGRPLLST  278 (514)
Q Consensus       244 l~~~~~~~~~~~~vGd~V~v~Vl~~d~---~grliLS~  278 (514)
                               ..|+.||.|+|.|..+..   .-+++||+
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                     348999999999998642   33567774

>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=97.30  E-value=0.00028  Score=56.79  Aligned_cols=57  Identities=28%  Similarity=0.546  Sum_probs=48.6

Q ss_pred             ceEEEEEEEEec--ceEEEEECCCceEEEEEeeccccccc---------cCcccccCCCCEEEEEEEEE
Q 010232          377 TLLEGTVKKIYP--YGAQIRIGDSNRSGLLHISNMSRTRV---------TSVSDLLNEGERVKVLVVKS  434 (514)
Q Consensus       377 ~iV~G~V~~I~~--~GaFV~I~~~gi~GLvh~Sels~~~v---------~~~~~~~kvGd~VkvkVi~v  434 (514)
                      .++.|+|.+|.+  .+|||+|+. +..||+|.+++...+.         .+..+.+++||.|-|.|.+-
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            589999999998  699999998 8999999999876543         24567799999999999863

>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=97.00  E-value=0.0012  Score=56.33  Aligned_cols=78  Identities=22%  Similarity=0.256  Sum_probs=53.6

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCC--------ceeEEeecccccccccchhhhhhhhhchhhhHHhhhccceeeecc
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGA--------DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD  239 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~--------k~~G~Lp~sEl~p~~~~e~~~~l~D~~~~~~e~~~~g~~~v~~~~  239 (514)
                      +-+++||+|.|+|+++....+.|+|..        ...|+++.+++...                             +.
T Consensus         3 ~vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~t-----------------------------e~   53 (125)
T d2nn6i1           3 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRAT-----------------------------EK   53 (125)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTC-----------------------------SS
T ss_pred             cCCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccc-----------------------------hh
Confidence            457899999999999999999999832        34455555554211                             00


Q ss_pred             ccccccCCCCCCCCcccCCCEEEEEEEEEcCC-CcEEEEehHH
Q 010232          240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRTLS-GRPLLSTRRL  281 (514)
Q Consensus       240 d~~~l~~~~~~~~~~~~vGd~V~v~Vl~~d~~-grliLS~kk~  281 (514)
                      +...+       ...|++||.|.|+|++.... ..+.||++..
T Consensus        54 d~~~m-------~~~fr~GDiV~A~Vis~~~~~~~~~Lst~~~   89 (125)
T d2nn6i1          54 DKVEI-------YKSFRPGDIVLAKVISLGDAQSNYLLTTAEN   89 (125)
T ss_dssp             CCCCG-------GGTCCSSSEEEEEEEEEETTTTEEEEECCSS
T ss_pred             hhhhH-------HHhcCCCCEEEEEEEEccCCCccEEEEecCC
Confidence            11111       24589999999999987554 3477998654

>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=95.62  E-value=0.02  Score=45.55  Aligned_cols=34  Identities=21%  Similarity=0.217  Sum_probs=30.1

Q ss_pred             CEEEEEEEEEeC--CeEEEEeCCceeEEeecccccc
Q 010232          174 DFVIGVVVSGNE--NKLDVNVGADLLGTMLTKEVLP  207 (514)
Q Consensus       174 diV~G~Vv~v~~--~Gv~VdIG~k~~G~Lp~sEl~p  207 (514)
                      ++..|+|.+|.+  .++|||+|.+..||||.+++.+
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            467899999988  6899999999999999999854

>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=93.24  E-value=0.15  Score=39.64  Aligned_cols=74  Identities=24%  Similarity=0.257  Sum_probs=57.3

Q ss_pred             CCCCceEEEEEEEEecceEEEEECCC-ceEEEEEee-ccccccccCcccccCCCCEEEEEEEEEe-CCCeEEEEEecCc
Q 010232          373 LREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLHIS-NMSRTRVTSVSDLLNEGERVKVLVVKSM-FPDKISLSIADLE  448 (514)
Q Consensus       373 l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh~S-els~~~v~~~~~~~kvGd~VkvkVi~vd-e~~rI~LSlK~l~  448 (514)
                      ..+|++.+|+|. +.++-.+|.+.+. |.++++-.+ ++-.++..++++.+ +|.+|+|+|+.+| -++-|++.-|...
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            468999999887 5667778999876 788987432 23334556666666 7999999999999 8899999998764

>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=92.64  E-value=1.4  Score=34.81  Aligned_cols=104  Identities=16%  Similarity=0.217  Sum_probs=65.2

Q ss_pred             EEEEEEEEEECCeEEEEECCEEEEEeccccccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehhhhhhhccCCCCce
Q 010232          299 PIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSEREAWATLNLREGTL  378 (514)
Q Consensus       299 iV~GkV~~v~~~G~fVdi~Gi~gFVP~sel~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K~~~~~~~l~~G~i  378 (514)
                      ++.|+|.+...+.+.++++++...+|.. +            .+|+.+.+.|   .++  .|.++....    .-.....
T Consensus         4 ~l~g~v~~~~~~~~~v~~~~~~l~~~~~-~------------~~g~~v~~~i---RPE--~i~l~~~~~----~~~~~N~   61 (119)
T d3d31a1           4 VLKGRVISAEQGLLRIRVGEVVIDAAGD-M------------EVGDQVYAFL---RPE--NIALSKSST----QSSIRNS   61 (119)
T ss_dssp             EEEEEEEEEETTEEEEEETTEEEEEESS-C------------CTTCEEEEEE---CGG--GEEEESSCC----CBSCSEE
T ss_pred             EEEEEEEEecCCEEEEEECCEEEECCCC-C------------CCCCEEEEEE---chH--Hcccccccc----ccccceE
Confidence            6899999999999999998887766621 1            3788876544   354  355554321    1122347


Q ss_pred             EEEEEEEEecceEEEEEC--C-CceEEEEEeeccccccccCcccccCCCCEEEEEE
Q 010232          379 LEGTVKKIYPYGAQIRIG--D-SNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLV  431 (514)
Q Consensus       379 V~G~V~~I~~~GaFV~I~--~-~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkV  431 (514)
                      +.|+|..+...|..+.+.  . ..+...+......       ...+++||+|.+.+
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            999999999988765542  1 0222222211111       12478999998865

>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=92.02  E-value=0.13  Score=40.94  Aligned_cols=62  Identities=21%  Similarity=0.252  Sum_probs=48.1

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCC-ceEEEEE-eeccccccccCcccccCCCCEEEEEEEEEe
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDS-NRSGLLH-ISNMSRTRVTSVSDLLNEGERVKVLVVKSM  435 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~-gi~GLvh-~Sels~~~v~~~~~~~kvGd~VkvkVi~vd  435 (514)
                      ++.+|++.+|+|. +.++-.+|.+.++ |.++++- --++-.++..++++.+ +|.+|+|+|+.+|
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            7899999999887 5677788999876 7888853 2344445666676766 7999999999876

>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=88.32  E-value=1.9  Score=31.68  Aligned_cols=58  Identities=21%  Similarity=0.328  Sum_probs=40.6

Q ss_pred             EEEEEEEec---ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEEEE
Q 010232          380 EGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISLSI  444 (514)
Q Consensus       380 ~G~V~~I~~---~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~LSl  444 (514)
                      .|+|+-..+   || ||...+ |-+-|+|+|.+.....    ..+..||+|...+.. .+++.-...+
T Consensus         3 ~G~Vk~fn~~kGfG-FI~~d~-g~DiF~H~s~l~~~~~----~~L~~G~~V~f~~~~-~~~G~~A~~V   63 (66)
T d1c9oa_           3 RGKVKWFNNEKGYG-FIEVEG-GSDVFVHFTAIQGEGF----KTLEEGQEVSFEIVQ-GNRGPQAANV   63 (66)
T ss_dssp             EEEEEEEETTTTEE-EEEETT-EEEEEEEGGGBCSSSC----CCCCTTCEEEEEEEE-ETTEEEEEEE
T ss_pred             CeEEEEEECCCCEE-EEEecC-CceEEEEehhcccccC----CcCCCCCEEEEEEEE-CCCCCEEEEE
Confidence            588888753   66 466676 7899999999964321    357899999998864 3555444444

>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=87.77  E-value=1.1  Score=33.68  Aligned_cols=31  Identities=29%  Similarity=0.461  Sum_probs=27.3

Q ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCceeE
Q 010232          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLG  198 (514)
Q Consensus       168 ~~ik~GdiV~G~Vv~v~~~Gv~VdIG~k~~G  198 (514)
                      -.++.|++=+|-+++....|+|||||....+
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            3588999999999999999999999976555

>d1k3ra1 b.40.4.10 (A:93-163) Hypothetical protein MTH1 (MT0001), insert domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Hypothetical protein MTH1 (MT0001), insert domain
domain: Hypothetical protein MTH1 (MT0001), insert domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=83.56  E-value=1.5  Score=32.94  Aligned_cols=49  Identities=20%  Similarity=0.201  Sum_probs=39.8

Q ss_pred             cCCCCceEEEEEEEEecceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEE
Q 010232          372 NLREGTLLEGTVKKIYPYGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKS  434 (514)
Q Consensus       372 ~l~~G~iV~G~V~~I~~~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~v  434 (514)
                      ..++|++-+|.+.+....|+||+|+-   +-+....           ..+.+|+++.++|.++
T Consensus         7 ~p~vGEiReG~~~rr~~~g~~vDiGl---D~la~~k-----------~~~~~~~r~tfrIvs~   55 (71)
T d1k3ra1           7 KPVTGEYRQGLTVKRVKKGTLVDIGA---DKLALCR-----------EKLTVNRIMSFRVVRL   55 (71)
T ss_dssp             SCCTTCEEEEEEEEECSSSEEEESSS---SCEEECS-----------SCCCSSCEEEEEEEEC
T ss_pred             CCcccceeeEEEEEecCCcEEEEecC---Cceeeee-----------cccccCcEEEEEEEEc
Confidence            47899999999999999999999974   3333322           3478999999999876

>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=82.15  E-value=2.3  Score=32.75  Aligned_cols=68  Identities=13%  Similarity=0.250  Sum_probs=46.6

Q ss_pred             cCCCEEEEEEEEEECCeEEEEE---CCEEEEEecc-cc-ccccCChhhHhhhcCCEEEEEEEEEeCCCCceEeehh
Q 010232          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKA-EL-LSRVNNFTELKEKVGRRMYVQITRINEDTNDLILSER  365 (514)
Q Consensus       295 k~GeiV~GkV~~v~~~G~fVdi---~Gi~gFVP~s-el-~~~i~~~~el~~~VGq~V~vkVl~vD~e~~rIiLS~K  365 (514)
                      ..|++.+|.|. ++++-+.|.+   .|.+|++-.. ++ .+++.+.++-  .+|..|+++|+++|.-++-|-+..|
T Consensus         7 nigdVtkGiVy-~kd~~fyV~L~dY~g~ea~l~dy~~~~~d~~~klk~k--LVGKtIkvqVIR~d~lKGYIDVr~~   79 (85)
T d1luza_           7 NAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDK--LVGKTVKVKVIRVDYTKGYIDVNYK   79 (85)
T ss_dssp             CTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHH--HTTCEEEEEEEEEETTTTEEEEEEE
T ss_pred             CCCceeeeEEE-EeCCEEEEEecCCCCceEEeeehhhhhhHHHHHHHHH--hcCceEEEEEEEEcceeeEEEehhh
Confidence            46788888775 3455666777   3688887643 22 2344444443  5999999999999998887766654

>d1mjca_ b.40.4.5 (A:) Major cold shock protein {Escherichia coli [TaxId: 562]}

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: Escherichia coli [TaxId: 562]

Probab=81.32  E-value=3.6  Score=30.33  Aligned_cols=59  Identities=20%  Similarity=0.287  Sum_probs=39.6

Q ss_pred             eEEEEEEEEec---ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCeEEE
Q 010232          378 LLEGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDKISL  442 (514)
Q Consensus       378 iV~G~V~~I~~---~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~rI~L  442 (514)
                      .++|+|+-..+   || |+.-.+.+-+-|+|+|.+....    ...+++||.|...+.. .+++.-..
T Consensus         3 r~~G~Vk~f~~~kGfG-FI~~d~g~~diFvH~s~l~~~~----~~~L~~G~~V~f~~~~-~~~G~~A~   64 (69)
T d1mjca_           3 KMTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIES-GAKGPAAG   64 (69)
T ss_dssp             CEEEEEEEEETTTTEE-EEEETTSCCCEEEEGGGBCCTT----TCCCCTTCEEEEEEEC-CSSSCEEE
T ss_pred             CEEEEEEEEeCCCCEE-EEEEcCCCccEEEEhHHhcccC----CCcCCCCCEEEEEEEe-CCCCcEEE
Confidence            47899998753   56 5555542578999999997432    2347889999998753 24444333

>d1h95a_ b.40.4.5 (A:) Y-box protein 1 cold shock domain (YB1-CSD) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Y-box protein 1 cold shock domain (YB1-CSD)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.79  E-value=3.4  Score=31.38  Aligned_cols=61  Identities=25%  Similarity=0.281  Sum_probs=41.2

Q ss_pred             ceEEEEEEEEec---ceEEEEECCCceEEEEEeeccccccccCcccccCCCCEEEEEEEEEeCCCe
Q 010232          377 TLLEGTVKKIYP---YGAQIRIGDSNRSGLLHISNMSRTRVTSVSDLLNEGERVKVLVVKSMFPDK  439 (514)
Q Consensus       377 ~iV~G~V~~I~~---~GaFV~I~~~gi~GLvh~Sels~~~v~~~~~~~kvGd~VkvkVi~vde~~r  439 (514)
                      ..+.|+|+-..+   || ||.-.+.+-+-|+|.|.|...-....-..+..||.|...+.. .++++
T Consensus         7 ~r~~G~VKwfn~~KGfG-FI~~ddg~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~-~~~G~   70 (79)
T d1h95a_           7 TKVLGTVKWFNVRNGYG-FINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVE-GEKGA   70 (79)
T ss_dssp             EEEEEEEEEEETTTTEE-EEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEE-CSSSE
T ss_pred             CcccEEEEEEcCCCCeE-EEEECCCCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEe-CCCCC
Confidence            457899988753   66 555544257899999999754322223457899999998764 34444