Citrus Sinensis ID: 015066

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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----
Protein Sequence
MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDISPADD
Secondary Structure (PSIPRED)
cHHHHHHHHcccccccccccccccccccEEEEEEEcccccccEEEEEEEccccHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHccccccccEEEEEEEEEEccEEEEEcccccEEEEEHHHHcccccccccccccccccEEEEEEEEEEccccEEEEEHHHHHHHHHHHHHHHHHccccEEEEEEEEEEccEEEEEEccEEEEEcccccccccccccccccEEEEEEEEEEcccccEEEEEHHHHHHHHHccccccEEEEEEEEEcccEEEEEcccccccHHHHHcccccccccccccccccEEEEEEEEEEccccEEEEEccccccccccccccccccccEEEEEEEEccccEEEEEEcccccEEEEEEcccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHcccccccccccccccccccccccccccccccccEEEHHHHHccccHHHHHHHHHHHHHHHHHcccccHcHHHcHHHHHHHHHHHHHHcccccEEEEEEEEEcccEEEEEEcccEEEEEEcHHcccccccccccEEEEcccEEEEEEEEEcccccEEEEEHHHHccccHHHHHHHHcccccEEEEEEEEEEccEEEEEEcccEEEEEccccccccccccccccEEEEEEEEEcccccEEEEEHHHHccccHHHcccccEEEEEEEEEccccEEEEEccccEEEEEEHccHHcccccccEEEcccEEEEEEEEEcccccEEEEEHHccccccHHHHHcccccHHHccccccccccEEEEEcccccEEEEcccccEEEEEccccccccccccccHHcEEccccccccc
Coil and Loop (DISEMBL)
matlaqqftglrcppishtrlsrRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCrtapmegvsFTLEEFHSALEkydfnselgtkvkgtvfctdnrgalVDITAkssaylptqEACIHKIKHveeagivpglkeeFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEglrgfvpfsqisskSTAEEllgkdlplkfvevdEEQSRLVLSNRKAMADSQAQLGIGSVVIGtvqslkpygafidigginGLLHVSQISHDRVADiatvlqpgdTLKVMILSHdrergrvslstkkleptpgdmirnpklVFEKAEEMAQTFRQRIAQAEAMARADMLrfqpesgltlnsdgilgplspdlpadgldltdispadd
Flexible Loop (DISEMBL)
matlaqqftglrcppishtrlsrrkSITQIQQKllnsrknktivsavaisnaetrerEELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMIlshdrergrvslstkkleptpgdmirnpKLVFEKAEEMAQTFRQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLspdlpadgldltdispadd
Low Complexity Region (SEG)
MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDvvvkgkvvgankggvvaevegLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDISPADD
Disordered region (IsUnstruct)
******************************************IVSAVAI************QLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQI********LLGKDLPLKFVEV*******************AQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILS**********************************************************************************************
Disordered Region (DISOPRED)
********TG*******************************TIVSAVAISNA*TREREELNQLFEEA*****************EFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARADMLRFQPESGLTLNSDGIL**LS******************
Disordered Region (DISEMBL)
MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDISPADD
Disordered Region (DISPRO)
********TGLRC**************************NKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDIS****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAIxxxxxxxxxxxxxxxxxxxxxCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVxxxxxxxxxxxxxxxxxxxxxARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDISPADD
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	414	2.2.26 [Sep-21-2011]
P29344	411	30S ribosomal protein S1,	N/A	no	0.983	0.990	0.830	0.0
P73530	328	30S ribosomal protein S1	N/A	no	0.702	0.887	0.503	3e-82
P46228	307	30S ribosomal protein S1	yes	no	0.702	0.947	0.501	9e-80
O33698	295	30S ribosomal protein S1	no	no	0.698	0.979	0.358	2e-47
P51345	263	30S ribosomal protein S1,	N/A	no	0.615	0.969	0.366	3e-44
Q1XDE2	263	30S ribosomal protein S1,	N/A	no	0.611	0.961	0.357	5e-44
P74142	305	30S ribosomal protein S1	N/A	no	0.649	0.881	0.341	3e-43
P50889	429	30S ribosomal protein S1	N/A	no	0.640	0.617	0.351	3e-33
P38494	382	30S ribosomal protein S1	yes	no	0.584	0.633	0.357	8e-32
O06147	481	30S ribosomal protein S1	yes	no	0.603	0.519	0.329	1e-30

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

 Score =  702 bits (1813), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 343/413 (83%), Positives = 382/413 (92%), Gaps = 6/413 (1%)

Query: 1   MATLAQQFTG-LRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREE 59
           MA+LAQQ  G LRCPP+S++ LS+  S     +  L  R +  IVSAVA+SNA+TRER++
Sbjct: 1   MASLAQQLAGGLRCPPLSNSNLSKPFS----PKHTLKPRFSP-IVSAVAVSNAQTRERQK 55

Query: 60  LNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDI 119
           L QLFE+AYERCR APMEGVSFT+++FH+AL+KYDFNSE+G++VKGTVFCTD  GALVDI
Sbjct: 56  LKQLFEDAYERCRNAPMEGVSFTIDDFHTALDKYDFNSEMGSRVKGTVFCTDANGALVDI 115

Query: 120 TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWE 179
           TAKSSAYLP  EACI++IK+VEEAGI+PG++EEFVIIGENEADDSL+LSLR IQYELAWE
Sbjct: 116 TAKSSAYLPLAEACIYRIKNVEEAGIIPGVREEFVIIGENEADDSLILSLRQIQYELAWE 175

Query: 180 RCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239
           RCRQLQ+EDVVVKGK+VGANKGGVVA VEGLRGFVPFSQISSKS+AEELL K++PLKFVE
Sbjct: 176 RCRQLQAEDVVVKGKIVGANKGGVVALVEGLRGFVPFSQISSKSSAEELLEKEIPLKFVE 235

Query: 240 VDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHD 299
           VDEEQSRLV+SNRKAMADSQAQLGIGSVV GTVQSLKPYGAFIDIGGINGLLHVSQISHD
Sbjct: 236 VDEEQSRLVMSNRKAMADSQAQLGIGSVVTGTVQSLKPYGAFIDIGGINGLLHVSQISHD 295

Query: 300 RVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT 359
           RV+DIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT
Sbjct: 296 RVSDIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT 355

Query: 360 FRQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDISPA 412
           FRQRIAQAEAMARADMLRFQPESGLTL+SDGILGPL+ DLPA+GLDL+ + PA
Sbjct: 356 FRQRIAQAEAMARADMLRFQPESGLTLSSDGILGPLTSDLPAEGLDLSVVPPA 408

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 =  305 bits (782), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 148/294 (50%), Positives = 211/294 (71%), Gaps = 3/294 (1%)

Query: 79  VSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK 138
           + FTLE+F + L+KYD++   G  V GTVF  ++RGAL+DI AK++AY+P QE  I+++ 
Sbjct: 10  IGFTLEDFAALLDKYDYHFSPGDIVAGTVFSMESRGALIDIGAKTAAYIPIQEMSINRVD 69

Query: 139 HVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGA 198
             EE  + P    EF I+ +   D  L LS+R I+Y  AWER RQLQ+ED  V+  V   
Sbjct: 70  DPEEV-LQPNETREFFILTDENEDGQLTLSIRRIEYMRAWERVRQLQAEDATVRSNVFAT 128

Query: 199 NKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADS 258
           N+GG +  +EGLRGF+P S IS++   E+L+G+DLPLKF+EVDEE++RLVLS+R+A+ + 
Sbjct: 129 NRGGALVRIEGLRGFIPGSHISAREAKEDLVGEDLPLKFLEVDEERNRLVLSHRRALVER 188

Query: 259 QAQ-LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVM 317
           +   L +  VV+G+V+ +KPYGAFIDIGG++GLLH+S+ISHD +    +V    D +KVM
Sbjct: 189 KMNGLEVAQVVVGSVRGIKPYGAFIDIGGVSGLLHISEISHDHIDTPHSVFNVNDEIKVM 248

Query: 318 ILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQ-RIAQAEAM 370
           I+  D ERGR+SLSTK+LEP PG M+++  LV E A+EMA+ FRQ R+A+A+ +
Sbjct: 249 IIDLDAERGRISLSTKQLEPEPGAMLKDRDLVNEMADEMAEIFRQKRLAEAQGI 302

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 =  297 bits (761), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 147/293 (50%), Positives = 213/293 (72%), Gaps = 2/293 (0%)

Query: 75  PMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI 134
           P   + FT E+F + L++YD++   G  V GTVF  + RGAL+DI AK++A+LP QE  I
Sbjct: 7   PAVDIGFTHEDFAALLDQYDYHFNPGDTVVGTVFNLEPRGALIDIGAKTAAFLPVQEMSI 66

Query: 135 HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGK 194
           ++++  EE  + P    EF I+ +   D  L LS+R I+Y  AWER RQLQ+ED  V+ +
Sbjct: 67  NRVESPEEV-LQPSEMREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQTEDATVRSE 125

Query: 195 VVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKA 254
           V   N+GG +  +EGLRGF+P S IS++   E+L+G++LPLKF+EVDE+++RLVLS+R+A
Sbjct: 126 VFATNRGGALVRIEGLRGFIPGSHISTRKAKEDLVGEELPLKFLEVDEDRNRLVLSHRRA 185

Query: 255 MADSQA-QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDT 313
           + + +  +L +G VV+G V+ +KPYGAFIDIGG++GLLH+S+ISHD +    +V    D 
Sbjct: 186 LVERKMNRLEVGEVVVGAVRGIKPYGAFIDIGGVSGLLHISEISHDHIETPHSVFNVNDE 245

Query: 314 LKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQ 366
           +KVMI+  D ERGR+SLSTK+LEP PGDM+RNP++V+EKAEEMA  +R+++ Q
Sbjct: 246 VKVMIIDLDAERGRISLSTKQLEPEPGDMVRNPEVVYEKAEEMAAQYREKLKQ 298

Binds mRNA.

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

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

 Score =  190 bits (482), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 105/293 (35%), Positives = 173/293 (59%), Gaps = 4/293 (1%)

Query: 74  APMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEAC 133
           +P    + + ++F  ALE    +S+ G  V+G V      GA +DI  K+ A+LP +EA 
Sbjct: 2   SPSAANTPSYDDFALALEAQSLDSQKGQLVRGKVCEYSTDGAYIDIGGKAPAFLPKREAA 61

Query: 134 IHKIKHVEEAGIVPGLKE-EFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVK 192
           +H +  +E    +P  +E EF++I +   D  + +SLR +  E AW R  +LQ     V+
Sbjct: 62  LHAVLDLEAH--LPKDEELEFLVIRDQNEDGQVTVSLRALALEQAWTRVAELQEGGQTVQ 119

Query: 193 GKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNR 252
            KV G+NKGGV A++EGLR F+P S ++ K   + L GK L + F+EV+    +LVLS R
Sbjct: 120 VKVTGSNKGGVTADLEGLRAFIPRSHLNEKEDLDSLKGKTLTVAFLEVNRADKKLVLSER 179

Query: 253 KAMADSQA-QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG 311
           +A   +   ++ +G ++ G V  LKP+G F+D+GG   LL ++QIS   VAD+  + + G
Sbjct: 180 QAARTALVREIEVGQLINGKVTGLKPFGVFVDLGGATALLPINQISQKFVADVGAIFKIG 239

Query: 312 DTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRI 364
           D ++ ++++ D  +GR+SLSTK LE  PG+++ N   +   A + A+  R+++
Sbjct: 240 DPIQALVVAIDNTKGRISLSTKVLENHPGEILENVAELQASAADRAERARKQL 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 =  179 bits (454), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 95/259 (36%), Positives = 157/259 (60%), Gaps = 4/259 (1%)

Query: 80  SFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK-IK 138
           SFT   F + L+KY ++  LG  V GT+F  +  G LVDI    SAYLP QE   ++ + 
Sbjct: 7   SFTHRNFAAVLQKYKYDLNLGDIVAGTIFSFELNGVLVDIGTPVSAYLPIQEVSSNQELN 66

Query: 139 HVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGA 198
           +     I      EF ++  N     L+LS+R ++Y  AW+R RQL +ED ++  ++ G 
Sbjct: 67  NFNSLNIND--TREFFLLDYNVESRQLILSIRRLEYIRAWKRIRQLLAEDSLLDVRIKGF 124

Query: 199 NKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAM-AD 257
           NKGG++  +EG+ GFVP S +++ S       K + LK + V+E+ + L+LS+R+A+ A 
Sbjct: 125 NKGGMIVNLEGISGFVPNSHLNNFSKNTSSTNKFIKLKLLNVEEKSNNLILSHRRALIAQ 184

Query: 258 SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVM 317
           + + L +G+++ G +  + PYG FI  G + GL+H+S+I+  +V  I +  + GDT+K +
Sbjct: 185 ASSNLIVGNIIEGVINQITPYGLFIKAGNLKGLVHISEINVKQVERIPSQFKIGDTIKAV 244

Query: 318 ILSHDRERGRVSLSTKKLE 336
           I+  D+++GR+SLS K L+
Sbjct: 245 IIHVDKKQGRLSLSMKHLK 263

Porphyra purpurea (taxid: 2787)

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

 Score =  179 bits (453), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 92/257 (35%), Positives = 156/257 (60%), Gaps = 4/257 (1%)

Query: 81  FTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK-IKH 139
           FT   F + L+KY ++  LG  V GT+F  +  G LVDI    SAYLP QE   ++ + +
Sbjct: 8   FTHRNFAAVLQKYKYDLNLGDIVAGTIFSFELNGVLVDIGTPISAYLPIQEVSSNQDLNN 67

Query: 140 VEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGAN 199
                I      EF ++  N     L+LS+R ++Y  AW+R RQL +ED ++   + G N
Sbjct: 68  FTSLNIND--TREFFLLDYNIQSKQLILSIRRLEYIRAWKRIRQLLAEDSLLNVMIKGFN 125

Query: 200 KGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAM-ADS 258
           KGG++  +EG+ GFVP S + +   +E+   K + LK + V+E+ + L+LS+R+A+ + +
Sbjct: 126 KGGMIINLEGISGFVPNSHLGNFQKSEQFNNKFIKLKLLNVEEKSNNLILSHRRALISQA 185

Query: 259 QAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMI 318
            + L +G+++ G +  + PYG FI +G + GL+H+S+I+   +  I++  + GDT+K +I
Sbjct: 186 SSNLIVGNIIEGIINQITPYGLFIKVGNLKGLVHISEINIKNLEQISSQFKIGDTIKAVI 245

Query: 319 LSHDRERGRVSLSTKKL 335
           +  D+++GR+SLS K L
Sbjct: 246 IHVDKKQGRLSLSMKHL 262

Porphyra yezoensis (taxid: 2788)

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

 Score =  176 bits (446), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 95/278 (34%), Positives = 159/278 (57%), Gaps = 9/278 (3%)

Query: 80  SFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKH 139
           +F+L+EF  AL+K+D+++E G  V G +    N G  VD   KS  ++P QE  +     
Sbjct: 9   AFSLDEFAKALDKHDYHAEKGQTVHGKICQHANEGVYVDFGGKSPGFVPVQELGLRPHAE 68

Query: 140 VEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGAN 199
           +E++  +     +F++  E   +  + LS R +Q + +WE   +L+     ++  V G N
Sbjct: 69  IEDSFPLDS-AWDFLVTSEQNDEGQVRLSRRQLQIQQSWENLAELEESGKTLEMVVTGTN 127

Query: 200 KGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRK-AMADS 258
           KGGVV +VEGLRGF+P S +  K   + L+G+ L    +E +++ ++LVL+ R+   A+S
Sbjct: 128 KGGVVGDVEGLRGFIPRSHLMHKDNMDALVGQVLKAHILEANQDNNKLVLTQRRIQQAES 187

Query: 259 QAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMI 318
             ++  G++  G V  ++PYG F++I G+ GLLHVSQ+S  RV  + T+   G  + V +
Sbjct: 188 MGKIAAGNIYEGKVAKIQPYGVFVEIEGVTGLLHVSQVSGTRVDSLNTLFAFGQAISVYV 247

Query: 319 LSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEM 356
              D  + R+SLST+ LE  PG+++       EK +EM
Sbjct: 248 QEIDEYKNRISLSTRILETYPGELV-------EKFDEM 278

Binds mRNA.

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

>sp|P50889|RS1_LEULA 30S ribosomal protein S1 OS=Leuconostoc lactis GN=rps1 PE=2 SV=2

 Score =  142 bits (359), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 101/287 (35%), Positives = 157/287 (54%), Gaps = 22/287 (7%)

Query: 71  CRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRG-ALVDITAKSSAYLPT 129
           CR   ++ +S T  EF +ALE      ++G  V G +   DN   A+V ++      +P 
Sbjct: 27  CRRT-LDVMSETNNEFLAALESAADQIKVGDVVTGELLAIDNDNQAVVGLSTGEEGVVPA 85

Query: 130 QEACIHK-IKHVEEAGIVPGLKEEFVIIGENEADD---SLVLSLRMIQYELAWERCRQLQ 185
           +E    + I   +E  I  G   E V+I    +D    + +LS + +    AWE     +
Sbjct: 86  REYSDDRNINLADELKI--GDTIEAVVISNVTSDKEGVAYLLSKKRLDARKAWENLSFAE 143

Query: 186 SEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVEVDEE 243
            +   V  KV+ A +GG++ +V G+RGFVP S ++ +  S   +   KD+  + +E+D  
Sbjct: 144 GD--TVDAKVINAVRGGLIVDVNGVRGFVPASMVAERFVSDLNQFKNKDIKAQVIEIDPA 201

Query: 244 QSRLVLSNRKAMADSQ---------AQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVS 294
            +RL+LS RKA+A  +         ++L +G VV GTV  L  +GAF+D+GG++GL+HVS
Sbjct: 202 NARLILS-RKAVAAQELAAQLAEVFSKLSVGEVVEGTVARLTDFGAFVDLGGVDGLVHVS 260

Query: 295 QISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGD 341
           +ISHDRV + A VL  GD + V IL+ D E+GR+SLS K  +  P D
Sbjct: 261 EISHDRVKNPADVLTKGDKVDVKILALDTEKGRISLSIKATQRGPWD 307

Exhibits preferential binding to single-stranded and double-stranded DNA and a low binding affinity for RNA.

Leuconostoc lactis (taxid: 1246)

>sp|P38494|RS1H_BACSU 30S ribosomal protein S1 homolog OS=Bacillus subtilis (strain 168) GN=ypfD PE=1 SV=1

 Score =  138 bits (348), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 92/257 (35%), Positives = 142/257 (55%), Gaps = 15/257 (5%)

Query: 98  ELGTKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVII 156
           E+G  VKG V   +++   V+I   K S  +P  E       HVE+A  V  + +E  + 
Sbjct: 14  EVGDVVKGIVTKVEDKHVDVEIINVKQSGIIPISELSS---LHVEKASDVVKVDDELDLK 70

Query: 157 GENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPF 216
                DD+L+LS R +  + AWE   +      V + +V    KGG+V ++ G+RGF+P 
Sbjct: 71  VTKVEDDALILSKRAVDADRAWEDLEKKFETKEVFEAEVKDVVKGGLVVDI-GVRGFIPA 129

Query: 217 SQISSKSTAE--ELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQ--------LGIGS 266
           S + +    +  +  GK L L  VE+D +++R++LS+R  +   QA         L +GS
Sbjct: 130 SLVEAHFVEDFTDYKGKTLSLLVVELDRDKNRVILSHRAVVESEQANKKQELLQSLEVGS 189

Query: 267 VVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERG 326
           V+ G VQ L  +GAF+DIGGI+GL+H+SQ+SH  V   + V++ G  +KV +LS DR+  
Sbjct: 190 VLDGKVQRLTDFGAFVDIGGIDGLVHISQLSHSHVEKPSDVVEEGQEVKVKVLSVDRDNE 249

Query: 327 RVSLSTKKLEPTPGDMI 343
           R+SLS K   P P + I
Sbjct: 250 RISLSIKDTLPGPWNQI 266

Plays a role in sporulation.

Bacillus subtilis (strain 168) (taxid: 224308)

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

 Score =  134 bits (338), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 89/270 (32%), Positives = 152/270 (56%), Gaps = 20/270 (7%)

Query: 84  EEFHSALEK---YDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI-HKIKH 139
           E+F +A++K   Y FN   G  V+GT+   D    L+DI  K+   +P +E  I H +  
Sbjct: 20  EDFLAAIDKTIKY-FND--GDIVEGTIVKVDRDEVLLDIGYKTEGVIPARELSIKHDVDP 76

Query: 140 VEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGAN 199
            E   +  G + E +++ + + +  L+LS +  QYE AW     L+ +D  VKG V+   
Sbjct: 77  NEVVSV--GDEVEALVLTKEDKEGRLILSKKRAQYERAWGTIEALKEKDEAVKGTVIEVV 134

Query: 200 KGGVVAEVEGLRGFVPFSQISSKSTAE--ELLGKDLPLKFVEVDEEQSRLVLSNRKAMAD 257
           KGG++ ++ GLRGF+P S +  +   +    +GK++  K +E+D+ ++ +VLS R  +  
Sbjct: 135 KGGLILDI-GLRGFLPASLVEMRRVRDLQPYIGKEIEAKIIELDKNRNNVVLSRRAWLEQ 193

Query: 258 SQAQ--------LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQ 309
           +Q++        L  G++  G V S+  +GAF+D+GG++GL+HVS++S   +   + V+Q
Sbjct: 194 TQSEVRSEFLNNLQKGTIRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVQ 253

Query: 310 PGDTLKVMILSHDRERGRVSLSTKKLEPTP 339
            GD + V +L  D +R RVSLS K  +  P
Sbjct: 254 VGDEVTVEVLDVDMDRERVSLSLKATQEDP 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)

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	414
133872	411	RecName: Full=30S ribosomal protein S1,	0.983	0.990	0.830	0.0
225432062	410	PREDICTED: 30S ribosomal protein S1, chl	0.987	0.997	0.852	0.0
255556496	412	tex protein-relatedtranscription accesso	0.992	0.997	0.838	0.0
224099083	421	predicted protein [Populus trichocarpa]	0.990	0.973	0.832	0.0
449459770	413	PREDICTED: 30S ribosomal protein S1, chl	0.990	0.992	0.810	0.0
224112036	412	predicted protein [Populus trichocarpa]	0.992	0.997	0.809	0.0
297813179	416	hypothetical protein ARALYDRAFT_489681 [	0.997	0.992	0.786	0.0
30692346	416	small subunit ribosomal protein S1 [Arab	0.997	0.992	0.781	0.0
358248430	412	uncharacterized protein LOC100812847 [Gl	0.925	0.929	0.793	0.0
321437419	415	ribosomal protein S4 [Musa acuminata AAA	1.0	0.997	0.795	1e-179

>gi|133872|sp|P29344.1|RR1_SPIOL RecName: Full=30S ribosomal protein S1, chloroplastic; AltName: Full=CS1; Flags: Precursor gi|18060|emb|CAA46927.1| ribosomal protein S1 [Spinacia oleracea] gi|170143|gb|AAA34045.1| chloroplast ribosomal protein S1 [Spinacia oleracea]

 Score =  702 bits (1813), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 343/413 (83%), Positives = 382/413 (92%), Gaps = 6/413 (1%)

Query: 1   MATLAQQFTG-LRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREE 59
           MA+LAQQ  G LRCPP+S++ LS+  S     +  L  R +  IVSAVA+SNA+TRER++
Sbjct: 1   MASLAQQLAGGLRCPPLSNSNLSKPFS----PKHTLKPRFSP-IVSAVAVSNAQTRERQK 55

Query: 60  LNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDI 119
           L QLFE+AYERCR APMEGVSFT+++FH+AL+KYDFNSE+G++VKGTVFCTD  GALVDI
Sbjct: 56  LKQLFEDAYERCRNAPMEGVSFTIDDFHTALDKYDFNSEMGSRVKGTVFCTDANGALVDI 115

Query: 120 TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWE 179
           TAKSSAYLP  EACI++IK+VEEAGI+PG++EEFVIIGENEADDSL+LSLR IQYELAWE
Sbjct: 116 TAKSSAYLPLAEACIYRIKNVEEAGIIPGVREEFVIIGENEADDSLILSLRQIQYELAWE 175

Query: 180 RCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239
           RCRQLQ+EDVVVKGK+VGANKGGVVA VEGLRGFVPFSQISSKS+AEELL K++PLKFVE
Sbjct: 176 RCRQLQAEDVVVKGKIVGANKGGVVALVEGLRGFVPFSQISSKSSAEELLEKEIPLKFVE 235

Query: 240 VDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHD 299
           VDEEQSRLV+SNRKAMADSQAQLGIGSVV GTVQSLKPYGAFIDIGGINGLLHVSQISHD
Sbjct: 236 VDEEQSRLVMSNRKAMADSQAQLGIGSVVTGTVQSLKPYGAFIDIGGINGLLHVSQISHD 295

Query: 300 RVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT 359
           RV+DIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT
Sbjct: 296 RVSDIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT 355

Query: 360 FRQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDISPA 412
           FRQRIAQAEAMARADMLRFQPESGLTL+SDGILGPL+ DLPA+GLDL+ + PA
Sbjct: 356 FRQRIAQAEAMARADMLRFQPESGLTLSSDGILGPLTSDLPAEGLDLSVVPPA 408

Source: Spinacia oleracea

Species: Spinacia oleracea

Genus: Spinacia

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225432062|ref|XP_002280604.1| PREDICTED: 30S ribosomal protein S1, chloroplastic [Vitis vinifera] gi|296083203|emb|CBI22839.3| unnamed protein product [Vitis vinifera]

 Score =  702 bits (1812), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 353/414 (85%), Positives = 382/414 (92%), Gaps = 5/414 (1%)

Query: 1   MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREEL 60
           MA LAQQFTGLRCPPIS +RLS+  S  Q Q+          IVSAVAISNA+T+ER +L
Sbjct: 1   MACLAQQFTGLRCPPISSSRLSKPFSPKQPQKPSF-----VRIVSAVAISNAQTKERLKL 55

Query: 61  NQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDIT 120
            ++FE+AYERCRTAP EGVSF+ ++F+SAL+KYDFNSE+GTKVKGTVFCTD  GALVDIT
Sbjct: 56  KEMFEDAYERCRTAPTEGVSFSADDFYSALDKYDFNSEIGTKVKGTVFCTDTNGALVDIT 115

Query: 121 AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWER 180
           AKSSAYLP  EACIHKIKHVEEAGIVPG++EEFVIIGENEADDSL+LSLR IQY+LAWER
Sbjct: 116 AKSSAYLPVYEACIHKIKHVEEAGIVPGVREEFVIIGENEADDSLILSLRSIQYDLAWER 175

Query: 181 CRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEV 240
           CRQLQ+EDVVVKGKVVGANKGGVVA VEGLRGFVPFSQISSK+TAEELL K+LP+KFVEV
Sbjct: 176 CRQLQAEDVVVKGKVVGANKGGVVALVEGLRGFVPFSQISSKTTAEELLDKELPVKFVEV 235

Query: 241 DEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDR 300
           DEEQSRLVLSNRKAMADSQAQLGIGSVV GTVQSLKPYGAFIDIGGINGLLHVSQISHDR
Sbjct: 236 DEEQSRLVLSNRKAMADSQAQLGIGSVVTGTVQSLKPYGAFIDIGGINGLLHVSQISHDR 295

Query: 301 VADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF 360
           V+DIATVLQPGD LKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF
Sbjct: 296 VSDIATVLQPGDILKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF 355

Query: 361 RQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDISPADD 414
           RQRIAQAEAMARADMLRFQPESGLTLNSDGILGP+S DLPA+GLDL+D+ PA+D
Sbjct: 356 RQRIAQAEAMARADMLRFQPESGLTLNSDGILGPVSADLPAEGLDLSDVPPAED 409

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556496|ref|XP_002519282.1| tex protein-relatedtranscription accessory protein, putative [Ricinus communis] gi|223541597|gb|EEF43146.1| tex protein-relatedtranscription accessory protein, putative [Ricinus communis]

 Score =  695 bits (1793), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 348/415 (83%), Positives = 385/415 (92%), Gaps = 4/415 (0%)

Query: 1   MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREEL 60
           MA+LAQQFTGLRC  +S+ R++++ S      +    RK++ +VSAVAISNA+T+ERE+L
Sbjct: 1   MASLAQQFTGLRCTALSNCRVTKKASSLLSSSR---PRKSRFVVSAVAISNAQTKEREKL 57

Query: 61  NQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDIT 120
            QLFE+AYERCRTAPMEGV+FT E+FHSALEKYDFNSE+GT VKGTVF TD  GA+VDIT
Sbjct: 58  KQLFEDAYERCRTAPMEGVAFTAEDFHSALEKYDFNSEIGTTVKGTVFMTDANGAVVDIT 117

Query: 121 AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWER 180
           AKSSAYLP QEACIHKIKHVEEAGIVPGL +EFVIIGENEADDSL+LSLR IQY+L+WER
Sbjct: 118 AKSSAYLPVQEACIHKIKHVEEAGIVPGLTQEFVIIGENEADDSLILSLRAIQYDLSWER 177

Query: 181 CRQLQSEDVVVKGKVVGANKGGVVAEVEG-LRGFVPFSQISSKSTAEELLGKDLPLKFVE 239
           CRQLQ+EDV+VKGKVVGANKGGVVA VEG LRGFVPFSQISSKSTAEELL K+LPLKFV+
Sbjct: 178 CRQLQAEDVIVKGKVVGANKGGVVAIVEGGLRGFVPFSQISSKSTAEELLEKELPLKFVD 237

Query: 240 VDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHD 299
           VDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHD
Sbjct: 238 VDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHD 297

Query: 300 RVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT 359
           RV+DIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT
Sbjct: 298 RVSDIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT 357

Query: 360 FRQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDISPADD 414
           FRQRIAQAEAMARADMLRFQPESGL+L+SDGILGP++ D+PA+GLDL+D+  A+D
Sbjct: 358 FRQRIAQAEAMARADMLRFQPESGLSLSSDGILGPVTSDMPAEGLDLSDVPSAED 412

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224099083|ref|XP_002311368.1| predicted protein [Populus trichocarpa] gi|118485696|gb|ABK94698.1| unknown [Populus trichocarpa] gi|222851188|gb|EEE88735.1| predicted protein [Populus trichocarpa]

 Score =  684 bits (1766), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 344/413 (83%), Positives = 376/413 (91%), Gaps = 3/413 (0%)

Query: 1   MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREEL 60
           MA+LAQQF GLRCPPIS +RL+ R +     ++  N         AVAISNA+T+ERE+L
Sbjct: 1   MASLAQQFAGLRCPPISISRLTERAATFSKPKRAANF---VVTAKAVAISNAQTKEREKL 57

Query: 61  NQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDIT 120
            QLFEEAYERCRTAPMEGVSFT+E+FHSAL+ YDFNSE+GT+VKGTVF TDN GALVDIT
Sbjct: 58  KQLFEEAYERCRTAPMEGVSFTVEDFHSALDAYDFNSEIGTRVKGTVFMTDNNGALVDIT 117

Query: 121 AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWER 180
           AKSSAYLP QEA IH+IK +EEAGIVPG++EEFVIIGENEADDSL+LSLR I YELAWER
Sbjct: 118 AKSSAYLPVQEASIHRIKRLEEAGIVPGMREEFVIIGENEADDSLILSLRSIHYELAWER 177

Query: 181 CRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEV 240
           CRQLQ+EDV+VKGKVVG NKGG+VA VEGLRGFVPFSQISSKST EELL K+ PLKFV+V
Sbjct: 178 CRQLQAEDVIVKGKVVGGNKGGLVAVVEGLRGFVPFSQISSKSTPEELLDKEFPLKFVDV 237

Query: 241 DEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDR 300
           DEEQSRL+LSNRKAMADSQAQLGIGSVV GTVQSLKPYGAFIDIGGINGLLHVSQISHDR
Sbjct: 238 DEEQSRLILSNRKAMADSQAQLGIGSVVTGTVQSLKPYGAFIDIGGINGLLHVSQISHDR 297

Query: 301 VADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF 360
           V+DIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF
Sbjct: 298 VSDIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF 357

Query: 361 RQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDISPAD 413
           RQRIAQAEAMARADMLRFQPESGLTL+SDGIL PL+ D+PA+GLDL+D+SPAD
Sbjct: 358 RQRIAQAEAMARADMLRFQPESGLTLSSDGILSPLNSDMPAEGLDLSDVSPAD 410

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449459770|ref|XP_004147619.1| PREDICTED: 30S ribosomal protein S1, chloroplastic-like [Cucumis sativus] gi|449517357|ref|XP_004165712.1| PREDICTED: 30S ribosomal protein S1, chloroplastic-like [Cucumis sativus]

 Score =  680 bits (1754), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 338/417 (81%), Positives = 379/417 (90%), Gaps = 7/417 (1%)

Query: 1   MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAV---AISNAETRER 57
           MA++AQQFTGLRC P+S +RLS+  S     +  LN  ++  + +AV    I + +TRER
Sbjct: 1   MASMAQQFTGLRCAPLSSSRLSKPFS----SKHFLNKSRSLPVQAAVISGPIPSPQTRER 56

Query: 58  EELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALV 117
            +L ++FEEAYERCR AP+EG+SFTLE+FH+ALEKYDF+SELGTKVKGTVFCTDN GALV
Sbjct: 57  FKLKEVFEEAYERCRNAPVEGISFTLEDFHAALEKYDFDSELGTKVKGTVFCTDNNGALV 116

Query: 118 DITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELA 177
           DITAKSSAYLP QEACIH+IKHVEEAG+ PGL+EEFVIIGENE+DDSL+LSLR IQY+LA
Sbjct: 117 DITAKSSAYLPLQEACIHRIKHVEEAGVFPGLREEFVIIGENESDDSLILSLRSIQYDLA 176

Query: 178 WERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKF 237
           WERCRQLQ+EDVVVKGKVV ANKGGVVA VEGLRGFVPFSQIS+KS AEELL K+LPLKF
Sbjct: 177 WERCRQLQAEDVVVKGKVVDANKGGVVAVVEGLRGFVPFSQISTKSNAEELLSKELPLKF 236

Query: 238 VEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQIS 297
           VEVDEEQSRLVLSNRKAMADSQAQLGIGSVV GTVQSLKPYGAFIDIGGINGLLHVSQIS
Sbjct: 237 VEVDEEQSRLVLSNRKAMADSQAQLGIGSVVTGTVQSLKPYGAFIDIGGINGLLHVSQIS 296

Query: 298 HDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMA 357
           HDR++DIATVLQPGD+LKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMA
Sbjct: 297 HDRISDIATVLQPGDSLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMA 356

Query: 358 QTFRQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDISPADD 414
           QTFRQRIAQAEA+ARADMLRFQPESGLTL +DGILGP++P+LP +GLDL D+ PA++
Sbjct: 357 QTFRQRIAQAEALARADMLRFQPESGLTLTTDGILGPITPELPVEGLDLNDVPPAEE 413

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224112036|ref|XP_002316061.1| predicted protein [Populus trichocarpa] gi|222865101|gb|EEF02232.1| predicted protein [Populus trichocarpa]

 Score =  663 bits (1711), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 335/414 (80%), Positives = 372/414 (89%), Gaps = 3/414 (0%)

Query: 1   MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREEL 60
           MA+LAQQF GL CPP+S +RL+ R +     ++  NS        AVAISN +T+ER +L
Sbjct: 1   MASLAQQFAGLICPPLSSSRLTERAATFSKPKRAANS---VVTAKAVAISNVQTKERHKL 57

Query: 61  NQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDIT 120
            +LFEEAYERCRTAP+EGVSFTLE+FH+AL+ YD+NSE+GT+VKGTVF TDN GA VDIT
Sbjct: 58  KELFEEAYERCRTAPLEGVSFTLEDFHAALDTYDYNSEIGTRVKGTVFMTDNNGAFVDIT 117

Query: 121 AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWER 180
           AKSSAYLP QEA IHKIK VEEAGIVPG++EEFVIIGENEADDSL+LSLR IQYELAWER
Sbjct: 118 AKSSAYLPVQEASIHKIKRVEEAGIVPGMREEFVIIGENEADDSLILSLRSIQYELAWER 177

Query: 181 CRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEV 240
           CRQLQ+ED +VKGKVVG N+GGVVA VEGL+GFVPFSQISSKS+AEELL K++PLKFV+V
Sbjct: 178 CRQLQAEDAIVKGKVVGGNRGGVVAVVEGLQGFVPFSQISSKSSAEELLDKEVPLKFVDV 237

Query: 241 DEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDR 300
           DEEQSRLVLSNRKAMADSQAQLGIGSVV GTVQSLKPYGAFIDIGGINGLLHVSQISHDR
Sbjct: 238 DEEQSRLVLSNRKAMADSQAQLGIGSVVTGTVQSLKPYGAFIDIGGINGLLHVSQISHDR 297

Query: 301 VADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF 360
           V+DI+TVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMA+TF
Sbjct: 298 VSDISTVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMARTF 357

Query: 361 RQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDISPADD 414
           RQRIAQAEAMARADMLRFQPESGL L+S GILGP   DLPA+GLDL+D+ PAD+
Sbjct: 358 RQRIAQAEAMARADMLRFQPESGLPLSSGGILGPNISDLPAEGLDLSDVPPADE 411

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297813179|ref|XP_002874473.1| hypothetical protein ARALYDRAFT_489681 [Arabidopsis lyrata subsp. lyrata] gi|297320310|gb|EFH50732.1| hypothetical protein ARALYDRAFT_489681 [Arabidopsis lyrata subsp. lyrata]

 Score =  654 bits (1686), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 327/416 (78%), Positives = 373/416 (89%), Gaps = 3/416 (0%)

Query: 1   MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREEL 60
           MA+LAQQFTGLRC P+S +    R       Q   ++  + TIV+AVAIS+ +T+ER EL
Sbjct: 1   MASLAQQFTGLRCSPLSSSSRLSRSVSKNFPQNK-SASVSPTIVAAVAISSGQTKERLEL 59

Query: 61  NQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDIT 120
            ++FE+AYERCRTAPMEGV+F++++F +A+E+YDFNSE+GT+VKGTVF TD  GALVDI+
Sbjct: 60  KKMFEDAYERCRTAPMEGVAFSVDDFAAAIEQYDFNSEIGTRVKGTVFKTDANGALVDIS 119

Query: 121 AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWER 180
           AKSSAYL  ++ACIH+IKHVEEAGIVPG+ EEFVIIGENE+DDSL+LSLR IQYELAWER
Sbjct: 120 AKSSAYLSVEQACIHRIKHVEEAGIVPGMVEEFVIIGENESDDSLLLSLRNIQYELAWER 179

Query: 181 CRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEV 240
           CRQLQ+EDV+VK KV+GANKGG+VA VEGLRGFVPFSQISSK+ AEELL K++PLKFVEV
Sbjct: 180 CRQLQAEDVIVKAKVIGANKGGLVALVEGLRGFVPFSQISSKAAAEELLEKEIPLKFVEV 239

Query: 241 DEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDR 300
           DEEQ++LVLSNRKA+ADSQAQLGIGSVV+G VQSLKPYGAFIDIGGINGLLHVSQISHDR
Sbjct: 240 DEEQTKLVLSNRKAVADSQAQLGIGSVVLGVVQSLKPYGAFIDIGGINGLLHVSQISHDR 299

Query: 301 VADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF 360
           V+DIATVLQPGDTLKVMILSHDR+RGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF
Sbjct: 300 VSDIATVLQPGDTLKVMILSHDRDRGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF 359

Query: 361 RQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLT--DISPADD 414
           RQRIAQAEAMARADMLRFQPESGLTL+SDGILGPL  +LP DG+DLT  DI  A D
Sbjct: 360 RQRIAQAEAMARADMLRFQPESGLTLSSDGILGPLGSELPDDGVDLTVDDIPSAVD 415

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30692346|ref|NP_850903.1| small subunit ribosomal protein S1 [Arabidopsis thaliana] gi|13877939|gb|AAK44047.1|AF370232_1 putative ribosomal protein S1 [Arabidopsis thaliana] gi|16649089|gb|AAL24396.1| Unknown protein [Arabidopsis thaliana] gi|21593804|gb|AAM65771.1| ribosomal protein S1 [Arabidopsis thaliana] gi|23296539|gb|AAN13122.1| putative ribosomal protein S1 [Arabidopsis thaliana] gi|332006494|gb|AED93877.1| small subunit ribosomal protein S1 [Arabidopsis thaliana]

 Score =  651 bits (1679), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 325/416 (78%), Positives = 375/416 (90%), Gaps = 3/416 (0%)

Query: 1   MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREEL 60
           MA+LAQQF+GLRC P+S +    R++     Q   ++  + TIV+AVA+S+ +T+ER EL
Sbjct: 1   MASLAQQFSGLRCSPLSSSSRLSRRASKNFPQNK-SASVSPTIVAAVAMSSGQTKERLEL 59

Query: 61  NQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDIT 120
            ++FE+AYERCRT+PMEGV+FT+++F +A+E+YDFNSE+GT+VKGTVF TD  GALVDI+
Sbjct: 60  KKMFEDAYERCRTSPMEGVAFTVDDFAAAIEQYDFNSEIGTRVKGTVFKTDANGALVDIS 119

Query: 121 AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWER 180
           AKSSAYL  ++ACIH+IKHVEEAGIVPG+ EEFVIIGENE+DDSL+LSLR IQYELAWER
Sbjct: 120 AKSSAYLSVEQACIHRIKHVEEAGIVPGMVEEFVIIGENESDDSLLLSLRNIQYELAWER 179

Query: 181 CRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEV 240
           CRQLQ+EDV+VK KV+GANKGG+VA VEGLRGFVPFSQISSK+ AEELL K++PLKFVEV
Sbjct: 180 CRQLQAEDVIVKAKVIGANKGGLVALVEGLRGFVPFSQISSKAAAEELLEKEIPLKFVEV 239

Query: 241 DEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDR 300
           DEEQ++LVLSNRKA+ADSQAQLGIGSVV+G VQSLKPYGAFIDIGGINGLLHVSQISHDR
Sbjct: 240 DEEQTKLVLSNRKAVADSQAQLGIGSVVLGVVQSLKPYGAFIDIGGINGLLHVSQISHDR 299

Query: 301 VADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF 360
           V+DIATVLQPGDTLKVMILSHDR+RGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF
Sbjct: 300 VSDIATVLQPGDTLKVMILSHDRDRGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTF 359

Query: 361 RQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLT--DISPADD 414
           RQRIAQAEAMARADMLRFQPESGLTL+SDGILGPL  +LP DG+DLT  DI  A D
Sbjct: 360 RQRIAQAEAMARADMLRFQPESGLTLSSDGILGPLGSELPDDGVDLTVDDIPSAVD 415

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248430|ref|NP_001239880.1| uncharacterized protein LOC100812847 [Glycine max] gi|255635364|gb|ACU18035.1| unknown [Glycine max]

 Score =  641 bits (1654), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 307/387 (79%), Positives = 348/387 (89%), Gaps = 4/387 (1%)

Query: 28  TQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFH 87
           TQ  QK    R + TI +++AI+NA+ +ER  L +LFEEAYERCR APMEGVSFT+E+F 
Sbjct: 29  TQQSQK----RVSITIANSIAIANAQNKERARLKKLFEEAYERCRNAPMEGVSFTIEDFT 84

Query: 88  SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVP 147
           +AL+KYDF+SE+G K+KGTVF TDN GA+VDITAKSSAYLP QEACIH++KHVEEAG+VP
Sbjct: 85  AALDKYDFDSEVGGKIKGTVFYTDNNGAVVDITAKSSAYLPLQEACIHRVKHVEEAGLVP 144

Query: 148 GLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEV 207
           G KEEF+IIGEN  DDSLVLSLR +Q++LAWERCRQLQ+EDV VKGK+VG NKGGVVAE+
Sbjct: 145 GFKEEFLIIGENSIDDSLVLSLRSLQFDLAWERCRQLQAEDVTVKGKIVGVNKGGVVAEL 204

Query: 208 EGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSV 267
           EGLRGFVP SQIS+ S  EELL K+LPLKFVEVDEEQSRLVLSNRKA+A +QAQLGIGSV
Sbjct: 205 EGLRGFVPLSQISTNSNVEELLDKELPLKFVEVDEEQSRLVLSNRKAVAGNQAQLGIGSV 264

Query: 268 VIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGR 327
           V G+VQSLKPYGAFIDIGGINGLLHVSQISHDRV DI+TVLQPGD LKVMILSHDRERGR
Sbjct: 265 VTGSVQSLKPYGAFIDIGGINGLLHVSQISHDRVTDISTVLQPGDILKVMILSHDRERGR 324

Query: 328 VSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARADMLRFQPESGLTLN 387
           VSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARADMLRFQPESGLT++
Sbjct: 325 VSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARADMLRFQPESGLTIS 384

Query: 388 SDGILGPLSPDLPADGLDLTDISPADD 414
            DGILGP + DLP +GLDL+++ PA++
Sbjct: 385 GDGILGPFTSDLPEEGLDLSEVPPAEE 411

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|321437419|gb|ADW83720.1| ribosomal protein S4 [Musa acuminata AAA Group]

 Score =  633 bits (1632), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 330/415 (79%), Positives = 368/415 (88%), Gaps = 1/415 (0%)

Query: 1   MATLA-QQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREE 59
           MA+    QF GLRCPP+S + LS+  S    +     S  +  +++      +  +ER++
Sbjct: 1   MASFVNHQFAGLRCPPLSSSPLSKPSSAASSKAPARPSFCSAAVIAGTYALTSAQKERQK 60

Query: 60  LNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDI 119
           L ++FEEAY+RCRTAPMEGV+FT+E+FHSALEKYDF+SE+GTKVKGTVF TD  GALVDI
Sbjct: 61  LKEVFEEAYDRCRTAPMEGVAFTVEDFHSALEKYDFDSEIGTKVKGTVFMTDMNGALVDI 120

Query: 120 TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWE 179
           TAKSSAYLP QEACIHKIKHV EAGI PGL EEFVIIGE  ADDSL+LSLR IQY+LAWE
Sbjct: 121 TAKSSAYLPVQEACIHKIKHVSEAGIYPGLVEEFVIIGEMNADDSLILSLRSIQYDLAWE 180

Query: 180 RCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239
           RCRQLQ+EDV+VKGKVVG NKGGVVA VEGLRGFVPFSQIS+KSTAEEL+ K+LPLKFVE
Sbjct: 181 RCRQLQAEDVIVKGKVVGGNKGGVVAIVEGLRGFVPFSQISAKSTAEELIDKELPLKFVE 240

Query: 240 VDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHD 299
           VDEEQSRLVLSNRKAMADSQAQLGIGSVV+GTVQSLKPYGAF+DIGGINGLLHVSQISHD
Sbjct: 241 VDEEQSRLVLSNRKAMADSQAQLGIGSVVLGTVQSLKPYGAFVDIGGINGLLHVSQISHD 300

Query: 300 RVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT 359
           RV+DI+TVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKA+EMAQ 
Sbjct: 301 RVSDISTVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKADEMAQI 360

Query: 360 FRQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLTDISPADD 414
           FRQRIAQAEAMARADMLRFQPESGLTLNS+GILGPL+ DLPA+GLDL++I PADD
Sbjct: 361 FRQRIAQAEAMARADMLRFQPESGLTLNSEGILGPLTSDLPAEGLDLSEIPPADD 415

Source: Musa acuminata AAA Group

Species: Musa acuminata

Genus: Musa

Family: Musaceae

Order: Zingiberales

Class: Liliopsida

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	414
TAIR|locus:2145860	416	RPS1 "ribosomal protein S1" [A	0.995	0.990	0.755	3.6e-160
TIGR_CMR|BA_1519	382	BA_1519 "ribosomal protein S1"	0.579	0.628	0.321	2.8e-27
UNIPROTKB|O06147	481	rpsA "30S ribosomal protein S1	0.630	0.542	0.296	2.7e-26
TIGR_CMR|SPO_0802	558	SPO_0802 "ribosomal protein S1	0.623	0.462	0.266	1.6e-20
TIGR_CMR|CPS_2335	553	CPS_2335 "ribosomal protein S1	0.611	0.457	0.261	1.5e-18
TIGR_CMR|GSU_2603	586	GSU_2603 "ribosomal protein S1	0.596	0.421	0.276	2.8e-18
TIGR_CMR|SO_2402	555	SO_2402 "ribosomal protein S1"	0.599	0.446	0.265	1.7e-17
UNIPROTKB|Q9KQT3	556	VC_1915 "30S ribosomal protein	0.603	0.449	0.266	2.2e-17
TIGR_CMR|VC_1915	556	VC_1915 "ribosomal protein S1"	0.603	0.449	0.266	2.2e-17
UNIPROTKB|P0AG67	557	rpsA "30S ribosomal subunit pr	0.596	0.443	0.260	9.3e-17

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

 Score = 1560 (554.2 bits), Expect = 3.6e-160, P = 3.6e-160
 Identities = 315/417 (75%), Positives = 360/417 (86%)

Query:     1 MATLAQQFTGLRCPPISHT-RLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREE 59
             MA+LAQQF+GLRC P+S + RLSRR S    Q K  ++  + TIV+AVA+S+ +T+ER E
Sbjct:     1 MASLAQQFSGLRCSPLSSSSRLSRRASKNFPQNK--SASVSPTIVAAVAMSSGQTKERLE 58

Query:    60 LNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDI 119
             L ++FE+AYERCRT+PMEGV+FT+++F +A+E+YDFNSE+GT+VKGTVF TD  GALVDI
Sbjct:    59 LKKMFEDAYERCRTSPMEGVAFTVDDFAAAIEQYDFNSEIGTRVKGTVFKTDANGALVDI 118

Query:   120 TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWE 179
             +AKSSAYL  ++ACIH+IKHVEEAGIVPG+ EEFVIIGENE+DDSL+LSLR IQYELAWE
Sbjct:   119 SAKSSAYLSVEQACIHRIKHVEEAGIVPGMVEEFVIIGENESDDSLLLSLRNIQYELAWE 178

Query:   180 RCRQLQSEDXXXXXXXXXXXXXXXXXXXXXLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239
             RCRQLQ+ED                     LRGFVPFSQISSK+ AEELL K++PLKFVE
Sbjct:   179 RCRQLQAEDVIVKAKVIGANKGGLVALVEGLRGFVPFSQISSKAAAEELLEKEIPLKFVE 238

Query:   240 VDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHD 299
             VDEEQ++LVLSNRKA+ADSQAQLGIGSVV+G VQSLKPYGAFIDIGGINGLLHVSQISHD
Sbjct:   239 VDEEQTKLVLSNRKAVADSQAQLGIGSVVLGVVQSLKPYGAFIDIGGINGLLHVSQISHD 298

Query:   300 RVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT 359
             RV+DIATVLQPGDTLKVMILSHDR+RGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT
Sbjct:   299 RVSDIATVLQPGDTLKVMILSHDRDRGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQT 358

Query:   360 FRQRIAQAEAMARADMLRFQPESGLTLNSDGILGPLSPDLPADGLDLT--DISPADD 414
             FRQRIAQAEAMARADMLRFQPESGLTL+SDGILGPL  +LP DG+DLT  DI  A D
Sbjct:   359 FRQRIAQAEAMARADMLRFQPESGLTLSSDGILGPLGSELPDDGVDLTVDDIPSAVD 415

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

GO:0005739 "mitochondrion" evidence=ISM

GO:0009507 "chloroplast" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

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

GO:0006364 "rRNA processing" evidence=RCA

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

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

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

GO:0034660 "ncRNA metabolic process" evidence=RCA

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

 Score = 306 (112.8 bits), Expect = 2.8e-27, P = 2.8e-27
 Identities = 83/258 (32%), Positives = 136/258 (52%)

Query:    98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKE--EFVI 155
             ++G  V G+V   + +  LV++  K+   +P  E  +  + H+E+A  V  L +  E  +
Sbjct:    16 QVGDVVTGSVTKVEEKQVLVNVGYKTDGVIPISE--LANV-HIEKASDVVELDQTLELKV 72

Query:   156 IGENEADDSLVLSLRMIQYELAWERCRQLQSEDXXXXXXXXXXXXXXXXXXXXXLRGFVP 215
             I   E D  LVLS R +  E AW   ++ +                        +RGF+P
Sbjct:    73 IKLEEND--LVLSKRAVDAEKAWVELQE-KFNSGHVFDVTVKDIVNGGLVVDLGVRGFIP 129

Query:   216 FSQISSKSTAE--ELLGKDLPLKFVEVDEEQSRLVLSNRKAMA---DSQAQLGI-----G 265
              S +      +  +  GK L +K VE+D E++R++LS++  +    DS+ +  I     G
Sbjct:   130 ASLVEVHYVEDFTDYKGKTLAVKIVELDREKNRVILSHKAVVELELDSKKKEAISSLKEG 189

Query:   266 SVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRER 325
              VV GTVQ L  +GAF+++GG++GL+H+SQISH+RV   + VL+ G  +KV +LS D + 
Sbjct:   190 DVVEGTVQRLTDFGAFVNVGGVDGLVHISQISHERVEQPSEVLEQGQKVKVKVLSVDADT 249

Query:   326 GRVSLSTKKLEPTPGDMI 343
              R+SLS K  +P P + +
Sbjct:   250 QRISLSIKAAQPGPWENV 267

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

GO:0006412 "translation" evidence=ISS

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

 Score = 300 (110.7 bits), Expect = 2.7e-26, P = 2.7e-26
 Identities = 84/283 (29%), Positives = 145/283 (51%)

Query:    73 TAPMEGVSF--TLEEFHSALEK---YDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYL 127
             T+P   V+   + E+F +A++K   Y FN   G  V+GT+   D    L+DI  K+   +
Sbjct:     7 TSPQVAVNDIGSSEDFLAAIDKTIKY-FND--GDIVEGTIVKVDRDEVLLDIGYKTEGVI 63

Query:   128 PTQEACI-HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQS 186
             P +E  I H +   E   +  G + E +++ + + +  L+LS +  QYE AW     L+ 
Sbjct:    64 PARELSIKHDVDPNEVVSV--GDEVEALVLTKEDKEGRLILSKKRAQYERAWGTIEALKE 121

Query:   187 EDXXXXXXXXXXXXXXXXXXXXXLRGFVPFSQISSKSTAE--ELLGKDLPLKFVEVDEEQ 244
             +D                     LRGF+P S +  +   +    +GK++  K +E+D+ +
Sbjct:   122 KDEAVKGTVIEVVKGGLILDIG-LRGFLPASLVEMRRVRDLQPYIGKEIEAKIIELDKNR 180

Query:   245 SRLVLSNRKAMADSQAQ--------LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQI 296
             + +VLS R  +  +Q++        L  G++  G V S+  +GAF+D+GG++GL+HVS++
Sbjct:   181 NNVVLSRRAWLEQTQSEVRSEFLNNLQKGTIRKGVVSSIVNFGAFVDLGGVDGLVHVSEL 240

Query:   297 SHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP 339
             S   +   + V+Q GD + V +L  D +R RVSLS K  +  P
Sbjct:   241 SWKHIDHPSEVVQVGDEVTVEVLDVDMDRERVSLSLKATQEDP 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|SPO_0802 SPO_0802 "ribosomal protein S1" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 264 (98.0 bits), Expect = 1.6e-20, P = 1.6e-20
 Identities = 73/274 (26%), Positives = 133/274 (48%)

Query:    82 TLEEFHSAL-EKYDFNS-ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKH 139
             ++EEF + L E ++ ++ E G+ VKG V   +   A++D+  K    +  +E        
Sbjct:     5 SMEEFEALLNESFEMDTPEEGSVVKGKVIAIEAGQAIIDVGYKMEGRVELKEFA----NP 60

Query:   140 VEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDXXXXXXXXXXX 199
              E   I  G + E  +     A    V+S  M + E AW+R  +  ++D           
Sbjct:    61 GEAPEISIGDEVEVYLRAAENARGEAVISREMARREEAWDRLEKAYADDQRVEGAIFGRV 120

Query:   200 XXXXXXXXXXLRGFVPFSQISSKST--AEELLGKDLPLKFVEVDEEQSRLVLSNRKAMAD 257
                          F+P SQ+  +    A  L+G   P + +++D  +  +V+S R  + +
Sbjct:   121 KGGFTVDLGGAVAFLPGSQVDVRPVRDAGPLMGLKQPFQILKMDRRRGNIVVSRRAILEE 180

Query:   258 SQAQ--------LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQ 309
             S+A+        L  G  V G V+++  YGAF+D+GG++GLLHV+ ++  RV     +L 
Sbjct:   181 SRAEQRAEVIGNLTEGQTVDGVVKNITEYGAFVDLGGVDGLLHVTDMAWRRVNHPNEILN 240

Query:   310 PGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMI 343
              G+T+KV ++  +++  R+SL  K+L+  P D++
Sbjct:   241 IGETVKVQVIKINKDTHRISLGMKQLQEDPWDLV 274

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

GO:0006412 "translation" evidence=ISS

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

 Score = 247 (92.0 bits), Expect = 1.5e-18, Sum P(2) = 1.5e-18
 Identities = 71/271 (26%), Positives = 129/271 (47%)

Query:    86 FHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE-EAG 144
             F  +L++ +  +  G+ ++GT+   +    +VD   KS + +      I + K+   E  
Sbjct:     9 FEESLKEIE--TRPGSIIRGTIVAVNKDNVIVDAGLKSESVIS-----IDQFKNAAGEVE 61

Query:   145 IVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDXXXXXXXXXXXXXXXX 204
             +V G + +  +   ++     +LS    +   AW+   +   E                 
Sbjct:    62 VVVGDEIDVALDATDDGFGETILSREKAKRHEAWQVLEKAYEEKETVIGVINGKVKGGFT 121

Query:   205 XXXXXLRGFVPFSQISSKSTAE--ELLGKDLPLKFVEVDEEQSRLVLSNRKAM-ADSQAQ 261
                  +R F+P S +  +   +   L GK L  K +++D++++ +V+S R  + A+  A+
Sbjct:   122 VEVSDIRAFLPGSLVDVRPVRDTAHLEGKPLEFKVIKLDQKRNNVVVSRRAVIEAEGSAE 181

Query:   262 -------LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTL 314
                    L  G  V G V++L  YGAF+D+GGI+GLLH++ ++  RV   + ++  GD +
Sbjct:   182 RDELLESLAEGQEVKGIVKNLTDYGAFVDLGGIDGLLHITDMAWKRVKHPSEIVNVGDEI 241

Query:   315 KVMILSHDRERGRVSLSTKKLEPTPGDMIRN 345
             +V +L  DRER RVSL  K+L   P   I N
Sbjct:   242 QVKVLKFDRERTRVSLGMKQLGEDPWVAIAN 272

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

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

 Score = 246 (91.7 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 74/268 (27%), Positives = 127/268 (47%)

Query:    85 EFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAG 144
             EF    ++   +  +G  VKG V    N   LVDI  KS   +P +E        ++EAG
Sbjct:    32 EFAELFQESIRHHHVGEVVKGKVVHISNDYVLVDIGYKSEGSIPVEE-------FLDEAG 84

Query:   145 -IVPGLKEEFVIIGENEADDS--LVLSLRMIQYELAWERCRQLQSEDXXXXXXXXXXXXX 201
              +   + +E   + E + +     VLS R      AW+       E              
Sbjct:    85 NLTVQVGDEVKALFERKENQKGYAVLSKRKADRLSAWDSIDAAGGEGGIVEGKITGKVKG 144

Query:   202 XXXXXXXXLRGFVPFSQISSK--STAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQ 259
                     ++ F+P SQ+  +     ++ +G     K +++++++  +VLS R  + + +
Sbjct:   145 GLTVDIG-VQAFLPASQVDLRPGGNLDKYIGVTDRFKVLKLNKKRGNIVLSRRVLLEEER 203

Query:   260 A--------QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG 311
             A         L  G    G V+++  YGAF+DIGG++GLLHV+ +S  R+   + +L+PG
Sbjct:   204 AGVRTETLANLAEGQTREGVVKNITDYGAFVDIGGVDGLLHVTDMSWGRLGHPSEMLKPG 263

Query:   312 DTLKVMILSHDRERGRVSLSTKKLEPTP 339
             D L V IL +D+E+G++SL  K++ P P
Sbjct:   264 DKLSVKILKYDQEKGKISLGLKQITPDP 291

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

GO:0006412 "translation" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

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

 Score = 239 (89.2 bits), Expect = 1.7e-17, P = 1.7e-17
 Identities = 70/264 (26%), Positives = 125/264 (47%)

Query:    86 FHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGI 145
             F  +L+  +F    G+ V+GTV   +N   LVD   KS + +P ++      + V E  +
Sbjct:     9 FEQSLQTLEFRP--GSIVRGTVVAIENGMVLVDAGLKSESPIPAEQ--FKNAQGVLEIAV 64

Query:   146 VPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDXXXXXXXXXXXXXXXXX 205
               G + +  +    +      LS    +   AW    +   +                  
Sbjct:    65 --GDEVDVALDSVEDGFGETQLSREKAKRHEAWIVLEKAYEDAETVIGIINGKVKGGFTV 122

Query:   206 XXXXLRGFVPFSQISSKSTAE--ELLGKDLPLKFVEVDEEQSRLVLSNRKAM-ADSQAQ- 261
                 +R F+P S +  +   +   L  K+L  K +++D++++ +V+S R  + ++S A+ 
Sbjct:   123 ELNGIRAFLPGSLVDVRPVRDTAHLEYKELEFKVIKLDQKRNNVVVSRRAVIESESSAER 182

Query:   262 ------LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLK 315
                   L  G  V G V++L  YGAF+D+GG++GLLH++ ++  RV   + ++  GD + 
Sbjct:   183 DALLENLQEGQAVKGIVKNLTDYGAFVDLGGVDGLLHITDMAWKRVKHPSEIVNVGDEIN 242

Query:   316 VMILSHDRERGRVSLSTKKLEPTP 339
             V +L +DRER RVSL  K+L   P
Sbjct:   243 VKVLKYDRERTRVSLGLKQLGEDP 266

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

GO:0006412 "translation" evidence=ISS

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

 Score = 238 (88.8 bits), Expect = 2.2e-17, P = 2.2e-17
 Identities = 72/270 (26%), Positives = 127/270 (47%)

Query:    84 EEFHSALEKY--DFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE 141
             E F    E++  +   + GT VKGTV   +N   LVD   KS + +P ++      K+  
Sbjct:     3 ESFAQLFEEFLNETQFQQGTIVKGTVVAIENGYVLVDAGLKSESAIPAEQ-----FKNAA 57

Query:   142 -EAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDXXXXXXXXXXXX 200
              E  +  G + +  +    +      LS    +   AW    +   E             
Sbjct:    58 GELEVQVGSQVDVALDAVEDGFGETQLSREKAKRHEAWIVLEKAYEEAATVIGIINGKVK 117

Query:   201 XXXXXXXXXLRGFVPFSQISSKSTAE--ELLGKDLPLKFVEVDEEQSRLVLSNRKAMADS 258
                      +R F+P S +  +   +   L  K+L  K +++D++++ +V+S R+A+ +S
Sbjct:   118 GGFTVELNGIRAFLPGSLVDVRPIRDTAHLENKELEFKVIKLDQKRNNVVVS-RRAVIES 176

Query:   259 QAQ---------LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQ 309
             ++          L  G+ V G V++L  YGAF+D+GG++GLLH++ ++  RV   + ++ 
Sbjct:   177 ESSVERDELLETLQEGTEVKGIVKNLTDYGAFVDLGGVDGLLHITDMAWKRVKHPSEIVN 236

Query:   310 PGDTLKVMILSHDRERGRVSLSTKKLEPTP 339
              GD + V +L  DR+R RVSL  K+L   P
Sbjct:   237 VGDEILVKVLKFDRDRTRVSLGLKQLGEDP 266

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

GO:0006412 "translation" evidence=ISS

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

 Score = 238 (88.8 bits), Expect = 2.2e-17, P = 2.2e-17
 Identities = 72/270 (26%), Positives = 127/270 (47%)

Query:    84 EEFHSALEKY--DFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE 141
             E F    E++  +   + GT VKGTV   +N   LVD   KS + +P ++      K+  
Sbjct:     3 ESFAQLFEEFLNETQFQQGTIVKGTVVAIENGYVLVDAGLKSESAIPAEQ-----FKNAA 57

Query:   142 -EAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDXXXXXXXXXXXX 200
              E  +  G + +  +    +      LS    +   AW    +   E             
Sbjct:    58 GELEVQVGSQVDVALDAVEDGFGETQLSREKAKRHEAWIVLEKAYEEAATVIGIINGKVK 117

Query:   201 XXXXXXXXXLRGFVPFSQISSKSTAE--ELLGKDLPLKFVEVDEEQSRLVLSNRKAMADS 258
                      +R F+P S +  +   +   L  K+L  K +++D++++ +V+S R+A+ +S
Sbjct:   118 GGFTVELNGIRAFLPGSLVDVRPIRDTAHLENKELEFKVIKLDQKRNNVVVS-RRAVIES 176

Query:   259 QAQ---------LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQ 309
             ++          L  G+ V G V++L  YGAF+D+GG++GLLH++ ++  RV   + ++ 
Sbjct:   177 ESSVERDELLETLQEGTEVKGIVKNLTDYGAFVDLGGVDGLLHITDMAWKRVKHPSEIVN 236

Query:   310 PGDTLKVMILSHDRERGRVSLSTKKLEPTP 339
              GD + V +L  DR+R RVSL  K+L   P
Sbjct:   237 VGDEILVKVLKFDRDRTRVSLGLKQLGEDP 266

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

GO:0006412 "translation" evidence=ISS

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

 Score = 233 (87.1 bits), Expect = 9.3e-17, Sum P(2) = 9.3e-17
 Identities = 69/265 (26%), Positives = 126/265 (47%)

Query:    86 FHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE-EAG 144
             F  +L++ +  +  G+ V+G V   D    LVD   KS + +P ++      K+ + E  
Sbjct:     9 FEESLKEIE--TRPGSIVRGVVVAIDKDVVLVDAGLKSESAIPAEQ-----FKNAQGELE 61

Query:   145 IVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDXXXXXXXXXXXXXXXX 204
             I  G + +  +    +     +LS    +   AW    +   +                 
Sbjct:    62 IQVGDEVDVALDAVEDGFGETLLSREKAKRHEAWITLEKAYEDAETVTGVINGKVKGGFT 121

Query:   205 XXXXXLRGFVPFSQISSKSTAE--ELLGKDLPLKFVEVDEEQSRLVLSNRKAM-ADSQAQ 261
                  +R F+P S +  +   +   L GK+L  K +++D++++ +V+S R  + +++ A+
Sbjct:   122 VELNGIRAFLPGSLVDVRPVRDTLHLEGKELEFKVIKLDQKRNNVVVSRRAVIESENSAE 181

Query:   262 -------LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTL 314
                    L  G  V G V++L  YGAF+D+GG++GLLH++ ++  RV   + ++  GD +
Sbjct:   182 RDQLLENLQEGMEVKGIVKNLTDYGAFVDLGGVDGLLHITDMAWKRVKHPSEIVNVGDEI 241

Query:   315 KVMILSHDRERGRVSLSTKKLEPTP 339
              V +L  DRER RVSL  K+L   P
Sbjct:   242 TVKVLKFDRERTRVSLGLKQLGEDP 266

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

GO:0003729 "mRNA binding" evidence=IDA

GO:0016020 "membrane" evidence=IDA

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

GO:0003723 "RNA binding" evidence=IDA

GO:0006412 "translation" evidence=IMP

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

GO:0005737 "cytoplasm" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P46228	RS1_SYNP6	No assigned EC number	0.5017	0.7028	0.9478	yes	no
P29344	RR1_SPIOL	No assigned EC number	0.8305	0.9830	0.9902	N/A	no

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	414
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	1e-117
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	4e-73
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	9e-57
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	4e-50
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	8e-50
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	2e-38
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	5e-31
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	4e-30
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	6e-29
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	1e-26
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	1e-26
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	2e-25
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	3e-23
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	2e-22
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	3e-21
cd04465	67	cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec	6e-21
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	1e-20
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-20
pfam00575	74	pfam00575, S1, S1 RNA binding domain	1e-19
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	4e-19
PRK08059	123	PRK08059, PRK08059, general stress protein 13; Val	6e-19
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	4e-17
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	5e-17
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	3e-16
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	3e-16
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	2e-15
COG1098	129	COG1098, VacB, Predicted RNA binding protein (cont	4e-15
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	7e-15
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	7e-15
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	7e-15
cd05708	77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	1e-14
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-14
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	7e-14
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	1e-13
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	2e-13
PRK05807	136	PRK05807, PRK05807, hypothetical protein; Provisio	1e-12
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	7e-12
COG2183	780	COG2183, Tex, Transcriptional accessory protein [T	9e-12
cd05684	79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	3e-11
cd05687	70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	4e-11
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	1e-10
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	1e-10
pfam00575	74	pfam00575, S1, S1 RNA binding domain	2e-10
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	4e-10
pfam00575	74	pfam00575, S1, S1 RNA binding domain	2e-09
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	3e-09
PRK07252	120	PRK07252, PRK07252, hypothetical protein; Provisio	4e-09
cd05698	70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	6e-09
cd05687	70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	7e-09
PRK08582	139	PRK08582, PRK08582, hypothetical protein; Provisio	2e-08
cd05691	73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	3e-08
cd04461	83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	5e-08
cd05690	69	cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: R	8e-08
PRK08563	187	PRK08563, PRK08563, DNA-directed RNA polymerase su	2e-07
PRK03987	262	PRK03987, PRK03987, translation initiation factor	2e-07
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	3e-07
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	3e-07
cd05689	72	cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: R	5e-07
cd05686	73	cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-b	7e-07
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	2e-06
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	3e-06
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	5e-06
cd04460	99	cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-bindi	8e-06
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	1e-05
cd04465	67	cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec	1e-04
COG1095	183	COG1095, RPB7, DNA-directed RNA polymerase, subuni	1e-04
TIGR02696	719	TIGR02696, pppGpp_PNP, guanosine pentaphosphate sy	2e-04
cd04453	88	cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase	2e-04
cd05697	69	cd05697, S1_Rrp5_repeat_hs5, S1_Rrp5_repeat_hs5: R	2e-04
cd05789	86	cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-bindin	5e-04
PLN00207	891	PLN00207, PLN00207, polyribonucleotide nucleotidyl	5e-04
COG1097	239	COG1097, RRP4, RNA-binding protein Rrp4 and relate	9e-04

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

 Score =  344 bits (883), Expect = e-117
 Identities = 150/299 (50%), Positives = 216/299 (72%), Gaps = 3/299 (1%)

Query: 72  RTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQE 131
           +    + + FT E+F + L+KYD++ + G  V GTVF  + RGAL+DI AK++A++P QE
Sbjct: 4   QNTDADDIGFTHEDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQE 63

Query: 132 ACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVV 191
             I++++  EE  + P    EF I+ +   D  L LS+R I+Y  AWER RQLQ ED  V
Sbjct: 64  MSINRVEGPEEV-LQPNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATV 122

Query: 192 KGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSN 251
           + +V   N+GG +  +EGLRGF+P S IS++   EEL+G++LPLKF+EVDEE++RLVLS+
Sbjct: 123 RSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKEELVGEELPLKFLEVDEERNRLVLSH 182

Query: 252 RKAMADSQA-QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQP 310
           R+A+ + +  +L +G VV+GTV+ +KPYGAFIDIGG++GLLH+S+ISH+ +    +V   
Sbjct: 183 RRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNV 242

Query: 311 GDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRI-AQAE 368
            D +KVMI+  D ERGR+SLSTK+LEP PGDM+++P+ VF+KAEEMA  +RQ + AQAE
Sbjct: 243 NDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDPQKVFDKAEEMAAKYRQMLLAQAE 301

Length = 318

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

 Score =  237 bits (608), Expect = 4e-73
 Identities = 104/293 (35%), Positives = 163/293 (55%), Gaps = 17/293 (5%)

Query: 82  TLEEFHSALEKYDFNSEL---GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK 138
             EEF    E+ D + E    G  VKGTV   +  G LVDI  KS   +P  E      +
Sbjct: 1   EEEEFAELFEESDKSDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEF---SNE 57

Query: 139 HVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGA 198
            VE+  +  G + E +++   + +  LVLS R  + E AWE+  +      +V+GK+ G 
Sbjct: 58  PVEDV-VQVGDEVEVLVLRVEDGEGELVLSRRKAERERAWEKLEEAFENGEIVEGKITGK 116

Query: 199 NKGGVVAEVEGLRGFVPFSQISSKS--TAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMA 256
            KGG+  ++EG+R F+P S +  +     + L+GK+L  K +E+D++++ +VLS R  + 
Sbjct: 117 VKGGLTVDIEGVRAFLPGSLVDVRPVRDLDPLIGKELEFKILELDKKRNNVVLSRRAVLE 176

Query: 257 DSQA--------QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVL 308
           + ++        +L +G VV G V+++  YGAF+DIGG++GLLH+S+IS  RV   + V+
Sbjct: 177 EERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDHPSEVV 236

Query: 309 QPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFR 361
           + GD +KV ++S D ERGRVSLS K+LE  P + I     V +K E       
Sbjct: 237 KVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLT 289

Length = 541

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

 Score =  190 bits (486), Expect = 9e-57
 Identities = 87/257 (33%), Positives = 143/257 (55%), Gaps = 12/257 (4%)

Query: 98  ELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVII 156
           E+G  V G V   +++   V+I   K    +P  E     I+ + +  +  G + E  ++
Sbjct: 16  EVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDV-VKVGDELEVYVL 74

Query: 157 GENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPF 216
              + + +L+LS R ++ E AW++  +   E  VV+ KV    KGG+V +VEG+RGF+P 
Sbjct: 75  KVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPA 134

Query: 217 SQISSK--STAEELLGKDLPLKFVEVDEEQSRLVLSNR--------KAMADSQAQLGIGS 266
           S IS++      +  GK L +K +E+D E++R++LS R            +  + L  G 
Sbjct: 135 SLISTRFVEDFSDFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGD 194

Query: 267 VVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERG 326
           VV GTV  L  +GAF+DIGG++GL+H+S++SH+RV   + V+  G  ++V +LS D E  
Sbjct: 195 VVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETE 254

Query: 327 RVSLSTKKLEPTPGDMI 343
           R+SLS K   P P + +
Sbjct: 255 RISLSLKDTLPGPWEGV 271

Length = 390

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

 Score =  177 bits (452), Expect = 4e-50
 Identities = 83/269 (30%), Positives = 139/269 (51%), Gaps = 18/269 (6%)

Query: 84  EEFHSALEKY--DFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE 141
           E F    E+   +  +  G+ VKGTV   D    LVD+  KS   +P +E      K+ +
Sbjct: 13  ESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEE-----FKNEQ 67

Query: 142 -EAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANK 200
            E  +  G + E  +    +     VLS    +   AW++  +      +V+G + G  K
Sbjct: 68  GELEVKVGDEVEVYVERIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVK 127

Query: 201 GGVVAEVEGLRGFVPFSQISSKST--AEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADS 258
           GG   ++ G+  F+P SQ+  +     + L GK+L  K +++D++++ +V+S R  + + 
Sbjct: 128 GGFTVDLNGVEAFLPGSQVDVRPVRDTDPLEGKELEFKVIKLDKKRNNIVVSRRAVLEEE 187

Query: 259 QA--------QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQP 310
           +A         L  G VV G V+++  YGAF+D+GG++GLLH++ IS  RV   + V+  
Sbjct: 188 RAEEREELLENLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVNHPSEVVNV 247

Query: 311 GDTLKVMILSHDRERGRVSLSTKKLEPTP 339
           GD +KV +L  D+E+ RVSL  K+L   P
Sbjct: 248 GDEVKVKVLKFDKEKKRVSLGLKQLGEDP 276

Length = 565

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

 Score =  177 bits (452), Expect = 8e-50
 Identities = 89/267 (33%), Positives = 142/267 (53%), Gaps = 12/267 (4%)

Query: 84  EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEA 143
            E    + + +     G  VKGTV   +     VD+  KS   +P +E  + +I  ++E+
Sbjct: 287 NEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKES 346

Query: 144 GIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGV 203
             V G + E  ++   + D  +VLS +    E AW+   +       VKGKV    KGG+
Sbjct: 347 VKV-GDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGL 405

Query: 204 VAEVEGLRGFVPFSQISSKSTAE--ELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQ 261
           + +  G+R F+P S +      +  E  G++L +K +E + ++ + V+ +RKA+ + + +
Sbjct: 406 LVDYGGVRAFLPASHVELGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKE 465

Query: 262 ---------LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGD 312
                    L  G VV G V+ L  +GAF+DIGG++GLLHVS+IS  RV   + VL+ GD
Sbjct: 466 KKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKVGD 525

Query: 313 TLKVMILSHDRERGRVSLSTKKLEPTP 339
            +KV IL  D+E  ++SLS KKL P P
Sbjct: 526 EIKVYILDIDKENKKLSLSLKKLLPDP 552

Length = 647

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

 Score =  144 bits (365), Expect = 2e-38
 Identities = 82/275 (29%), Positives = 136/275 (49%), Gaps = 20/275 (7%)

Query: 84  EEFHSALEK-YDFNSEL-GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE 141
           E F   LE+         G+ VKGTV   +     VD+  KS   +P +E          
Sbjct: 1   ESFAQLLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEE--FLDAPLEI 58

Query: 142 EAGIVPGLKEEFVIIGENEADDSL-VLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANK 200
           + G      E  V +   E      VLS    Q    W +  +   E  +V+GK+VG  K
Sbjct: 59  QVG-----DEVEVYLDRVEDRFGETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVK 113

Query: 201 GGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVEVDEEQSRLVLS-------- 250
           GG + ++ G+  F+P SQ+  K     + L+GK L  K +++D++++ +V+S        
Sbjct: 114 GGFIVDLNGVEAFLPGSQVDVKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEE 173

Query: 251 NRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQP 310
             +A  +    L  G VV G V+++  +GAF+D+GG++GLLH++ +S  RV   +  ++ 
Sbjct: 174 RSQAREELLENLKEGDVVKGVVKNITDFGAFVDLGGVDGLLHITDMSWKRVKHPSEYVKV 233

Query: 311 GDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRN 345
           G  +KV ++  D+E+GR+SLS K+L   P + I  
Sbjct: 234 GQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEK 268

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

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

 Score =  123 bits (311), Expect = 5e-31
 Identities = 89/267 (33%), Positives = 153/267 (57%), Gaps = 22/267 (8%)

Query: 82  TLEEFHSALE---KYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK 138
           + E+F +A++   KY FN   G  V+GTV   D    L+DI  K+   +P++E     IK
Sbjct: 18  SAEDFLAAIDKTIKY-FND--GDIVEGTVVKVDRDEVLLDIGYKTEGVIPSREL---SIK 71

Query: 139 H-VEEAGIVP-GLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVV 196
           H V+   +V  G + E +++ + + +  L+LS +  QYE AW    +++ +D VV G V+
Sbjct: 72  HDVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVI 131

Query: 197 GANKGGVVAEVEGLRGFVPFSQISSKSTA--EELLGKDLPLKFVEVDEEQSRLVLSNRKA 254
              KGG++ ++ GLRGF+P S +  +     +  +G+++  K +E+D+ ++ +VLS R  
Sbjct: 132 EVVKGGLILDI-GLRGFLPASLVEMRRVRDLQPYIGQEIEAKIIELDKNRNNVVLSRRAW 190

Query: 255 MADSQA--------QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIAT 306
           +  +Q+        QL  G V  G V S+  +GAF+D+GG++GL+HVS++S   +   + 
Sbjct: 191 LEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSE 250

Query: 307 VLQPGDTLKVMILSHDRERGRVSLSTK 333
           V++ G  + V +L  D +R RVSLS K
Sbjct: 251 VVEVGQEVTVEVLDVDMDRERVSLSLK 277

Length = 486

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

 Score =  121 bits (306), Expect = 4e-30
 Identities = 73/262 (27%), Positives = 130/262 (49%), Gaps = 18/262 (6%)

Query: 98  ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157
           E G  V+G +      G  VDI     A+LP     +  ++ ++    + G + EF I+ 
Sbjct: 104 ENGEIVEGKITGKVKGGLTVDIEG-VRAFLPGSLVDVRPVRDLDP---LIGKELEFKILE 159

Query: 158 ENEADDSLVLSLRMIQYELAWERCRQLQSEDV----VVKGKVVGANKGGVVAEVEGLRGF 213
            ++  +++VLS R +  E      R+     +    VV+G V      G   ++ G+ G 
Sbjct: 160 LDKKRNNVVLSRRAVL-EEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGGVDGL 218

Query: 214 VPFSQISSKSTA--EELL--GKDLPLKFVEVDEEQSRLVLSNRKAMADS----QAQLGIG 265
           +  S+IS K      E++  G ++ +K + +DEE+ R+ LS ++   D     + +  +G
Sbjct: 219 LHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVG 278

Query: 266 SVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRE 324
             V G V +L  YGAF++I  G+ GL+HVS+IS  +    + V++ G  ++V +L  D E
Sbjct: 279 DKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPE 338

Query: 325 RGRVSLSTKKLEPTPGDMIRNP 346
           R R+SL  K+L+  P +   + 
Sbjct: 339 RRRISLGLKQLKENPWEEFADK 360

Length = 541

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

 Score =  107 bits (269), Expect = 6e-29
 Identities = 42/70 (60%), Positives = 55/70 (78%), Gaps = 2/70 (2%)

Query: 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323
           GSVV GTV  LKP+GAF+++G GI+GL+H+SQI+H RV D+  VL+ GD +KV +LS D 
Sbjct: 1   GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID- 59

Query: 324 ERGRVSLSTK 333
            RGR+SLS K
Sbjct: 60  ARGRISLSIK 69

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 69

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

 Score =  109 bits (275), Expect = 1e-26
 Identities = 69/239 (28%), Positives = 120/239 (50%), Gaps = 25/239 (10%)

Query: 152 EFVIIGENEADDSLVLSLRMI-QYELAWERCRQLQS--EDVVVKGKVVGANKGGVVAEVE 208
           E  II  +   + ++LS R + + E A ++   L S  E  VV+G V      G   ++ 
Sbjct: 154 EVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG 213

Query: 209 GLRGFVPFSQISSK--STAEELL--GKDLPLKFVEVDEEQSRLVLSNRKAMADS----QA 260
           G+ G V  S++S +      E++  G+++ +K + +D E  R+ LS +  +       + 
Sbjct: 214 GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEE 273

Query: 261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMIL 319
           +L  G V+ GTV+ L  +GAF+++  G+ GL+H+SQISH  +A  + VL+ G  +KV +L
Sbjct: 274 KLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVL 333

Query: 320 SHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEA--MARADML 376
             + E  R+SLS K LE  P            + E+  + +RQ     E    +  D++
Sbjct: 334 EVNEEEKRISLSIKALEEAP-----------AEEEDRREEYRQYELPEEETGFSLGDLI 381

Length = 390

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

 Score =  111 bits (281), Expect = 1e-26
 Identities = 80/261 (30%), Positives = 132/261 (50%), Gaps = 25/261 (9%)

Query: 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN 159
           G  VKG V      G LVD      A+LP       ++ +VE+     G + E  II  N
Sbjct: 390 GEPVKGKVKEVVKGGLLVDY-GGVRAFLPASHV---ELGYVEDLSEYKGQELEVKIIEFN 445

Query: 160 EADD-SLVLSLRMI-------QYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLR 211
                 +VLS + I       + E  W     L+ E  VV+G+V      G   ++ G+ 
Sbjct: 446 RKRRKKVVLSRKAILEEEKEKKKEETWNS---LE-EGDVVEGEVKRLTDFGAFVDIGGVD 501

Query: 212 GFVPFSQIS---SKSTAEEL-LGKDLPLKFVEVDEEQSRLVLSNRKAMADS----QAQLG 263
           G +  S+IS    +  ++ L +G ++ +  +++D+E  +L LS +K + D     + +  
Sbjct: 502 GLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYP 561

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           +GS+V+G V  + P+GAF+++  G++GL+H+SQIS  R+     VL  G+ +K  IL  D
Sbjct: 562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVD 621

Query: 323 RERGRVSLSTKKLEPTPGDMI 343
            E  R+ LS K++E  PGD+ 
Sbjct: 622 PEEKRIRLSIKEVEEEPGDIE 642

Length = 647

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

 Score =  107 bits (270), Expect = 2e-25
 Identities = 75/276 (27%), Positives = 137/276 (49%), Gaps = 19/276 (6%)

Query: 87  HSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIV 146
           H    K +   E G+ V+G +      G +VD+     A+LP  +  +  IK ++    +
Sbjct: 88  HELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNG-VEAFLPGSQVDVKPIKDLDS---L 143

Query: 147 PGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQS---EDVVVKGKVVGANKGGV 203
            G   +F II  ++  +++V+S R    E   +   +L     E  VVKG V      G 
Sbjct: 144 IGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGA 203

Query: 204 VAEVEGLRGFVPFSQISSKSTA--EELL--GKDLPLKFVEVDEEQSRLVLSNRKAMADS- 258
             ++ G+ G +  + +S K      E +  G+++ +K ++ D+E+ R+ LS ++   D  
Sbjct: 204 FVDLGGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPW 263

Query: 259 ---QAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR-VADIATVLQPGDT 313
              + +  +G  + G V +L  YG F++I  GI GL+HVS++S  +  +  + V++ GD 
Sbjct: 264 EAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDE 323

Query: 314 LKVMILSHDRERGRVSLSTKKLEPTPGDMI--RNPK 347
           ++VMIL  D ER R+SL  K+ +  P +    ++P 
Sbjct: 324 VEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPV 359

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

 Score = 91.9 bits (229), Expect = 3e-23
 Identities = 32/68 (47%), Positives = 48/68 (70%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323
            G VV GTV+S+  +GAF+D+GG++GLLH+S +S  RV   + V+  GD ++V +L  D+
Sbjct: 1   EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDK 60

Query: 324 ERGRVSLS 331
           ER R+SL 
Sbjct: 61  ERKRISLG 68

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 68

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

 Score = 99.0 bits (247), Expect = 2e-22
 Identities = 79/282 (28%), Positives = 125/282 (44%), Gaps = 32/282 (11%)

Query: 84  EEFHSALEKY--DFNSEL--GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKH 139
           E F   LE Y  +  +EL  G K+ GTV         VD  +K        +  + + + 
Sbjct: 15  ESFAELLEAYEGERKTELRVGDKITGTVIAITEDSVFVDTGSKV-------DGVVDRAEL 67

Query: 140 VEEAGIVP---GLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVV 196
           ++  G +    G + E  ++  N     + LS  +     A     +     V V+GKV 
Sbjct: 68  LDADGELTVAVGDEVELYVVSVN--GQEIRLSKALSGQGGA-AMLEEAYENGVPVEGKVT 124

Query: 197 GANKGGVVAEVEGLRGFVPFSQISSKST--AEELLGKDLPLKFVEVDEEQSRLVLSNRKA 254
           G  KGG   EV G R F P SQI  +     E  +G+        V+E    +V+S R  
Sbjct: 125 GTCKGGFNVEVLGRRAFCPVSQIDLRYVEDPESYVGQTFQFLITRVEENGRNIVVSRRAL 184

Query: 255 MADSQAQ--------LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIA 305
           +   Q +        +  G VV GTV  L P+GAF+++  G+ G++H+S++S  RV    
Sbjct: 185 LEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKAD 244

Query: 306 TVLQPGDTLKVMILSHDRERG----RVSLSTKKLEPTPGDMI 343
             +  GDT++V +L  +R +     R+SLS K+    P D +
Sbjct: 245 EAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTV 286

Length = 491

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

 Score = 95.4 bits (238), Expect = 3e-21
 Identities = 82/269 (30%), Positives = 140/269 (52%), Gaps = 16/269 (5%)

Query: 83  LEEFHSALEKYDFNS-ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE 141
           LEE  S   +   N  E+G  V+G V    + GA VDI       L   E    ++ H  
Sbjct: 175 LEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISWKRVDHPS 233

Query: 142 EAGIV-PGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANK 200
           E  +V  G + +  +I  +E    + LSL+ ++ E  WE   +       V+GKV     
Sbjct: 234 E--VVKVGDEVKVKVISLDEERGRVSLSLKQLE-EDPWEGIEKKYPVGDKVEGKVTNLTD 290

Query: 201 GGVVAEV-EGLRGFVPFSQIS--SKSTAEELL--GKDLPLKFVEVDEEQSRLVLSNRKAM 255
            G   E+ EG+ G V  S+IS   K+   E++  G+++ +K +++D E+ R+ L  ++  
Sbjct: 291 YGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGLKQLK 350

Query: 256 ADSQAQLG----IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQP 310
            +   +      +G VV G V+S+  +GAF+++ GGI+GL+H+S +S DR  + A   + 
Sbjct: 351 ENPWEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKK 410

Query: 311 GDTLKVMILSHDRERGRVSLSTKKLEPTP 339
           GD ++  +L+ D+E+ R+SL  K+LE +P
Sbjct: 411 GDEVEAKVLAVDKEKERISLGIKQLEESP 439

Length = 541

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

 Score = 85.6 bits (213), Expect = 6e-21
 Identities = 26/67 (38%), Positives = 44/67 (65%), Gaps = 2/67 (2%)

Query: 188 DVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKST--AEELLGKDLPLKFVEVDEEQS 245
             +V+GKV    KGG++ ++EG+R F+P SQ+  +     +E +GK+L  K +E+D E++
Sbjct: 1   GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERN 60

Query: 246 RLVLSNR 252
            +VLS R
Sbjct: 61  NIVLSRR 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|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain

 Score = 85.0 bits (211), Expect = 1e-20
 Identities = 35/71 (49%), Positives = 49/71 (69%), Gaps = 1/71 (1%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           +G VV GTV  + P GAF+D+G G+ GL+ +S++S  RV D   VL+ GD +KV +LS D
Sbjct: 2   VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVD 61

Query: 323 RERGRVSLSTK 333
            E+GR+ LS K
Sbjct: 62  EEKGRIILSLK 72

Length = 72

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

 Score = 92.9 bits (232), Expect = 2e-20
 Identities = 62/227 (27%), Positives = 118/227 (51%), Gaps = 35/227 (15%)

Query: 137 IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR-MIQYELAWERCRQLQS--EDVVVKG 193
           ++ V +   + G + EF +I  ++  +++V+S R +++ E A ER   L++  E  VV+G
Sbjct: 148 VRPVRDTDPLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEG 207

Query: 194 KVV-----GA--NKGGVVAEVEGL--------RGFVPFSQISSKSTAEELLGKDLPLKFV 238
            V      GA  + GGV    +GL        +     S++ +       +G ++ +K +
Sbjct: 208 VVKNITDYGAFVDLGGV----DGLLHITDISWKRVNHPSEVVN-------VGDEVKVKVL 256

Query: 239 EVDEEQSRLVLSNRKAMADS----QAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHV 293
           + D+E+ R+ L  ++   D     + +  +GS V G V ++  YGAF+++  GI GL+HV
Sbjct: 257 KFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHV 316

Query: 294 SQISHD-RVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP 339
           S++S   +    + V+  G  ++VM+L  D E+ R+SL  K+ +  P
Sbjct: 317 SEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENP 363

Length = 565

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

 Score = 82.3 bits (204), Expect = 1e-19
 Identities = 33/73 (45%), Positives = 47/73 (64%), Gaps = 1/73 (1%)

Query: 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
              G VV GTV  +   GAF+D+G G+ G + +S+IS DRV D   VL+ GD ++V +L 
Sbjct: 2   PEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLK 61

Query: 321 HDRERGRVSLSTK 333
            D+ERGR+ LS +
Sbjct: 62  VDKERGRIILSIR 74

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

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

 Score = 88.6 bits (220), Expect = 4e-19
 Identities = 75/274 (27%), Positives = 131/274 (47%), Gaps = 15/274 (5%)

Query: 84  EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEA 143
           EE   A E+   N + G  VKG V    + GA VD+       L   +    ++KH  E 
Sbjct: 172 EERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEY 230

Query: 144 GIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGV 203
             V G + +  +I  ++    + LSL+ +  E  WE   +       + G+V      GV
Sbjct: 231 VKV-GQEVKVKVIKFDKEKGRISLSLKQLG-EDPWEAIEKKFPVGDKITGRVTNLTDYGV 288

Query: 204 VAEV-EGLRGFVPFSQIS-----SKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMAD 257
             E+ EG+ G V  S++S     S  +     G ++ +  +++D E+ RL L  ++  A+
Sbjct: 289 FVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKAN 348

Query: 258 SQAQLG----IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVL-QPG 311
              Q      +G  V G ++ +  +GAF+++  GI+GL+H+S IS D+    A  L + G
Sbjct: 349 PWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKG 408

Query: 312 DTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRN 345
           D ++ ++L+ D+E+ R+SL  K+L   P +    
Sbjct: 409 DEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAA 442

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

 Score = 82.0 bits (203), Expect = 6e-19
 Identities = 36/81 (44%), Positives = 52/81 (64%), Gaps = 1/81 (1%)

Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMI 318
           +Q  +GSVV G V  ++PYGAF+ +     GL+H+S+I+H  V DI   L  GD +KV +
Sbjct: 3   SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKV 62

Query: 319 LSHDRERGRVSLSTKKLEPTP 339
           LS D E+G++SLS +  E  P
Sbjct: 63  LSVDEEKGKISLSIRATEEAP 83

Length = 123

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

 Score = 82.9 bits (205), Expect = 4e-17
 Identities = 79/264 (29%), Positives = 126/264 (47%), Gaps = 28/264 (10%)

Query: 97  SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVII 156
            E G  V+G V  T   G  V++  +  A+ P  +  +    +VE+     G   +F+I 
Sbjct: 113 YENGVPVEGKVTGTCKGGFNVEVLGRR-AFCPVSQIDLR---YVEDPESYVGQTFQFLIT 168

Query: 157 GENEADDSLVLSLRMIQYELAWERCRQLQS------EDVVVKGKVVG-ANKGGVVAEVEG 209
              E   ++V+S R +   L  E+   L++      E  VV+G V   A  G  V    G
Sbjct: 169 RVEENGRNIVVSRRAL---LEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPG 225

Query: 210 LRGFVPFSQIS-SKS-TAEELL--GKDLPLKFVEVDE----EQSRLVLSNRKAMAD---S 258
           + G V  S++S S+   A+E +  G  + +K + ++     +  R+ LS ++A  D   +
Sbjct: 226 VEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDT 285

Query: 259 QA-QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH-DRVADIATVLQPGDTLK 315
              +L  G  V G V  L P+GAF++I  GI GL+HVS++S   RV     V+ PGD + 
Sbjct: 286 VGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVA 345

Query: 316 VMILSHDRERGRVSLSTKKLEPTP 339
           V I   D  + R+SLS +  E  P
Sbjct: 346 VKIKDIDPAKRRISLSLRDAEGDP 369

Length = 491

>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 = 74.6 bits (184), Expect = 5e-17
 Identities = 28/68 (41%), Positives = 47/68 (69%), Gaps = 1/68 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323
           G V+ G V ++  +GAF+DIG   +GL+H+S+++   V+  + V+  GD ++V ++S D 
Sbjct: 1   GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDE 60

Query: 324 ERGRVSLS 331
           ERGR+SLS
Sbjct: 61  ERGRISLS 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|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed

 Score = 80.2 bits (199), Expect = 3e-16
 Identities = 51/162 (31%), Positives = 93/162 (57%), Gaps = 12/162 (7%)

Query: 190 VVKGKVVGANKGGVVAEVE-GLRGFVPFSQIS----SKSTAEEL-LGKDLPLKFVEVDEE 243
            VKGKV      G   E+E G+ G V  S++S    +K  ++ + +G+++ +  +E+DEE
Sbjct: 289 KVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEE 348

Query: 244 QSRLVLSNRKAMADSQAQLG----IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISH 298
           + R+ L  ++   +   +      +G VV G V+++  +GAF+ + GGI+GL+H+S IS 
Sbjct: 349 KRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISW 408

Query: 299 DR-VADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP 339
           D+   +   + + GD ++ ++L  D E+ R+SL  K+LE  P
Sbjct: 409 DKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDP 450

Length = 565

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

 Score = 72.6 bits (179), Expect = 3e-16
 Identities = 29/68 (42%), Positives = 47/68 (69%), Gaps = 2/68 (2%)

Query: 265 GSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323
           G +  G V  +K +GAF++I  G +GL+H+S++S +RV  +  VL+ GD +KV ++  D 
Sbjct: 1   GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD- 59

Query: 324 ERGRVSLS 331
           +RGR+SLS
Sbjct: 60  DRGRISLS 67

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|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 78.2 bits (194), Expect = 2e-15
 Identities = 29/74 (39%), Positives = 48/74 (64%), Gaps = 2/74 (2%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           +G +  G V  +  +GAF++I  G +GL+H+S+I+ +RV  +  VL+ GD +KV +L  D
Sbjct: 621 VGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID 680

Query: 323 RERGRVSLSTKKLE 336
            +RGR+ LS K + 
Sbjct: 681 -KRGRIRLSRKAVL 693

Length = 693

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

 Score = 71.5 bits (176), Expect = 4e-15
 Identities = 38/105 (36%), Positives = 60/105 (57%), Gaps = 2/105 (1%)

Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMI 318
             + +GS + G +  + PYGAF+++ GG  GL+H+S+I+   V DI   L+ G  +KV +
Sbjct: 1   MSMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKV 60

Query: 319 LSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQR 363
           L  D E G++SLS +KLE  P    R P+    + +E  +T   R
Sbjct: 61  LDID-ENGKISLSIRKLEEEPEKQHRKPRFSKSRPKEGFETLLSR 104

Length = 129

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

 Score = 75.8 bits (187), Expect = 7e-15
 Identities = 71/250 (28%), Positives = 117/250 (46%), Gaps = 21/250 (8%)

Query: 98  ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157
            +G KV+G V    + GA V+I       +   E    K     E  +  G + E  ++ 
Sbjct: 276 PVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEV-VKVGQEVEVKVLD 334

Query: 158 ENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPF 216
            +     + L L+ ++ E  WE          VV+GKV      G   E+E G+ G V  
Sbjct: 335 IDPERRRISLGLKQLK-ENPWEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHL 393

Query: 217 SQISSKSTAEELL----GKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQ-----LGIGSV 267
           S +S     EE      G ++  K + VD+E+ R+ L   K + +S  +        GSV
Sbjct: 394 SDLSWDRPGEEAEKYKKGDEVEAKVLAVDKEKERISLG-IKQLEESPWEEFSEKYKKGSV 452

Query: 268 VIGTVQSLKPYGAFID-IGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERG 326
           V G V+S+K  GAF++  GG+ GL+ +S++S D        L+ GD ++ +++S D++  
Sbjct: 453 VKGKVKSVKDKGAFVELGGGVEGLIRLSELSRDV-------LKVGDEVEAVVVSIDKKNR 505

Query: 327 RVSLSTKKLE 336
           ++ LS K LE
Sbjct: 506 KILLSIKALE 515

Length = 541

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

 Score = 75.9 bits (187), Expect = 7e-15
 Identities = 65/247 (26%), Positives = 115/247 (46%), Gaps = 16/247 (6%)

Query: 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQE-ACIHKIKHVEEAGIVPGLKEEFVIIGE 158
           G K+ G V    + G  V+I       +   E + + K  H  +     G + E +I+  
Sbjct: 273 GDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKK-GDEVEVMILDI 331

Query: 159 NEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFS 217
           +     L L L+  +    WE+  +       V GK+      G   E+E G+ G +  S
Sbjct: 332 DPERRRLSLGLKQCK-ANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLS 390

Query: 218 QIS---SKSTAEELL--GKDLPLKFVEVDEEQSRLVLSNRKAMADS-----QAQLGIGSV 267
            IS       A+ L   G ++    + VD+E+ R+ L   K + ++      A+  +GSV
Sbjct: 391 DISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLG-VKQLTENPWEKFAAKYKVGSV 449

Query: 268 VIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERG 326
           V G V  +K +GAF+++ GG+ GL+  S++S +R  D    ++ GD ++  ++  D++  
Sbjct: 450 VKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNR 509

Query: 327 RVSLSTK 333
           +VSLS K
Sbjct: 510 KVSLSVK 516

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

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

 Score = 68.6 bits (168), Expect = 7e-15
 Identities = 26/65 (40%), Positives = 43/65 (66%), Gaps = 1/65 (1%)

Query: 268 VIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERG 326
           V G V S+  +G F+++  G+ GL+H+S++S   V D + V + GD ++V +L  D E+G
Sbjct: 1   VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKG 60

Query: 327 RVSLS 331
           R+SLS
Sbjct: 61  RISLS 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|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 = 68.5 bits (168), Expect = 1e-14
 Identities = 31/71 (43%), Positives = 45/71 (63%), Gaps = 2/71 (2%)

Query: 265 GSVVIGTVQSLKPYGAFIDIGGIN--GLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           G  + GTV+ ++ YG FIDI G N  GL H S+IS +RVAD + + + GD ++  +L  D
Sbjct: 3   GQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKID 62

Query: 323 RERGRVSLSTK 333
            E+ R+SL  K
Sbjct: 63  AEKKRISLGLK 73

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Length = 77

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

 Score = 74.8 bits (185), Expect = 2e-14
 Identities = 54/159 (33%), Positives = 84/159 (52%), Gaps = 13/159 (8%)

Query: 190 VVKGKVVGANKGGVVAEVE-GLRGFVPFSQIS---SKSTAEELL--GKDLPLKFVEVDEE 243
           VV+GKV      G    +E G+ G V  S IS       A EL   G ++    ++VD E
Sbjct: 376 VVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVE 435

Query: 244 QSRLVLSNRKAMADS-----QAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQIS 297
           + R+ L   K + +        +   GS+V GTV  +K  GAF+++  G+ GL+  S++S
Sbjct: 436 KERISLG-IKQLEEDPFEEFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELS 494

Query: 298 HDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE 336
            DRV D   VL+ GD ++  +++ DR+  R+SLS K L+
Sbjct: 495 RDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALD 533

Length = 565

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

 Score = 73.0 bits (180), Expect = 7e-14
 Identities = 28/75 (37%), Positives = 49/75 (65%), Gaps = 2/75 (2%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           +G V  GTV  +  +GAF+++  G +GL+H+SQ++ +RV  +  VL+ GD +KV ++  D
Sbjct: 619 VGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEID 678

Query: 323 RERGRVSLSTKKLEP 337
            ++GR+ LS K +  
Sbjct: 679 -KQGRIRLSIKAVLE 692

Length = 692

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

 Score = 72.8 bits (178), Expect = 1e-13
 Identities = 73/268 (27%), Positives = 128/268 (47%), Gaps = 31/268 (11%)

Query: 100 GTKVKGTV--FCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVI-- 155
           GT V+G +        G  VD+ A   A+LP  ++   K+   E    + GL  +F I  
Sbjct: 399 GTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPES---LIGLTSKFYIER 455

Query: 156 ---IGENEADDSLVLSLRMIQYELAWERCRQLQSE---DVVVKGKVVGANKG----GVVA 205
                ++  +D++V++ R        ER RQ + E    V ++  V G  K     G   
Sbjct: 456 ISQSKQHRGNDNIVINRR----RYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFI 511

Query: 206 EVEGLRGFVPFSQISSKSTAE--ELL--GKDLPLKFVEVDEEQSRLVLSNRKAMADS--- 258
           ++ G  G +  + +S    A   E +  G+ + LK + +D+ + R+ LS +    D    
Sbjct: 512 DLGGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLE 571

Query: 259 -QAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH-DRVADIATVLQPGDTLK 315
            + + G+  VV G V  +  +GAFI++  GI GL H+S+ S   + +  + +++ GD ++
Sbjct: 572 FENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVE 631

Query: 316 VMILSHDRERGRVSLSTKKLEPTPGDMI 343
            MIL +D + GRVSL  K++   P + I
Sbjct: 632 CMILGYDIQAGRVSLGLKQVTANPWEEI 659

Length = 863

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

 Score = 71.4 bits (176), Expect = 2e-13
 Identities = 26/68 (38%), Positives = 46/68 (67%), Gaps = 2/68 (2%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           +G +  G V  +  +GAF++I  G +GL+H+S+I+++RV  +  VL+ GD +KV +L  D
Sbjct: 618 VGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEID 677

Query: 323 RERGRVSL 330
           + +GR+ L
Sbjct: 678 K-QGRIKL 684

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family) [Transcription, Degradation of RNA]. Length = 684

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

 Score = 64.4 bits (157), Expect = 1e-12
 Identities = 28/77 (36%), Positives = 49/77 (63%), Gaps = 1/77 (1%)

Query: 262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSH 321
           L  GS++ GTV ++  +GAF+++ G  GL+H+S+++   V DI   L+  D +KV ++S 
Sbjct: 3   LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISI 62

Query: 322 DRERGRVSLSTKKLEPT 338
           D + G++SLS K+    
Sbjct: 63  D-DNGKISLSIKQAMKQ 78

Length = 136

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

 Score = 67.0 bits (163), Expect = 7e-12
 Identities = 74/275 (26%), Positives = 125/275 (45%), Gaps = 44/275 (16%)

Query: 91  EKYDFNS-ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGL 149
           E+Y F + E G+   GTV   +     VDI  KS   +P +E      +   +AG    +
Sbjct: 312 ERYSFEAPEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEE-----FEAPPKAGDGVRV 366

Query: 150 KEEFVI-----IGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVV 204
             E V      + + +AD    L L++        + R  + +   V+G++V   +    
Sbjct: 367 YVERVTPYGPELSKTKADR---LGLKV--------KLRDAERDGTPVEGRIVRLTEKKSG 415

Query: 205 AEVE---GLRGFVPFSQISSKS--TAEELLGKDLPLKFVEVDEEQSR-------LVLSNR 252
            EV+   G+  F+P SQ   +     E L+G  L  KF      QS+       +V++ R
Sbjct: 416 FEVDLGAGMMAFLPISQSDCQKVDAPESLIG--LTSKFYIERISQSKQHRGNDNIVINRR 473

Query: 253 KAMADSQAQ--------LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADI 304
           + + +   Q        + I   V G V+S   +GAFID+GG +GLLHV+ +S   VA  
Sbjct: 474 RYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVARP 533

Query: 305 ATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP 339
              ++ G T+++ ++  D+   R++LS K  +P P
Sbjct: 534 REFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDP 568

Length = 863

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

 Score = 66.5 bits (163), Expect = 9e-12
 Identities = 37/122 (30%), Positives = 62/122 (50%), Gaps = 11/122 (9%)

Query: 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
           L  G ++ GTV+++  +GAF+DIG   +GL+H+SQ+S   V D   V++ GD +KV ++ 
Sbjct: 656 LKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIE 715

Query: 321 HDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQR---------IAQAEAMA 371
            D  R R++L + +L+   G +        E+     +               A A+A A
Sbjct: 716 VDTARKRIAL-SMRLDEEEGKLNSGRGFCRERGLCRPRRAPVIEHPVYPGRNGAMADAFA 774

Query: 372 RA 373
           RA
Sbjct: 775 RA 776

Length = 780

>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 = 58.8 bits (143), Expect = 3e-11
 Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 7/74 (9%)

Query: 265 GSVVIGTVQSLKPYGAFIDIGGIN----GLLHVSQISHD-RVADIATVLQPGDTLKVMIL 319
           G +  G V S+  +G F+ + G+     GL+H+SQ+S + RVA+ + V++ G  +KV ++
Sbjct: 1   GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVI 60

Query: 320 SHDRERGRVSLSTK 333
           S   + G++SLS K
Sbjct: 61  S--IQNGKISLSMK 72

The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae. Length = 79

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

 Score = 58.3 bits (142), Expect = 4e-11
 Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN 159
           G  VKGTV   D+   LVDI  KS   +P  E     I++ E+  +  G + E  ++   
Sbjct: 1   GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDE-VKVGDEVEVYVLRVE 59

Query: 160 EADDSLVLSLR 170
           + + ++VLS R
Sbjct: 60  DEEGNVVLSKR 70

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 70

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

 Score = 62.8 bits (153), Expect = 1e-10
 Identities = 77/257 (29%), Positives = 128/257 (49%), Gaps = 43/257 (16%)

Query: 103 VKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD 162
           V GTV      G ++DI  +   +LP   A + +++ V +     G + E  II  ++  
Sbjct: 126 VTGTVIEVVKGGLILDIGLR--GFLP---ASLVEMRRVRDLQPYIGQEIEAKIIELDKNR 180

Query: 163 DSLVLSLRMIQYELAWERCRQLQSE------DVVVKGKVVGANKGGVVAEV--------- 207
           +++VLS R      AW    Q QSE      + + KG+V    + GVV+ +         
Sbjct: 181 NNVVLSRR------AW--LEQTQSEVRSEFLNQLQKGQV----RKGVVSSIVNFGAFVDL 228

Query: 208 EGLRGFVPFSQISSK-----STAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQL 262
            G+ G V  S++S K     S   E+ G+++ ++ ++VD ++ R+ LS +    D   Q 
Sbjct: 229 GGVDGLVHVSELSWKHIDHPSEVVEV-GQEVTVEVLDVDMDRERVSLSLKATQEDPWQQF 287

Query: 263 G----IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVM 317
                IG +V G V  L P+GAF+ +  GI GL+H+S+++   V     V+Q GD + V 
Sbjct: 288 ARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVK 347

Query: 318 ILSHDRERGRVSLSTKK 334
           ++  D ER R+SLS K+
Sbjct: 348 VIDIDLERRRISLSLKQ 364

Length = 486

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

 Score = 62.8 bits (153), Expect = 1e-10
 Identities = 46/175 (26%), Positives = 77/175 (44%), Gaps = 11/175 (6%)

Query: 178 WERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQIS-----SKSTAEELLGK 231
           W+           V GKVV     G   E+  G+ G V  S++S     +K       G 
Sbjct: 283 WDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGD 342

Query: 232 DLPLKFVEVDEEQSRLVLSNRKAMADSQA----QLGIGSVVIGTVQSLKPYGAFIDIG-G 286
            + +K  ++D  + R+ LS R A  D  A    +   G+ V GTV+    +G F+++  G
Sbjct: 343 AVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPG 402

Query: 287 INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGD 341
           + GLL  S IS          L+PGD++ +++   D  + ++SL+      +  D
Sbjct: 403 VTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGAAGSGAD 457

Length = 491

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

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 5/71 (7%)

Query: 187 EDVVVKGKVVGANKGGVVAEV-EGLRGFVPFSQISSK----STAEELLGKDLPLKFVEVD 241
           E  VVKG V    KGG   ++  G+ GF+P S+IS            +G ++ +K ++VD
Sbjct: 4   EGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLKVD 63

Query: 242 EEQSRLVLSNR 252
           +E+ R++LS R
Sbjct: 64  KERGRIILSIR 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|239899 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

 Score = 55.3 bits (134), Expect = 4e-10
 Identities = 22/74 (29%), Positives = 44/74 (59%), Gaps = 3/74 (4%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
            G +V+ TV+S+   GA++ +   G I G++ +S++S  R+  I  +++ G    V ++ 
Sbjct: 3   EGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIR 62

Query: 321 HDRERGRVSLSTKK 334
            D+E+G + LS K+
Sbjct: 63  VDKEKGYIDLSKKR 76

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

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 98  ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157
           E G  VKGTV      GA VD+      ++P  E    +++  +E  +  G + E  ++ 
Sbjct: 3   EEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDE-VLKVGDEVEVKVLK 61

Query: 158 ENEADDSLVLSLR 170
            ++    ++LS+R
Sbjct: 62  VDKERGRIILSIR 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|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

 Score = 56.9 bits (138), Expect = 3e-09
 Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
            G +V+GTV+ +  YGA++++    G  G +H+S+++   V +I   ++ G  +   +L 
Sbjct: 11  EGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLR 70

Query: 321 HDRERGRVSLSTKK 334
            D +RG + LS K+
Sbjct: 71  VDPKRGHIDLSLKR 84

Length = 269

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

 Score = 53.9 bits (130), Expect = 4e-09
 Identities = 27/74 (36%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           IG  + GT+  +KPYGAF+ +  G  GL+H+S+I    + +I  +L+ G+ + V ++  D
Sbjct: 3   IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFD 62

Query: 323 RERGRVSLSTKKLE 336
              G+ SLS + LE
Sbjct: 63  EYTGKASLSLRTLE 76

Length = 120

>gnl|CDD|240203 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

 Score = 51.8 bits (125), Expect = 6e-09
 Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323
           G    GT+  +KP G  +     + G L  S++S   + D     + G  +KV +LS D 
Sbjct: 1   GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDP 60

Query: 324 ERGRVSLSTK 333
           E+ R+ LS K
Sbjct: 61  EQQRLLLSCK 70

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Length = 70

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

 Score = 51.8 bits (125), Expect = 7e-09
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323
           G +V GTV S+      +DIG    G++ +S+ S D + +    ++ GD ++V +L  + 
Sbjct: 1   GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVED 60

Query: 324 ERGRVSLS 331
           E G V LS
Sbjct: 61  EEGNVVLS 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 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 70

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

 Score = 52.3 bits (126), Expect = 2e-08
 Identities = 29/107 (27%), Positives = 57/107 (53%), Gaps = 6/107 (5%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           +GS + G V  +  +GAF+++  G  GL+H+S+++ + V DI   L+ GD ++V +L+ +
Sbjct: 5   VGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE 64

Query: 323 RERGRVSLSTKKLEPTPGDMIRNPK----LVFEKAEEMAQTFRQRIA 365
            + G++ LS KK +  P      P+              + F Q+++
Sbjct: 65  DD-GKIGLSIKKAKDRPKRQHDRPRHEDNRGGGNDVAPKEDFEQKMS 110

Length = 139

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

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323
           GS+V G V  +   GA + +G G+ G L  +++S DRV D     + GD ++  I + DR
Sbjct: 1   GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60

Query: 324 ERGRVSLSTKKLE 336
           +  ++SLS K  E
Sbjct: 61  KNRKISLSIKAKE 73

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 73

>gnl|CDD|239908 cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains

 Score = 49.5 bits (119), Expect = 5e-08
 Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323
           G VV G V+++ PYG F++  GG+ GL   S IS + V D +   + G ++   + S D 
Sbjct: 15  GMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE 74

Query: 324 ERGRVSLS 331
           E+ R  LS
Sbjct: 75  EKQRFLLS 82

Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Length = 83

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

 Score = 48.6 bits (116), Expect = 8e-08
 Identities = 26/68 (38%), Positives = 45/68 (66%), Gaps = 2/68 (2%)

Query: 265 GSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQIS-HDRVADIATVLQPGDTLKVMILSHD 322
           G+VV G ++S+  +G F+ + GGI+GL+H+S IS   RV   + + + G  ++ ++L+ D
Sbjct: 1   GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID 60

Query: 323 RERGRVSL 330
            ER R+SL
Sbjct: 61  VERERISL 68

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 69

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

 Score = 50.6 bits (122), Expect = 2e-07
 Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 22/86 (25%)

Query: 267 VVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA-----------DIATVLQPGDTLK 315
           VV G V  +  +GAF+ IG ++GLLH+SQI  D ++           +   VL+ GD ++
Sbjct: 84  VVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVR 143

Query: 316 VMILSHDRERGRVSLSTKKLEPTPGD 341
             I         V++S K  E  P  
Sbjct: 144 ARI---------VAVSLK--ERRPRG 158

Length = 187

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

 Score = 51.7 bits (125), Expect = 2e-07
 Identities = 21/73 (28%), Positives = 42/73 (57%), Gaps = 3/73 (4%)

Query: 265 GSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSH 321
           G +V+GTV+ +K +GAF+ +    G  G +H+S+++   V +I   ++ G  +   ++  
Sbjct: 9   GELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRV 68

Query: 322 DRERGRVSLSTKK 334
           D  +G + LS K+
Sbjct: 69  DPRKGHIDLSLKR 81

Length = 262

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

 Score = 51.8 bits (125), Expect = 3e-07
 Identities = 26/82 (31%), Positives = 50/82 (60%), Gaps = 2/82 (2%)

Query: 257 DSQAQLGIGSVVIGTVQSLKPYGAFIDIGG--INGLLHVSQISHDRVADIATVLQPGDTL 314
           +S  ++ +G VV G V  ++    F++I G  + G++ +S++S+D + DI  V++ GD L
Sbjct: 10  NSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDEL 69

Query: 315 KVMILSHDRERGRVSLSTKKLE 336
           +V +L  +   G + LS ++LE
Sbjct: 70  EVYVLKVEDGEGNLLLSKRRLE 91

Length = 390

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

 Score = 47.2 bits (113), Expect = 3e-07
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 190 VVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKSTAEE----LLGKDLPLKFVEVDEEQ 244
           VV+G V     GG   ++  G+ G +P S++S K   +      +G ++ +K + VDEE+
Sbjct: 5   VVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEK 64

Query: 245 SRLVLSNR 252
            R++LS +
Sbjct: 65  GRIILSLK 72

Length = 72

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

 Score = 46.4 bits (110), Expect = 5e-07
 Identities = 25/68 (36%), Positives = 43/68 (63%), Gaps = 2/68 (2%)

Query: 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQIS-HDRVADIATVLQPGDTLKVMILSHD 322
           G+ + G V +L  YG F+++  G+ GL+HVS++   ++    + V+  GD ++VM+L  D
Sbjct: 4   GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDID 63

Query: 323 RERGRVSL 330
            ER R+SL
Sbjct: 64  EERRRISL 71

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 72

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

 Score = 45.9 bits (109), Expect = 7e-07
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 3/70 (4%)

Query: 266 SVVIGTVQSLKPYGAFIDIGGI--NGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323
            +  G V S+  YGAF+ I G    GL+H S +S  RV D + V+  G+ + V ++  + 
Sbjct: 5   QIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGRE- 63

Query: 324 ERGRVSLSTK 333
            + ++ LS  
Sbjct: 64  MKDKMKLSLS 73

pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis. Length = 73

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 98  ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG 157
           E+G  V+GTV      GA VD+       +P  E    ++K  EE  +  G + +  ++ 
Sbjct: 1   EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV-LKVGDEVKVKVLS 59

Query: 158 ENEADDSLVLSLR 170
            +E    ++LSL+
Sbjct: 60  VDEEKGRIILSLK 72

Length = 72

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

 Score = 49.3 bits (117), Expect = 3e-06
 Identities = 54/208 (25%), Positives = 96/208 (46%), Gaps = 17/208 (8%)

Query: 152 EFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVG-ANKGGVVAEVEGL 210
           E  +I  ++A+  + LSL+  Q +   E   +    DVV KG+V   A+ G  +   EG+
Sbjct: 544 ELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVV-KGRVTKIADFGAFIELAEGI 602

Query: 211 RGFVPFSQIS-----SKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADS----QAQ 261
            G    S+ S     SK +    +G ++    +  D +  R+ L  ++  A+     +A+
Sbjct: 603 EGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEAR 662

Query: 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQIS---HDRVADIATVLQPGDTLKVM 317
             +G+     +  +   GAFI++  GI+G LHV  +S     R AD    L+ G  ++ M
Sbjct: 663 YPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHE--LEVGKEIECM 720

Query: 318 ILSHDRERGRVSLSTKKLEPTPGDMIRN 345
           ++  D +  R+ L  K+L   P  +  N
Sbjct: 721 VIECDPQARRIRLGVKQLSDNPWQVFAN 748

Length = 863

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

 Score = 48.6 bits (115), Expect = 5e-06
 Identities = 40/152 (26%), Positives = 75/152 (49%), Gaps = 15/152 (9%)

Query: 199 NKGGVVAEVEGLRGFVPFSQIS----SKSTAEEL-LGKDLPLKFVEVDEEQSRLVLSNRK 253
           N G  +   EG+ GF+    +S    ++    EL +GK++    +E D +  R+ L   K
Sbjct: 678 NAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLG-VK 736

Query: 254 AMADSQAQL-----GIGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATV 307
            ++D+  Q+     G+GS V G V S+  +G F+ + GG+ GL+    +  +R  D    
Sbjct: 737 QLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEA 796

Query: 308 LQP---GDTLKVMILSHDRERGRVSLSTKKLE 336
           L+    GD +K +I+  + +  +V+ S +  +
Sbjct: 797 LRKYAVGDRVKAVIVDMNVKDRKVAFSVRDYQ 828

Length = 863

>gnl|CDD|239907 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding domain

 Score = 43.8 bits (104), Expect = 8e-06
 Identities = 17/35 (48%), Positives = 24/35 (68%)

Query: 267 VVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV 301
           VV G V  +  +GAF+ IG ++GLLH+SQI  D +
Sbjct: 2   VVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYI 36

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. Length = 99

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

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 26/65 (40%), Positives = 37/65 (56%), Gaps = 5/65 (7%)

Query: 191 VKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKST--AEELL--GKDLPLKFVEVDEEQS 245
           V GKVV   K GV  E+E G+ G V  S++S K      E+   G ++ +K +EVD E+ 
Sbjct: 1   VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKG 60

Query: 246 RLVLS 250
           R+ LS
Sbjct: 61  RISLS 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|239911 cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain

 Score = 39.7 bits (94), Expect = 1e-04
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 2/55 (3%)

Query: 279 GAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK 333
           G  +DI G+   L  SQ+    V D+   +  G  LK  I+  DRER  + LS +
Sbjct: 15  GLIVDIEGVRAFLPASQVDLRPVEDLDEYV--GKELKFKIIEIDRERNNIVLSRR 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|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription]

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 31/132 (23%), Positives = 48/132 (36%), Gaps = 39/132 (29%)

Query: 265 GSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRE 324
           G VV G V  +  +GAF+ IG ++GL+HVSQI  D +                   +D +
Sbjct: 82  GEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYI------------------DYDEK 123

Query: 325 RGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARADMLRFQPESGL 384
              +     K     GD +R                    A+   ++       + + GL
Sbjct: 124 NKVLIGEETKRVLKVGDKVR--------------------ARIVGVSLKSRRPRESKIGL 163

Query: 385 TLNSDGILGPLS 396
           T+   G LG L 
Sbjct: 164 TMRQPG-LGKLE 174

Length = 183

>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 6/72 (8%)

Query: 264 IGSVVIGTVQSLKPYGAFID-IGGINGLLHVSQISH----DRVADIATVLQPGDTLKVMI 318
           +G   +GTV     +GAF+  + G +GLLH+SQI       RV ++  VL  G  ++V I
Sbjct: 647 VGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEI 706

Query: 319 LSHDRERGRVSL 330
              D +RG++SL
Sbjct: 707 ADID-DRGKLSL 717

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. Length = 719

>gnl|CDD|239900 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 6/61 (9%)

Query: 264 IGSVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISH---DRVADIATVLQPGDTLKVM 317
           +G++ +G V+ + P    AF+DIG G NG LH+S I      +   IA +L+ G  + V 
Sbjct: 7   VGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQ 66

Query: 318 I 318
           +
Sbjct: 67  V 67

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 that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay. Length = 88

>gnl|CDD|240202 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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323
           G VV GT++ L+P G F+ +   I GL+    ++  R+       +PG  +K  +LS + 
Sbjct: 1   GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEP 60

Query: 324 ERGRVSL 330
           ER R+ L
Sbjct: 61  ERKRLVL 67

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. Length = 69

>gnl|CDD|240215 cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-binding domain

 Score = 38.3 bits (90), Expect = 5e-04
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 10/77 (12%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVA----DIATVLQPGD--TLKV 316
           +G VVIG V  +      +DI    + +L +S+++  R      ++ + L  GD    +V
Sbjct: 6   VGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEV 65

Query: 317 MILSHDRERGRVSLSTK 333
             +  D   G VSL T+
Sbjct: 66  QSVDSD---GSVSLHTR 79

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". Length = 86

>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase; Provisional

 Score = 42.2 bits (99), Expect = 5e-04
 Identities = 22/69 (31%), Positives = 42/69 (60%), Gaps = 2/69 (2%)

Query: 272 VQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSL 330
           ++S+ PYGAF++I  G  GL H+S++S + +A      + GD + V ++  + ++G++ L
Sbjct: 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVN-DKGQLRL 820

Query: 331 STKKLEPTP 339
           S + L P  
Sbjct: 821 SRRALLPEA 829

Length = 891

>gnl|CDD|224022 COG1097, RRP4, RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

 Score = 40.4 bits (95), Expect = 9e-04
 Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 8/76 (10%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIAT-----VLQPGDTLKVM 317
           +G VVIG +  + P G  +DIG     LL +S     R  + A       L  GD +   
Sbjct: 64  VGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLR-RKFENAEKDLRPFLNVGDLVYAK 122

Query: 318 ILSHDRERGRVSLSTK 333
           ++  DR+ G V L+ K
Sbjct: 123 VVDVDRD-GEVELTLK 137

Length = 239

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	414
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
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	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
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	100.0
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	100.0
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	100.0
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	100.0
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	100.0
PRK07400	318	30S ribosomal protein S1; Reviewed	99.89
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.83
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.78
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.77
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.76
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.69
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.66
PRK08582	139	hypothetical protein; Provisional	99.65
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.61
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.59
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.59
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.59
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.58
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.58
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.58
PRK07252	120	hypothetical protein; Provisional	99.57
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.57
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	99.55
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.55
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.55
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.54
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.54
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.54
PHA02945	88	interferon resistance protein; Provisional	99.53
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.53
PRK05807	136	hypothetical protein; Provisional	99.52
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.51
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.5
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.5
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.49
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.49
PRK08059	123	general stress protein 13; Validated	99.47
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.45
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.44
PRK03987	262	translation initiation factor IF-2 subunit alpha;	99.43
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.41
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.4
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.4
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.39
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.39
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.38
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.38
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.37
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.36
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.33
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.32
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.31
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.3
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.28
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.27
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.27
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.27
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	99.27
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.27
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.26
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.24
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.23
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.23
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.23
COG2183	780	Tex Transcriptional accessory protein [Transcripti	99.22
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.21
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.21
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.19
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.18
PRK07252	120	hypothetical protein; Provisional	99.17
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.17
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	99.16
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	99.15
COG2183	780	Tex Transcriptional accessory protein [Transcripti	99.15
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.15
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.15
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.14
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	99.14
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	99.14
PRK08582	139	hypothetical protein; Provisional	99.1
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.1
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	99.1
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.09
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.07
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.04
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.03
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.03
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.03
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.02
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.02
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	99.0
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	99.0
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.99
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.99
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.99
PRK05807	136	hypothetical protein; Provisional	98.99
PRK08059	123	general stress protein 13; Validated	98.98
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.96
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	98.95
PRK09202	470	nusA transcription elongation factor NusA; Validat	98.95
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.94
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.92
PHA02945	88	interferon resistance protein; Provisional	98.91
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.9
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.88
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.87
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	98.86
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.86
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.85
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.84
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.84
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.84
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.81
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.79
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.7
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.69
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.67
KOG2916	304	consensus Translation initiation factor 2, alpha s	98.64
TIGR01953	341	NusA transcription termination factor NusA. This m	98.6
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.59
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.59
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	98.58
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.57
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.55
PRK11642	813	exoribonuclease R; Provisional	98.55
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.54
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	98.52
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.44
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.44
TIGR01953	341	NusA transcription termination factor NusA. This m	98.44
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.32
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.3
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.25
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	98.03
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.98
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	97.96
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	97.95
PRK05054	644	exoribonuclease II; Provisional	97.92
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	97.9
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	97.89
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.87
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	97.83
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.8
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.8
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	97.8
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	97.72
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	97.69
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	97.66
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	97.59
PRK11642	813	exoribonuclease R; Provisional	97.57
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.55
COG0557	706	VacB Exoribonuclease R [Transcription]	97.44
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	97.44
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.41
PRK12329	449	nusA transcription elongation factor NusA; Provisi	97.38
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	97.35
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.35
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.29
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.28
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	97.27
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.24
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.23
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.11
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	97.11
KOG2916	304	consensus Translation initiation factor 2, alpha s	97.07
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.06
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	96.84
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	96.78
PRK10811	1068	rne ribonuclease E; Reviewed	96.64
PRK05054	644	exoribonuclease II; Provisional	96.48
PRK11712	489	ribonuclease G; Provisional	96.4
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.33
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	96.21
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	96.2
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	95.93
PRK10811	1068	rne ribonuclease E; Reviewed	95.81
PRK11712	489	ribonuclease G; Provisional	95.79
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	95.2
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	94.99
COG0557	706	VacB Exoribonuclease R [Transcription]	94.86
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	94.58
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	93.97
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	93.71
PRK12442	87	translation initiation factor IF-1; Reviewed	93.17
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	93.02
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	92.9
TIGR00008	68	infA translation initiation factor IF-1. This fami	92.6
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	92.28
KOG4078	173	consensus Putative mitochondrial ribosomal protein	91.63
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	89.41
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	88.85
PRK12442	87	translation initiation factor IF-1; Reviewed	88.38
TIGR00008	68	infA translation initiation factor IF-1. This fami	86.62
cd05700	65	S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a t	85.95
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	83.99
COG0361	75	InfA Translation initiation factor 1 (IF-1) [Trans	82.55
KOG1004	230	consensus Exosomal 3'-5' exoribonuclease complex s	82.45
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	81.01

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=2.9e-56  Score=439.74  Aligned_cols=295  Identities=49%  Similarity=0.877  Sum_probs=278.7

Q ss_pred             cCCCCCCCCCHHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEE
Q 015066           73 TAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEE  152 (414)
Q Consensus        73 ~~~~~~~~~~~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~  152 (414)
                      +.++.++.|++++|+++|++|++.++.|++|+|+|+++.++|+||+||++.+||||.+|+++.+..++.+. +++|+.++
T Consensus         5 ~~~~~~~~~~~~~f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~-~~~G~~v~   83 (318)
T PRK07400          5 NTDADDIGFTHEDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEV-LQPNETRE   83 (318)
T ss_pred             cCcccccCCCHHHHHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHc-cCCCCEEE
Confidence            45667889999999999999887899999999999999999999999999999999999999888888887 89999999


Q ss_pred             EEEEEEeCCCCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCCccccccCCe
Q 015066          153 FVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKD  232 (414)
Q Consensus       153 v~Vl~id~~~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~~~~~~vGq~  232 (414)
                      |+|++++++++++.||+|+......|+.+.+++..|.+++|+|++++++|+||+++|++||||.||++|....+.++|+.
T Consensus        84 ~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~Gv~gfip~s~ls~~~~~~~~vG~~  163 (318)
T PRK07400         84 FFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKEELVGEE  163 (318)
T ss_pred             EEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCccCCccccCCCE
Confidence            99999999999999999998877899999999999999999999999999999999999999999999875555679999


Q ss_pred             EEEEEEEeecccceEEeehhhhhhh-HHhhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCC
Q 015066          233 LPLKFVEVDEEQSRLVLSNRKAMAD-SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG  311 (414)
Q Consensus       233 V~vkVl~vD~e~~ri~LS~K~~l~~-~~~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G  311 (414)
                      ++|+|+++|++++++.||+|+++.+ ...++++|++|.|+|++|++||+||+++|++||+|+++++|.++.++.+.|++|
T Consensus       164 i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~~~~~~~~~~~vG  243 (318)
T PRK07400        164 LPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVN  243 (318)
T ss_pred             EEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccccccChhhccCCC
Confidence            9999999999999999999987654 567899999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEEEEEeCCCCeEEEEEeeCCCCCCcccCCchhhhhhHHHHHHHHHHHHHHHH
Q 015066          312 DTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAE  368 (414)
Q Consensus       312 ~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  368 (414)
                      |.|+|+|+++|.++++|.||+|+++++||+++++++.+|++|++|++++++++.++.
T Consensus       244 d~VkvkVl~iD~e~~rI~LS~K~l~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  300 (318)
T PRK07400        244 DEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDPQKVFDKAEEMAAKYRQMLLAQA  300 (318)
T ss_pred             CEEEEEEEEEeCCCCEEEEEEeccccChhhhhhhHHHHHHHHHHHHHHHHHHhhhhh
Confidence            999999999999999999999999999999999999999999999999999998763

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

Probab=100.00  E-value=1.3e-47  Score=393.43  Aligned_cols=254  Identities=38%  Similarity=0.627  Sum_probs=237.3

Q ss_pred             hhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066           92 KYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (414)
Q Consensus        92 ~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~  171 (414)
                      ...+.+++|++|+|+|+++.+++++|++|++++|++|.+|++......   . +++|+.+++.|..+.+..+.++||+++
T Consensus        14 ~~~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~~~~~~---~-~~~gd~v~v~v~~~e~~~g~~~lS~~k   89 (541)
T COG0539          14 KSDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVED---V-VQVGDEVEVLVLRVEDGEGELVLSRRK   89 (541)
T ss_pred             cchhccCCCCEEEEEEEEEeCCeEEEEecCccccEeEHHHhccccccc---e-ecCCCEEEEEEEEEecCCceEEeeHHH
Confidence            345689999999999999999999999999999999999998765433   2 889999999999999888999999999


Q ss_pred             hhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--CccccccCCeEEEEEEEeecccceEEe
Q 015066          172 IQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVEVDEEQSRLVL  249 (414)
Q Consensus       172 ~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~~~vGq~V~vkVl~vD~e~~ri~L  249 (414)
                      +...++|..+++.+..|++++|+|+..+++|++|+++|++||+|.|+++..  .+...++|++++++|+++|.+++++++
T Consensus        90 ~~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~gvr~FlP~S~v~~r~v~d~~~~~Gk~~~~kiie~d~~~n~vv~  169 (541)
T COG0539          90 AERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEGVRAFLPGSLVDVRPVRDLDPLIGKELEFKILELDKKRNNVVL  169 (541)
T ss_pred             HHHHHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEECCEEEeccHHHhcccccccccccCCceEEEEEEEEccccCcEEE
Confidence            999999999999999999999999999999999999999999999999977  677788999999999999999999999


Q ss_pred             ehhhhhhh--------HHhhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEE
Q 015066          250 SNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSH  321 (414)
Q Consensus       250 S~K~~l~~--------~~~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~i  321 (414)
                      |+|..+.+        ..+++++|++|.|+|++|++||+||+|+|++||+|+++|||.|+.+|+++|++||+|+|+|+++
T Consensus       170 SrR~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~  249 (541)
T COG0539         170 SRRAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISL  249 (541)
T ss_pred             EhHHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEecCeeeEEehhhccccccCCHHHhcccCCEEEEEEEEE
Confidence            99988753        2479999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCCCeEEEEEeeCCCCCCcccCCchhh
Q 015066          322 DRERGRVSLSTKKLEPTPGDMIRNPKLV  349 (414)
Q Consensus       322 d~e~~ri~LS~K~~~~~p~~~~~~~~~~  349 (414)
                      |++++||+||||++.++||+.+.+...+
T Consensus       250 D~e~~RVsLSlK~l~~dPw~~i~~~~~~  277 (541)
T COG0539         250 DEERGRVSLSLKQLEEDPWEGIEKKYPV  277 (541)
T ss_pred             ccCCCeEEEEehhcccCcHHHHhhhcCC
Confidence            9999999999999999999988775544

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=8.1e-46  Score=382.05  Aligned_cols=260  Identities=32%  Similarity=0.538  Sum_probs=240.7

Q ss_pred             CHHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCC
Q 015066           82 TLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA  161 (414)
Q Consensus        82 ~~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~  161 (414)
                      |.++|.++++++...++.|++|+|+|++++++|++|+||++.+|+||.+|+++....++++. +++|++++|+|+++++.
T Consensus        18 ~~e~f~~~~e~~~~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~-~~vGd~Ie~~V~~~~~~   96 (486)
T PRK07899         18 SAEDFLAAIDKTIKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEV-VEVGDEVEALVLQKEDK   96 (486)
T ss_pred             CHHHHHHHHHHHHhcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccccCChhhc-CCCCCEEEEEEEEEECC
Confidence            66788888877766799999999999999999999999999999999999999877778776 89999999999999999


Q ss_pred             CCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--CccccccCCeEEEEEEE
Q 015066          162 DDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVE  239 (414)
Q Consensus       162 ~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~~~vGq~V~vkVl~  239 (414)
                      ++++.||+|++.....|..++++++.|++++|+|++++++|++|++ |++||||.|++++.  .++..++|++|+|+|++
T Consensus        97 ~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl-Gi~gflP~Sel~~~~~~~~~~~vGq~V~vkVle  175 (486)
T PRK07899         97 EGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-GLRGFLPASLVEMRRVRDLQPYIGQEIEAKIIE  175 (486)
T ss_pred             CCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEE-CCEEEEEhhHhcccccCChhhcCCCEEEEEEEE
Confidence            9999999999988889999999998899999999999999999999 79999999999976  35566899999999999


Q ss_pred             eecccceEEeehhhhhhh--------HHhhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCC
Q 015066          240 VDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG  311 (414)
Q Consensus       240 vD~e~~ri~LS~K~~l~~--------~~~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G  311 (414)
                      +|++++++.||+|..+.+        ....+++|+++.|+|+++++||+||+|+|++||||+|+++|.++.++.+.|++|
T Consensus       176 id~~~~~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v~~~~~~~kvG  255 (486)
T PRK07899        176 LDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVG  255 (486)
T ss_pred             EECCCCEEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCCHHHhcCCC
Confidence            999999999999975432        236899999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066          312 DTLKVMILSHDRERGRVSLSTKKLEPTPGDMI  343 (414)
Q Consensus       312 ~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~  343 (414)
                      |.|+|+|+++|++++||.||+|++.++||+.+
T Consensus       256 d~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~  287 (486)
T PRK07899        256 QEVTVEVLDVDMDRERVSLSLKATQEDPWQQF  287 (486)
T ss_pred             CEEEEEEEEEECCCCEEEEEEeeccccchhhh
Confidence            99999999999999999999999999999754

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

Probab=100.00  E-value=1.7e-45  Score=377.71  Aligned_cols=257  Identities=30%  Similarity=0.447  Sum_probs=233.1

Q ss_pred             HHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCe
Q 015066           85 EFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS  164 (414)
Q Consensus        85 ~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~  164 (414)
                      +.+..|++....++.|.+|+|+|+...++|+.|++++ .+||+|.|+++..++++..   ..+|.+++++|+++|..+++
T Consensus        91 ~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~g-vr~FlP~S~v~~r~v~d~~---~~~Gk~~~~kiie~d~~~n~  166 (541)
T COG0539          91 ERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEG-VRAFLPGSLVDVRPVRDLD---PLIGKELEFKILELDKKRNN  166 (541)
T ss_pred             HHHHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEECC-EEEeccHHHhccccccccc---ccCCceEEEEEEEEccccCc
Confidence            5678899988899999999999999999999999986 9999999999988776655   35899999999999999999


Q ss_pred             EEEEeeehhhhHH----HHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--Cccccc--cCCeEEEE
Q 015066          165 LVLSLRMIQYELA----WERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEEL--LGKDLPLK  236 (414)
Q Consensus       165 i~LS~k~~~~~~~----~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~~~--vGq~V~vk  236 (414)
                      +++|+|.......    .+.+.+ .+.|++++|+|++++++|+||+++|++||+|.+||+|.  .+|+++  +||+|+|+
T Consensus       167 vv~SrR~~~e~~~~~~r~e~~~~-l~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~rv~~P~~vvkvGd~Vkvk  245 (541)
T COG0539         167 VVLSRRAVLEEERSEQREELLNK-LEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKVK  245 (541)
T ss_pred             EEEEhHHHhhHHHHHHHHHHHhc-CCCCceEEEEEEEeecCcEEEEecCeeeEEehhhccccccCCHHHhcccCCEEEEE
Confidence            9999999876322    223433 46778999999999999999999999999999999997  456665  79999999


Q ss_pred             EEEeecccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCC
Q 015066          237 FVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPG  311 (414)
Q Consensus       237 Vl~vD~e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G  311 (414)
                      |+++|++++|+.||+|++..++|    ..+++|+.+.|+|+++++|||||+++ |++||+|+|||||.+...|++++++|
T Consensus       246 Vi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~G  325 (541)
T COG0539         246 VISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVG  325 (541)
T ss_pred             EEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHhcccC
Confidence            99999999999999999987766    68899999999999999999999998 99999999999999988899999999


Q ss_pred             CEEEEEEEEEeCCCCeEEEEEeeCCCCCCcccCCc
Q 015066          312 DTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNP  346 (414)
Q Consensus       312 ~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~~~~  346 (414)
                      |+|.|+|+++|++++||+||+|++..+||+....+
T Consensus       326 q~V~V~Vl~id~e~rRIsL~iKq~~~~pw~~~~~~  360 (541)
T COG0539         326 QEVEVKVLDIDPERRRISLGLKQLKENPWEEFADK  360 (541)
T ss_pred             CEEEEEEEeeCchhceEEeeehhhhcChhhhhhhh
Confidence            99999999999999999999999999999866554

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=2.8e-42  Score=366.41  Aligned_cols=264  Identities=31%  Similarity=0.487  Sum_probs=239.8

Q ss_pred             CCCCCCCHHHHHHHHHhhc--ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEE
Q 015066           76 MEGVSFTLEEFHSALEKYD--FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEF  153 (414)
Q Consensus        76 ~~~~~~~~~~f~~~l~~~~--~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v  153 (414)
                      +++..-+.++|+++++++.  +.++.|++|+|+|++++++|++|++|++.+||||.+|++...   ... .+++|++++|
T Consensus         5 ~~~~~~~~~~f~~~l~~~~~~~~~~~G~~v~G~V~~v~~~~~~Vdig~k~~g~lp~~e~~~~~---~~~-~~~vG~~i~~   80 (565)
T PRK06299          5 AQNQNDMEESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQ---GEL-EVKVGDEVEV   80 (565)
T ss_pred             ccccccchHHHHHHHHhhcccccCCCCCEEEEEEEEEECCEEEEEeCCCeEEEEEHHHhcCcc---ccc-cCCCCCEEEE
Confidence            3444456778999998876  568999999999999999999999999999999999998432   122 2899999999


Q ss_pred             EEEEEeCCCCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC--ccccccCC
Q 015066          154 VIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEELLGK  231 (414)
Q Consensus       154 ~Vl~id~~~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~--~~~~~vGq  231 (414)
                      +|+.+++.++++.||+++......|+.+.++++.|++++|+|++++++|++|+++|++||||.+|+++..  ++..++|+
T Consensus        81 ~V~~~~~~~~~i~lS~k~~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~~~g~~gfip~s~~~~~~~~~~~~~vG~  160 (565)
T PRK06299         81 YVERIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAFLPGSQVDVRPVRDTDPLEGK  160 (565)
T ss_pred             EEEEEECCCCcEEEechHHHHHHHHHHHHHHhhCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHccCcCCCChHHhCCC
Confidence            9999999899999999999988999999999999999999999999999999999999999999999863  44457999


Q ss_pred             eEEEEEEEeecccceEEeehhhhhhh--------HHhhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccC
Q 015066          232 DLPLKFVEVDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVAD  303 (414)
Q Consensus       232 ~V~vkVl~vD~e~~ri~LS~K~~l~~--------~~~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~  303 (414)
                      +++|+|+++|++++++.||+|+++.+        ...++++|+++.|+|+++.+||+||+++|++||+|+++++|.++.+
T Consensus       161 ~i~~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~g~~glv~~se~s~~~~~~  240 (565)
T PRK06299        161 ELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVNH  240 (565)
T ss_pred             EEEEEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEECCEEEEEEHHHhcccccCC
Confidence            99999999999999999999987642        2468999999999999999999999999999999999999999999


Q ss_pred             cccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066          304 IATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMI  343 (414)
Q Consensus       304 ~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~  343 (414)
                      +.+.|++||+|+|+|+++|++++++.||+|.+.++||+.+
T Consensus       241 ~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~~p~~~~  280 (565)
T PRK06299        241 PSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAI  280 (565)
T ss_pred             HhhcCCCCCEEEEEEEEEeCCCCeEEEEEEecccChhHHH
Confidence            9999999999999999999999999999999999999754

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1.5e-41  Score=345.68  Aligned_cols=259  Identities=35%  Similarity=0.597  Sum_probs=237.9

Q ss_pred             HHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEe-CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCC
Q 015066           83 LEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA  161 (414)
Q Consensus        83 ~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdi-g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~  161 (414)
                      +++|++.++... ++++|++|+|+|.+++++|++|++ +++.+|+||.+|+++....++.+. +++|+.++|+|++++.+
T Consensus         2 ~~~~~~~~~~~~-~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~-~~vGd~v~~~V~~v~~~   79 (390)
T PRK06676          2 MEEFEESLNSVK-EVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDV-VKVGDELEVYVLKVEDG   79 (390)
T ss_pred             hHHHHHHhhhhh-cccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccccccCcccc-cCCCCEEEEEEEEEECC
Confidence            467888887544 899999999999999999999999 878999999999998777777766 89999999999999988


Q ss_pred             CCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--CccccccCCeEEEEEEE
Q 015066          162 DDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVE  239 (414)
Q Consensus       162 ~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~~~vGq~V~vkVl~  239 (414)
                      ++++.||+++......|+.+.+.+..|++++|+|+++.++|+||+++|++||||.+++++.  .+++.++|++++|+|++
T Consensus        80 ~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~G~~gflp~~el~~~~~~~~~~~vG~~v~~~Vl~  159 (390)
T PRK06676         80 EGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLISTRFVEDFSDFKGKTLEVKIIE  159 (390)
T ss_pred             CCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCCccCCChHHcCCCEEEEEEEE
Confidence            8999999999888889999999989999999999999999999999999999999999976  34566799999999999


Q ss_pred             eecccceEEeehhhhhhh--------HHhhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCC
Q 015066          240 VDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG  311 (414)
Q Consensus       240 vD~e~~ri~LS~K~~l~~--------~~~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G  311 (414)
                      +|++++++.||+|.+...        ...++++|++|.|+|+++.++|+||+++|++|++|++++++.++.++.+.|++|
T Consensus       160 ~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~~~~~~~~~vG  239 (390)
T PRK06676        160 LDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVG  239 (390)
T ss_pred             EECCCCEEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCccccCCHHHhcCCC
Confidence            999999999999986432        236789999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066          312 DTLKVMILSHDRERGRVSLSTKKLEPTPGDMI  343 (414)
Q Consensus       312 ~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~  343 (414)
                      |.|+|+|+++|+++++|.||+|++.++||+.+
T Consensus       240 d~i~~~Vl~vd~~~~~i~lS~k~~~~~~~~~~  271 (390)
T PRK06676        240 QEVEVKVLSIDWETERISLSLKDTLPGPWEGV  271 (390)
T ss_pred             CEEEEEEEEEeCCCCEEEEEEeecccCccccc
Confidence            99999999999999999999999999999754

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=4e-41  Score=350.76  Aligned_cols=247  Identities=26%  Similarity=0.394  Sum_probs=223.4

Q ss_pred             HHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC----C
Q 015066           88 SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD----D  163 (414)
Q Consensus        88 ~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~----~  163 (414)
                      +.|+.+...+++|++++|+|+++.++|+||+++++.+||+|.+|+++.+..++.+. |++|+.++|+|+++|.++    +
T Consensus       191 ~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~-~~vGd~i~vkVl~id~~~~~~~~  269 (491)
T PRK13806        191 EALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEA-VSVGDTVRVKVLGIERAKKGKGL  269 (491)
T ss_pred             HHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHh-cCCCCEEEEEEEEEecccCCcce
Confidence            45555555789999999999999999999999878999999999999888888877 899999999999999776    4


Q ss_pred             eEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCC---Ccccc--ccCCeEEEEE
Q 015066          164 SLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEE--LLGKDLPLKF  237 (414)
Q Consensus       164 ~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~---~~~~~--~vGq~V~vkV  237 (414)
                      ++.||+|++.. .+|..+.+.+..|++++|+|+++.++|+||+++ |++||+|.|+++|.   .++..  .+||.|+|+|
T Consensus       270 ri~lS~K~~~~-~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkV  348 (491)
T PRK13806        270 RISLSIKQAGG-DPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKI  348 (491)
T ss_pred             EEEEEehhhhc-ccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEE
Confidence            79999998854 689998888888999999999999999999997 99999999999984   22333  2799999999


Q ss_pred             EEeecccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCC
Q 015066          238 VEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGD  312 (414)
Q Consensus       238 l~vD~e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~  312 (414)
                      +++|++++++.||+|++..+++    ..+++|++|+|+|+++++||+||++. |++||||+|+++|.+..++.+.|++||
T Consensus       349 l~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~~~~~~~~~~~~Gd  428 (491)
T PRK13806        349 KDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGD  428 (491)
T ss_pred             EEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCcccccchhhcCCCCC
Confidence            9999999999999998866554    57889999999999999999999997 999999999999999999999999999


Q ss_pred             EEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          313 TLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       313 ~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      +|+|+|+.+|++++||+||+|++.
T Consensus       429 ~v~~~V~~id~e~~ri~Ls~~~~~  452 (491)
T PRK13806        429 SVTLVVEEIDTAKRKISLAPAGAA  452 (491)
T ss_pred             EEEEEEEEEeCCCCEEEEEeehhh
Confidence            999999999999999999999773

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

Probab=100.00  E-value=4.1e-40  Score=353.68  Aligned_cols=290  Identities=31%  Similarity=0.509  Sum_probs=255.6

Q ss_pred             EEEeCCcchhHHHHHHHHHHHHhhcccC-CCCCCCCCHHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeE
Q 015066           47 VAISNAETREREELNQLFEEAYERCRTA-PMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSA  125 (414)
Q Consensus        47 ~~~~~~~~~~~~~l~~iiee~~~~~~~~-~~~~~~~~~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g  125 (414)
                      +.|..|-..+    +.+|++++..++.. .+.  ..+.+++.+.|+.....+++|++|+|+|.+++++|++|+++++.+|
T Consensus       255 vgitagaStP----~~~i~~v~~~l~~~~~~~--~~~~~~~~~~~~~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G  328 (647)
T PRK00087        255 IGVTAGASTP----DWIIEEVIKKMSELDNME--EVEENEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEG  328 (647)
T ss_pred             EEEEeccCCC----HHHHHHHHHHHHHhcccc--ccCHHHHHHHHHHHHhhccCCCEEEEEEEEEECCEEEEEECCCeEE
Confidence            5555555334    45666666666542 111  2345667777888778999999999999999999999999999999


Q ss_pred             EEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEE
Q 015066          126 YLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVA  205 (414)
Q Consensus       126 ~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V  205 (414)
                      ++|.+|+++....++.+. +++|+.++|+|++++++++++.||++.......|+.+.+.++.|++++|+|++++++|+||
T Consensus       329 ~lp~~els~~~~~~~~~~-~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V  407 (647)
T PRK00087        329 VIPLRELTLDEISSLKES-VKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLV  407 (647)
T ss_pred             EEEHHHhcccccCChhhc-cCCCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEE
Confidence            999999998887777776 8999999999999998999999999999888899999999999999999999999999999


Q ss_pred             EECCEEEEEeccccCCCC--ccccccCCeEEEEEEEeecccce-EEeehhhhhh--------hHHhhccccEEEEEEEEE
Q 015066          206 EVEGLRGFVPFSQISSKS--TAEELLGKDLPLKFVEVDEEQSR-LVLSNRKAMA--------DSQAQLGIGSVVIGTVQS  274 (414)
Q Consensus       206 ~i~gi~GfIp~sels~~~--~~~~~vGq~V~vkVl~vD~e~~r-i~LS~K~~l~--------~~~~~l~~G~iv~g~V~~  274 (414)
                      +++|++||||.+++++..  ++..++|+.+.|+|+++|+++++ +.+|+|..+.        ..++++++|++|.|+|++
T Consensus       408 ~lggi~gfiP~sel~~~~~~d~~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~  487 (647)
T PRK00087        408 DYGGVRAFLPASHVELGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKR  487 (647)
T ss_pred             EECCEEEEEEHHHhCccccCCHHHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEE
Confidence            999999999999999763  55567999999999999999998 9999998753        234678999999999999


Q ss_pred             EeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066          275 LKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMI  343 (414)
Q Consensus       275 i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~  343 (414)
                      +.++|+||+++|++|++|+++++|.++.++.+.|++||.|+|+|+++|++++++.||+|++.++||+.+
T Consensus       488 v~~~G~fV~l~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~~~~~p~~~~  556 (647)
T PRK00087        488 LTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENV  556 (647)
T ss_pred             EeCCcEEEEECCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeeccccChhhhh
Confidence            999999999999999999999999999999999999999999999999999999999999999999754

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=2e-39  Score=334.66  Aligned_cols=249  Identities=27%  Similarity=0.407  Sum_probs=221.4

Q ss_pred             HHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeE
Q 015066           86 FHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL  165 (414)
Q Consensus        86 f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i  165 (414)
                      +...|+.+...++.|++|+|+|+++.++|++|++|  .+||||.+++++.+..++.+   ++|+.++|+|+++|.+++++
T Consensus       109 ~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~VdlG--i~gflP~Sel~~~~~~~~~~---~vGq~V~vkVleid~~~~~i  183 (486)
T PRK07899        109 YERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDIG--LRGFLPASLVEMRRVRDLQP---YIGQEIEAKIIELDKNRNNV  183 (486)
T ss_pred             ccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEEC--CEEEEEhhHhcccccCChhh---cCCCEEEEEEEEEECCCCEE
Confidence            35678887766679999999999999999999994  79999999998876666553   58999999999999999999


Q ss_pred             EEEeeehhh---hHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC--ccccc--cCCeEEEEEE
Q 015066          166 VLSLRMIQY---ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEEL--LGKDLPLKFV  238 (414)
Q Consensus       166 ~LS~k~~~~---~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~--~~~~~--vGq~V~vkVl  238 (414)
                      .||+|..+.   ...|+.+...+..|++++|+|++++++|+||+++|++||||.|+++|..  ++..+  +||.|+|+|+
T Consensus       184 vLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl  263 (486)
T PRK07899        184 VLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVL  263 (486)
T ss_pred             EEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEE
Confidence            999997543   3567777667788899999999999999999999999999999999863  44443  7999999999


Q ss_pred             EeecccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCE
Q 015066          239 EVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDT  313 (414)
Q Consensus       239 ~vD~e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~  313 (414)
                      ++|+++++|.||+|+...+++    ..+++|++|.|+|+++.+||+||++. |++||+|++++++.++.++.+.|++||+
T Consensus       264 ~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~  343 (486)
T PRK07899        264 DVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDE  343 (486)
T ss_pred             EEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCE
Confidence            999999999999998876554    45778999999999999999999997 8999999999999999999999999999


Q ss_pred             EEEEEEEEeCCCCeEEEEEeeCCCCC
Q 015066          314 LKVMILSHDRERGRVSLSTKKLEPTP  339 (414)
Q Consensus       314 V~vkVl~id~e~~ri~LS~K~~~~~p  339 (414)
                      |+|+|+++|++++||.||+|++.++-
T Consensus       344 V~VkIi~ID~e~rrI~LSlK~~~~~~  369 (486)
T PRK07899        344 VFVKVIDIDLERRRISLSLKQANEGV  369 (486)
T ss_pred             EEEEEEEEECCCCEEEEEEEEcccCC
Confidence            99999999999999999999987553

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=2.7e-40  Score=359.87  Aligned_cols=250  Identities=23%  Similarity=0.370  Sum_probs=225.3

Q ss_pred             HhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           91 EKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        91 ~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      +++..++++|++|+|+|.++.++|+||+++ +.+||+|.+++++.+..++.+. +++|++++|+|+++|++++++.||+|
T Consensus       485 ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~-~kvGq~v~vkVi~iD~e~~rI~LSlK  562 (863)
T PRK12269        485 EEFFNSVHIEDSVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREF-VKKGQTIELKVIRLDQAEKRINLSLK  562 (863)
T ss_pred             HHHHhcCCCCCEEEEEEEEEeCCcEEEEEC-CEEEEEEchhccccccCCHHHh-ccCCCEEEEEEEEEecCCCeEEEEEe
Confidence            333346889999999999999999999996 5999999999999988888877 88999999999999999999999999


Q ss_pred             ehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCC---Cccccc--cCCeEEEEEEEeeccc
Q 015066          171 MIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEEL--LGKDLPLKFVEVDEEQ  244 (414)
Q Consensus       171 ~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~---~~~~~~--vGq~V~vkVl~vD~e~  244 (414)
                      .... .+|..+.+.++.|++++|+|+++.++|+||+++ |++||+|.|+++|.   .++.+.  +||+|+|+|+.+|+++
T Consensus       563 ~l~~-~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~  641 (863)
T PRK12269        563 HFQP-DPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQA  641 (863)
T ss_pred             cccc-chhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEeccc
Confidence            8754 689998888889999999999999999999997 99999999999983   244443  7999999999999999


Q ss_pred             ceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccc-cCcccccCCCCEEEEEE
Q 015066          245 SRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV-ADIATVLQPGDTLKVMI  318 (414)
Q Consensus       245 ~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~-~~~~~~~~~G~~V~vkV  318 (414)
                      +++.||+|++..++|    ..+++|++++|+|+++++||+||+++ |++||||.|+++|.+. .++...|++||.|+|+|
T Consensus       642 ~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkV  721 (863)
T PRK12269        642 GRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMV  721 (863)
T ss_pred             CceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEEEE
Confidence            999999999866544    57889999999999999999999997 9999999999999765 44566899999999999


Q ss_pred             EEEeCCCCeEEEEEeeCCCCCCccc
Q 015066          319 LSHDRERGRVSLSTKKLEPTPGDMI  343 (414)
Q Consensus       319 l~id~e~~ri~LS~K~~~~~p~~~~  343 (414)
                      +++|++++||.||+|++.++||+.+
T Consensus       722 l~ID~e~rrI~LS~K~l~~dpw~~~  746 (863)
T PRK12269        722 IECDPQARRIRLGVKQLSDNPWQVF  746 (863)
T ss_pred             EEEeccCCEEEEEecccccChHHHH
Confidence            9999999999999999999999754

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=6.3e-40  Score=356.94  Aligned_cols=258  Identities=27%  Similarity=0.413  Sum_probs=228.1

Q ss_pred             HHHHHHHHhhcccCCCCCEEEEEEEEEe--CCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeC-
Q 015066           84 EEFHSALEKYDFNSELGTKVKGTVFCTD--NRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENE-  160 (414)
Q Consensus        84 ~~f~~~l~~~~~~l~~G~iV~G~V~~v~--~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~-  160 (414)
                      .+....|++....++.|++|+|+|++++  ++|++|+++.+.+||||.+|+......++.   ..+|+.++|.|+.++. 
T Consensus       383 ~~~~~~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~~~~~~---~~vG~~ie~~V~~~~~~  459 (863)
T PRK12269        383 ADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPE---SLIGLTSKFYIERISQS  459 (863)
T ss_pred             hhhhHHHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhccccccchH---HhCCCeEEEEEEEEecc
Confidence            3566789888888999999999999984  579999998889999999999766554443   3589999999999864 


Q ss_pred             ----CCCeEEEEeeehhhhHHHHHhhhccc---CCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC--ccccc--c
Q 015066          161 ----ADDSLVLSLRMIQYELAWERCRQLQS---EDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEEL--L  229 (414)
Q Consensus       161 ----~~~~i~LS~k~~~~~~~~~~l~~~~~---~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~--~~~~~--v  229 (414)
                          ++++++||+|+...+..|+.+.+++.   .|++++|+|++++++|+||+++|++||||.|+++|..  ++.+.  +
T Consensus       460 ~~~~~~~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~Gv~Gfvp~SeiS~~~v~~~~~~~kv  539 (863)
T PRK12269        460 KQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVARPREFVKK  539 (863)
T ss_pred             cccCCCCeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEchhccccccCCHHHhccC
Confidence                34689999999988888888776553   5789999999999999999999999999999999863  44443  7


Q ss_pred             CCeEEEEEEEeecccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCc-ccccC
Q 015066          230 GKDLPLKFVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH-DRVAD  303 (414)
Q Consensus       230 Gq~V~vkVl~vD~e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~-~~~~~  303 (414)
                      ||+++|+|+++|++++++.||+|+...+.+    +.+++|++|+|+|+++.+||+||+++ |++||+|+|+++| .++.+
T Consensus       540 Gq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~  619 (863)
T PRK12269        540 GQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSK  619 (863)
T ss_pred             CCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCC
Confidence            999999999999999999999998865543    57899999999999999999999997 9999999999999 57899


Q ss_pred             cccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCCCcccC
Q 015066          304 IATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIR  344 (414)
Q Consensus       304 ~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~~  344 (414)
                      |.+.|++||+|+|+|+++|++++|++||+|++.+|||+.+.
T Consensus       620 p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~  660 (863)
T PRK12269        620 PSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIE  660 (863)
T ss_pred             HHHcCCCCCEEEEEEEEEecccCceEEEehhcccCchHHHH
Confidence            99999999999999999999999999999999999998663

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=2.4e-39  Score=337.45  Aligned_cols=255  Identities=30%  Similarity=0.460  Sum_probs=226.0

Q ss_pred             HHHHHHHHHhhcc----cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEE
Q 015066           83 LEEFHSALEKYDF----NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE  158 (414)
Q Consensus        83 ~~~f~~~l~~~~~----~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~i  158 (414)
                      .++|+++++++.+    .++.|++|+|+|++++++|++|++|.+.+||||.+|+....    .+..+++|++++|+|+++
T Consensus        14 ~~~f~~~l~~~~~~~~~~~~~G~~v~G~V~~v~~~~v~Vdig~k~eg~ip~~e~~~~~----~~~~~~~G~~i~~~Vi~~   89 (491)
T PRK13806         14 SESFAELLEAYEGERKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDAD----GELTVAVGDEVELYVVSV   89 (491)
T ss_pred             hHHHHHHHHhhhhhccccCCCCCEEEEEEEEEECCEEEEEECCCcEEEEEHHHhcCcc----ccccccCCCEEEEEEEEE
Confidence            3579999987753    38999999999999999999999999999999999986432    122378999999999998


Q ss_pred             eCCCCeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--CccccccCCeEEEE
Q 015066          159 NEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLK  236 (414)
Q Consensus       159 d~~~~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~~~vGq~V~vk  236 (414)
                      ++  +.+.||++.. ....|+.+.+++..|++++|+|++++++|++|+++|++||||.||+++.  .++..++|++++|+
T Consensus        90 ~~--~~~~lS~~~~-~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~i~g~~~flP~s~~~~~~~~~~~~~vG~~i~~~  166 (491)
T PRK13806         90 NG--QEIRLSKALS-GQGGAAMLEEAYENGVPVEGKVTGTCKGGFNVEVLGRRAFCPVSQIDLRYVEDPESYVGQTFQFL  166 (491)
T ss_pred             cC--CEEEEEhHHh-hhhhHHHHHHHHhCCCEEEEEEEEEEcCCEEEEECCEEEEEEHHHhccccCCChHHcCCCeEEEE
Confidence            74  5799997643 4578999999999999999999999999999999999999999999975  45666799999999


Q ss_pred             EEEeecccceEEeehhhhhhh--------HHhhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccc
Q 015066          237 FVEVDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATV  307 (414)
Q Consensus       237 Vl~vD~e~~ri~LS~K~~l~~--------~~~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~  307 (414)
                      |+.+|++++++.||+|+.+..        ....+++|++|+|+|+++.+||+||+++ |+.||||+|+++|.++.++.+.
T Consensus       167 V~~id~~~~~v~lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~  246 (491)
T PRK13806        167 ITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEA  246 (491)
T ss_pred             EEEEECCCCeEEEEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHh
Confidence            999999999999999987532        2357999999999999999999999997 8999999999999999999999


Q ss_pred             cCCCCEEEEEEEEEeCCC----CeEEEEEeeCCCCCCcccC
Q 015066          308 LQPGDTLKVMILSHDRER----GRVSLSTKKLEPTPGDMIR  344 (414)
Q Consensus       308 ~~~G~~V~vkVl~id~e~----~ri~LS~K~~~~~p~~~~~  344 (414)
                      |++||.|+|+|+++|+++    +||.||+|++.++||+.+.
T Consensus       247 ~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~~  287 (491)
T PRK13806        247 VSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVG  287 (491)
T ss_pred             cCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhhh
Confidence            999999999999999876    4899999999999997653

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1.2e-38  Score=324.21  Aligned_cols=253  Identities=29%  Similarity=0.447  Sum_probs=224.7

Q ss_pred             HHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEE
Q 015066           88 SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVL  167 (414)
Q Consensus        88 ~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~L  167 (414)
                      ..|+++...++.|++++|+|+++.++|++|++++ .+||+|.+|+++.+..++.+   .+|+.++|+|+++|.+++++.|
T Consensus        94 ~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~G-~~gflp~~el~~~~~~~~~~---~vG~~v~~~Vl~~d~~~~~i~l  169 (390)
T PRK06676         94 KAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEG-VRGFIPASLISTRFVEDFSD---FKGKTLEVKIIELDPEKNRVIL  169 (390)
T ss_pred             hhHHHHHHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCCccCCChHH---cCCCEEEEEEEEEECCCCEEEE
Confidence            4577666677999999999999999999999964 69999999999877766654   3899999999999999999999


Q ss_pred             Eeeehhhh---HHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC--ccccc--cCCeEEEEEEEe
Q 015066          168 SLRMIQYE---LAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEEL--LGKDLPLKFVEV  240 (414)
Q Consensus       168 S~k~~~~~---~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~--~~~~~--vGq~V~vkVl~v  240 (414)
                      |+|.....   ..|..+...+..|++++|+|+++.++|+||.+++++||||.+++++..  ++...  +|+.|+|+|+++
T Consensus       170 S~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~v  249 (390)
T PRK06676        170 SRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSI  249 (390)
T ss_pred             EeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEE
Confidence            99986542   467766666678899999999999999999999999999999999863  33332  799999999999


Q ss_pred             ecccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEE
Q 015066          241 DEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLK  315 (414)
Q Consensus       241 D~e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~  315 (414)
                      |++++++.||+|+...+++    +++++|+++.|+|+++.+||+||++. |+.||+|+|++++.++.++.+.|++||.|+
T Consensus       250 d~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~  329 (390)
T PRK06676        250 DWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVK  329 (390)
T ss_pred             eCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEE
Confidence            9999999999998765443    57899999999999999999999997 899999999999999999999999999999


Q ss_pred             EEEEEEeCCCCeEEEEEeeCCCCCCcccC
Q 015066          316 VMILSHDRERGRVSLSTKKLEPTPGDMIR  344 (414)
Q Consensus       316 vkVl~id~e~~ri~LS~K~~~~~p~~~~~  344 (414)
                      |+|+++|++++++.||+|++.++||+...
T Consensus       330 v~V~~id~e~~~i~ls~k~~~~~~~~~~~  358 (390)
T PRK06676        330 VKVLEVNEEEKRISLSIKALEEAPAEEED  358 (390)
T ss_pred             EEEEEEECCCCEEEEEEEecccChhhhhh
Confidence            99999999999999999999999997653

>TIGR00717 rpsA ribosomal protein S1

Probab=100.00  E-value=1e-38  Score=335.85  Aligned_cols=253  Identities=32%  Similarity=0.533  Sum_probs=230.0

Q ss_pred             HHHHHHHhh--cccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC
Q 015066           85 EFHSALEKY--DFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD  162 (414)
Q Consensus        85 ~f~~~l~~~--~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~  162 (414)
                      +|+++++++  ...+++|++|+|+|++++++|++|++|++.+|+||.+|++...     +. +++|++++++|++++++.
T Consensus         2 ~f~~~~~~~~~~~~~~~G~~v~g~V~~i~~~~~~v~~g~k~~g~i~~~E~~~~~-----~~-~~vGd~i~~~V~~~~~~~   75 (516)
T TIGR00717         2 SFAQLLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAP-----LE-IQVGDEVEVYLDRVEDRF   75 (516)
T ss_pred             hHHHHHhhhcccccCCCCCEEEEEEEEEECCEEEEEcCCCcEEEEEHHHhcCCc-----cC-CCCCCEEEEEEEEEeCCC
Confidence            688888765  3468999999999999999999999999999999999997532     23 789999999999998888


Q ss_pred             CeEEEEeeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--CccccccCCeEEEEEEEe
Q 015066          163 DSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVEV  240 (414)
Q Consensus       163 ~~i~LS~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~~~vGq~V~vkVl~v  240 (414)
                      +++.||+++......|..+++++..|++++|+|++++++|++|+++|++||||.+|++..  .+...++|++++|+|+++
T Consensus        76 g~i~lS~~~~~~~~~~~~l~~a~~~g~~v~g~V~~~~~~g~~V~i~g~~~flP~s~~~~~~~~~~~~~vG~~i~~~v~~~  155 (516)
T TIGR00717        76 GETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGSQVDVKPIKDLDSLIGKTLKFKIIKL  155 (516)
T ss_pred             CcEEEEHHHhhhhHHHHHHHHHhhCCCeEEEEEEEEECCEEEEEECCEEEEEeHHHhcCcccCchhhhCCCEEEEEEEEE
Confidence            999999998887789999999999999999999999999999999999999999999865  244557999999999999


Q ss_pred             ecccceEEeehhhhhhhH--------HhhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCC
Q 015066          241 DEEQSRLVLSNRKAMADS--------QAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGD  312 (414)
Q Consensus       241 D~e~~ri~LS~K~~l~~~--------~~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~  312 (414)
                      |+.++++.+|+|+++.+.        ...+++|++++|+|+++.++|+||+++|++|++|.++++|.++.++.+.|++||
T Consensus       156 ~~~~~~iv~Srk~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~g~~g~lp~~e~s~~~~~~~~~~~~vG~  235 (516)
T TIGR00717       156 DQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLGGVDGLLHITDMSWKRVKHPSEYVKVGQ  235 (516)
T ss_pred             ECCCCcEEEEHHHHHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCCCCCCCHHHhccCCC
Confidence            999999999999875432        368999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066          313 TLKVMILSHDRERGRVSLSTKKLEPTPGDMI  343 (414)
Q Consensus       313 ~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~  343 (414)
                      .|.|+|+++|++++++.||+|.+.++||+.+
T Consensus       236 ~v~v~Vl~~d~~~~~i~lS~k~~~~~p~~~~  266 (516)
T TIGR00717       236 EVKVKVIKFDKEKGRISLSLKQLGEDPWEAI  266 (516)
T ss_pred             EEEEEEEEEECCCCcEEEEEEecchhHHHHH
Confidence            9999999999999999999999988888643

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

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=9e-38  Score=331.98  Aligned_cols=251  Identities=27%  Similarity=0.455  Sum_probs=226.9

Q ss_pred             HHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066           90 LEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus        90 l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      |..+..++++|++++|+|+++.++|+||+++ +.+|++|.+|+++.+..++.+. +++|+.++|+|+++|++++++.||+
T Consensus       192 ~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~-~kvG~~v~v~V~~~d~~~~~i~lS~  269 (565)
T PRK06299        192 REELLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEV-VNVGDEVKVKVLKFDKEKKRVSLGL  269 (565)
T ss_pred             HHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhc-CCCCCEEEEEEEEEeCCCCeEEEEE
Confidence            3333446889999999999999999999998 6999999999999888888877 8999999999999999999999999


Q ss_pred             eehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCC---cccc--ccCCeEEEEEEEeecc
Q 015066          170 RMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS---TAEE--LLGKDLPLKFVEVDEE  243 (414)
Q Consensus       170 k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~---~~~~--~vGq~V~vkVl~vD~e  243 (414)
                      |.... .+|+.+.+.+..|++++|+|++++++|+||+++ |++||+|.++++|..   ++..  .+|+.|+|+|+++|++
T Consensus       270 k~~~~-~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~  348 (565)
T PRK06299        270 KQLGE-DPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEE  348 (565)
T ss_pred             Eeccc-ChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCC
Confidence            98776 689998877888999999999999999999997 999999999999752   3333  2799999999999999


Q ss_pred             cceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccc-cCcccccCCCCEEEEE
Q 015066          244 QSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV-ADIATVLQPGDTLKVM  317 (414)
Q Consensus       244 ~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~-~~~~~~~~~G~~V~vk  317 (414)
                      ++++.||+|++..+++    ..+++|++|.|+|+++.++|+||+++ +++|++|++++++.+. .++.+.|++||.|+|+
T Consensus       349 ~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~  428 (565)
T PRK06299        349 KRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAV  428 (565)
T ss_pred             CCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEE
Confidence            9999999998755433    57889999999999999999999998 8999999999999876 8899999999999999


Q ss_pred             EEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066          318 ILSHDRERGRVSLSTKKLEPTPGDMI  343 (414)
Q Consensus       318 Vl~id~e~~ri~LS~K~~~~~p~~~~  343 (414)
                      |+++|+++++|.||+|++..+||...
T Consensus       429 Il~vd~~~~~i~ls~k~~~~~p~~~~  454 (565)
T PRK06299        429 VLKVDVEKERISLGIKQLEEDPFEEF  454 (565)
T ss_pred             EEEEeCCCCEEEEEEehhhcCchhHH
Confidence            99999999999999999999999643

>TIGR00717 rpsA ribosomal protein S1

Probab=100.00  E-value=5.9e-37  Score=322.47  Aligned_cols=252  Identities=27%  Similarity=0.453  Sum_probs=224.3

Q ss_pred             HHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066           89 ALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (414)
Q Consensus        89 ~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS  168 (414)
                      .++.....+++|++++|+|.++.++|+||++++ .+||+|.+|+++....++.+. +++|+.++|+|+++|++++++.||
T Consensus       177 ~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~g-~~g~lp~~e~s~~~~~~~~~~-~~vG~~v~v~Vl~~d~~~~~i~lS  254 (516)
T TIGR00717       177 AREELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEY-VKVGQEVKVKVIKFDKEKGRISLS  254 (516)
T ss_pred             HHHHHHHhccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCCCCCCCHHHh-ccCCCEEEEEEEEEECCCCcEEEE
Confidence            344444578999999999999999999999975 999999999999888888776 899999999999999999999999


Q ss_pred             eeehhhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCC---cccc--ccCCeEEEEEEEeec
Q 015066          169 LRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS---TAEE--LLGKDLPLKFVEVDE  242 (414)
Q Consensus       169 ~k~~~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~---~~~~--~vGq~V~vkVl~vD~  242 (414)
                      +|.... .+|+.+.+.+..|++++|+|++++++|+||+++ |++||+|.++++|..   ++..  .+||.++|+|+++|+
T Consensus       255 ~k~~~~-~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~  333 (516)
T TIGR00717       255 LKQLGE-DPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDP  333 (516)
T ss_pred             EEecch-hHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcC
Confidence            998765 689988877788999999999999999999997 999999999999752   3332  389999999999999


Q ss_pred             ccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccc-ccCcccccCCCCEEEE
Q 015066          243 EQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR-VADIATVLQPGDTLKV  316 (414)
Q Consensus       243 e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~-~~~~~~~~~~G~~V~v  316 (414)
                      +++++.||+|++..+++    +.+++|+++.|+|+++.+||+||+++ |++||+|+++++|.+ ..++...|++||.|.|
T Consensus       334 ~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~  413 (516)
T TIGR00717       334 ERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEA  413 (516)
T ss_pred             CCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEE
Confidence            99999999998755443    46889999999999999999999998 899999999999975 4567788999999999


Q ss_pred             EEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066          317 MILSHDRERGRVSLSTKKLEPTPGDMI  343 (414)
Q Consensus       317 kVl~id~e~~ri~LS~K~~~~~p~~~~  343 (414)
                      +|+++|+++++|.||+|++.++||+..
T Consensus       414 ~Vl~vd~~~~~i~ls~K~~~~~p~~~~  440 (516)
T TIGR00717       414 VVLAVDKEKKRISLGVKQLTENPWEKF  440 (516)
T ss_pred             EEEEEeCcCCEEEEeeccccCCchhhh
Confidence            999999999999999999999998644

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

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

Probab=100.00  E-value=2.5e-35  Score=316.65  Aligned_cols=252  Identities=32%  Similarity=0.496  Sum_probs=221.4

Q ss_pred             HHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCe-E
Q 015066           87 HSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS-L  165 (414)
Q Consensus        87 ~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~-i  165 (414)
                      ...|+++...+++|++++|+|+++.++|++|++++ .+||+|.+|+++.+..++.+   .+|+.++|+|+++|+++++ +
T Consensus       377 ~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lgg-i~gfiP~sel~~~~~~d~~~---~vG~~v~v~Vl~vd~e~~~~l  452 (647)
T PRK00087        377 EKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGG-VRAFLPASHVELGYVEDLSE---YKGQELEVKIIEFNRKRRKKV  452 (647)
T ss_pred             hhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHhCccccCCHHH---hCCCEEEEEEEEEEcCCCcEE
Confidence            45677776678999999999999999999999997 99999999999877666653   3899999999999998888 9


Q ss_pred             EEEeeehhh---hHHHHHhhhcccCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC--cccc-c-cCCeEEEEEE
Q 015066          166 VLSLRMIQY---ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEE-L-LGKDLPLKFV  238 (414)
Q Consensus       166 ~LS~k~~~~---~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~--~~~~-~-vGq~V~vkVl  238 (414)
                      .+|+|....   ...|....+.+..|++++|+|+++.++|+||+++|++||+|.++++|..  ++.. + +|+.++++|+
T Consensus       453 ~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~  532 (647)
T PRK00087        453 VLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYIL  532 (647)
T ss_pred             EEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEE
Confidence            999988753   2334444444567899999999999999999999999999999999863  2322 2 7999999999


Q ss_pred             EeecccceEEeehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCE
Q 015066          239 EVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDT  313 (414)
Q Consensus       239 ~vD~e~~ri~LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~  313 (414)
                      ++|++++++.||+|+.+.+++    .++++|+++.|+|+++.+||+||+++ |+.||+|++++++.++.++.+.|++||.
T Consensus       533 ~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~  612 (647)
T PRK00087        533 DIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEE  612 (647)
T ss_pred             EEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCE
Confidence            999999999999998865543    56889999999999999999999997 8999999999999999999999999999


Q ss_pred             EEEEEEEEeCCCCeEEEEEeeCCCCCCcc
Q 015066          314 LKVMILSHDRERGRVSLSTKKLEPTPGDM  342 (414)
Q Consensus       314 V~vkVl~id~e~~ri~LS~K~~~~~p~~~  342 (414)
                      |+|+|+++|++++++.||+|++.++|++.
T Consensus       613 V~vkV~~id~e~~rI~lslk~~~~~~~~~  641 (647)
T PRK00087        613 VKAKILEVDPEEKRIRLSIKEVEEEPGDI  641 (647)
T ss_pred             EEEEEEEEeCCCCEEEEEEeecccCcccc
Confidence            99999999999999999999999999653

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.89  E-value=5.5e-22  Score=196.15  Aligned_cols=157  Identities=21%  Similarity=0.288  Sum_probs=132.7

Q ss_pred             HHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCC--ccccc--cCCeEEEEEEEeecccceEEee
Q 015066          176 LAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS--TAEEL--LGKDLPLKFVEVDEEQSRLVLS  250 (414)
Q Consensus       176 ~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~--~~~~~--vGq~V~vkVl~vD~e~~ri~LS  250 (414)
                      ..|+.+...+..|++++|+|+++.++|++|++| +.+||||.+++++..  ++.+.  +|++++|+|+++|.+++++.||
T Consensus        20 ~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS   99 (318)
T PRK07400         20 ALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLS   99 (318)
T ss_pred             HHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEe
Confidence            345444444678899999999999999999998 699999999999864  34443  6999999999999999999999


Q ss_pred             hhhhhh-hHH----hhccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCC
Q 015066          251 NRKAMA-DSQ----AQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRER  325 (414)
Q Consensus       251 ~K~~l~-~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~  325 (414)
                      +|++.. +.|    +..+.|++|.|+|+++.++|+||+++|+.||||+|+++|.+..   +. .+|+.+.|+|+.+|+++
T Consensus       100 ~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~Gv~gfip~s~ls~~~~~---~~-~vG~~i~~kVl~id~~~  175 (318)
T PRK07400        100 IRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPK---EE-LVGEELPLKFLEVDEER  175 (318)
T ss_pred             hhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCccCCc---cc-cCCCEEEEEEEEEEccc
Confidence            998642 333    2445699999999999999999999999999999999986432   33 49999999999999999


Q ss_pred             CeEEEEEeeCC
Q 015066          326 GRVSLSTKKLE  336 (414)
Q Consensus       326 ~ri~LS~K~~~  336 (414)
                      ++|.||+|...
T Consensus       176 ~~i~lS~K~~~  186 (318)
T PRK07400        176 NRLVLSHRRAL  186 (318)
T ss_pred             CEEEEEhhHhh
Confidence            99999999653

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

Probab=99.83  E-value=5.3e-20  Score=200.61  Aligned_cols=246  Identities=23%  Similarity=0.296  Sum_probs=206.2

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEc-CccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh-
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLP-TQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ-  173 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp-~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~-  173 (414)
                      ...+|++.-|+|..+..+++.++++.+..|-.. ..++++.+..+|.+. |..++.+.+.++.++..++.+.||++... 
T Consensus      1064 ~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~~~~P~~~-f~~~~~v~~~~L~vs~~n~~leLslr~sr~ 1142 (1710)
T KOG1070|consen 1064 NPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSYSMTPVEH-FTKIQIVYVCVLSVSALNKGLELSLRESRT 1142 (1710)
T ss_pred             CCCcchhhcceeeeeccceeEEecCCccccceEEeeehhccccCChHHh-cccccEEEEEEEEEecccccceeecccccc
Confidence            445999999999999999999999999988444 447888777777776 88899999999999987777999999433 


Q ss_pred             ------h-hHHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCC--ccc-cc-cCCeEEEEEEEee
Q 015066          174 ------Y-ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS--TAE-EL-LGKDLPLKFVEVD  241 (414)
Q Consensus       174 ------~-~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~--~~~-~~-vGq~V~vkVl~vD  241 (414)
                            . .......+++ ..|+++.|.|..+.+.|+|+.++ ++.||+|.|++++.+  ..+ .+ +|+.+..+|+.+|
T Consensus      1143 ~~t~~~~kd~~iks~eDl-k~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve 1221 (1710)
T KOG1070|consen 1143 KITPVDSKDGSIKSIEDL-KIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVE 1221 (1710)
T ss_pred             cCccccccCCcccchhhc-ccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhhhhccCCccceeeeEEEEee
Confidence                  1 1222334444 56789999999999999999998 999999999998653  222 22 7999999999999


Q ss_pred             cccceEEeehhhhhh-------hHHhhccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCC
Q 015066          242 EEQSRLVLSNRKAMA-------DSQAQLGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPG  311 (414)
Q Consensus       242 ~e~~ri~LS~K~~l~-------~~~~~l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G  311 (414)
                      +..+|+.||++..-.       ....++++|+.+.|+|..+.+||.||++.   ++.|++|++++++.+..+....+..|
T Consensus      1222 ~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~ 1301 (1710)
T KOG1070|consen 1222 EDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMVGLCHISEEADDRGENITALYYAG 1301 (1710)
T ss_pred             ccCceEEEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEEEecCcceecccccceeecchhhhhcccceecc
Confidence            999999999998632       12368999999999999999999999998   37999999999999999999999999


Q ss_pred             CEEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066          312 DTLKVMILSHDRERGRVSLSTKKLEPTPGDMI  343 (414)
Q Consensus       312 ~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~  343 (414)
                      +.|++.++.++.+++||+|.+|..--.-.++.
T Consensus      1302 ~~V~a~~lk~~~ek~rIsl~~k~s~~~~~dd~ 1333 (1710)
T KOG1070|consen 1302 DRVKACVLKEDSEKKRISLGLKSSYLSSEDDA 1333 (1710)
T ss_pred             ceeeeEeeeccchhhhhhhhhhhhccCChhhh
Confidence            99999999999999999999998754433333

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

Probab=99.78  E-value=1.2e-19  Score=151.05  Aligned_cols=80  Identities=39%  Similarity=0.730  Sum_probs=76.4

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCC
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP  339 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p  339 (414)
                      .+++|++++|+|++|++|||||+|+ |-.|||||||+++.++.++.+.+++||.|+|+|+++|. +++|+||+|.++..|
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 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSIRKLEEEP   80 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceehHHhhhCc
Confidence            4789999999999999999999998 79999999999999999999999999999999999997 999999999999877


Q ss_pred             Cc
Q 015066          340 GD  341 (414)
Q Consensus       340 ~~  341 (414)
                      -.
T Consensus        81 e~   82 (129)
T COG1098          81 EK   82 (129)
T ss_pred             cc
Confidence            64

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

Probab=99.77  E-value=4.8e-18  Score=185.56  Aligned_cols=221  Identities=20%  Similarity=0.293  Sum_probs=187.0

Q ss_pred             EEEEeCCCe-eEEEcCccccccccCCccc---cCccCCcEEEEEEEEEeCCCCeEEEEeeehhhhHHHHHhhhcccCCeE
Q 015066          115 ALVDITAKS-SAYLPTQEACIHKIKHVEE---AGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVV  190 (414)
Q Consensus       115 ~~Vdig~k~-~g~lp~sEls~~~~~~~~e---~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~~~~~~l~~~~~~g~i  190 (414)
                      ++++..... .+|+...++++.++.....   -.+.+|.++.+++..+-+.+..+.+|.++......+.++.+ .+-|+.
T Consensus       434 v~~~sK~pvis~y~~~~~~t~~~l~~v~q~~v~~~e~~te~~~rv~~v~~v~~v~~v~~~~svl~lk~~~~nD-I~iG~~  512 (1710)
T KOG1070|consen  434 VLCVSKLPVISMYADAVKLTHGMLSKVPQGMVPIYEVGTEVKSRVWQVFYVGKVVIVSVRESVLGLKFLRVND-IEIGQL  512 (1710)
T ss_pred             eeEeecCcceEEEeeccccCcchhhccccCCCCceecCCcccCccceecccCcEEEEEEehHhhccccccccc-ccccce
Confidence            667665544 7888888877766654422   12678999999999999999999999987665555555666 477899


Q ss_pred             EEEEEEEEecCcEEEEE--CCEEEEEeccccCCCC----ccccccCCeEEEEEEEeecccceEEeehhhhhhhH------
Q 015066          191 VKGKVVGANKGGVVAEV--EGLRGFVPFSQISSKS----TAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADS------  258 (414)
Q Consensus       191 v~G~V~~v~~~G~~V~i--~gi~GfIp~sels~~~----~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~~~------  258 (414)
                      |.|+|.++++.|+.|.+  +++.|++|.+|+++..    .....+|..+++||+.++.+.+++.|++|.++.+.      
T Consensus       513 V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~~~~~p~~~f~v~~~~k~RVl~~~~~~~~v~l~~K~slv~~~~plp~  592 (1710)
T KOG1070|consen  513 VPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLSDHPLQPPLRDFKVGSGVKLRVLSVNRDRNRVALTLKKSLVNTQLPLPS  592 (1710)
T ss_pred             eeeEEEEecCCcEEEEEecCceeeecChHhhhhcccccccceeeeccccEEEEEEEEccCCeeEEEechhhhcccCCCcc
Confidence            99999999999999987  3699999999999752    22234788888899999999999999999987543      


Q ss_pred             -HhhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          259 -QAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       259 -~~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                       ..+..+|+++.|+|.++.++||||+|. |++|+.|.+++++.++.++++.|.+||+|.|+|.++|.+++|+.+++|+..
T Consensus       593 d~~~~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r~s~  672 (1710)
T KOG1070|consen  593 DFEQAIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLRASS  672 (1710)
T ss_pred             chhhcCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhhhhh
Confidence             367789999999999999999999997 799999999999999999999999999999999999999999999999764

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

Probab=99.76  E-value=1.9e-16  Score=148.69  Aligned_cols=209  Identities=19%  Similarity=0.173  Sum_probs=169.7

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCe-eEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKS-SAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~-~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      +..+|++.+..|.+..++|+|++=+... .-++|.++...        ....+|+.|++.|+-  +.+++++++.+....
T Consensus         2 ~~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~--------~e~evGdev~vFiY~--D~~~rl~aTt~~p~~   71 (287)
T COG2996           2 MIKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEE--------DELEVGDEVTVFIYV--DSEDRLIATTREPKA   71 (287)
T ss_pred             cccccceEEEEEEEeeceeEEEecCCCceEEeccccCCcC--------CccccCcEEEEEEEE--CCCCceeheeecceE
Confidence            4679999999999999999999987654 66777775532        226789999999966  568899999886654


Q ss_pred             hHHHHHhhhcccCCeEEEEEEEEEe-cCcEEEEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehh
Q 015066          175 ELAWERCRQLQSEDVVVKGKVVGAN-KGGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNR  252 (414)
Q Consensus       175 ~~~~~~l~~~~~~g~iv~G~V~~v~-~~G~~V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K  252 (414)
                                 ..|+.-+++|+.++ +-|+|+++| .-+.|+|.+++....+.+..+|+.+-|. +.+|.. +|+.-.++
T Consensus        72 -----------tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~~~wpq~Gd~l~v~-l~~Dkk-~Ri~g~~a  138 (287)
T COG2996          72 -----------TVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLKSLWPQKGDKLLVY-LYVDKK-GRIWGTLA  138 (287)
T ss_pred             -----------eecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccccccCCCCCCEEEEE-EEEccC-CcEEEEec
Confidence                       45678899999998 789999999 8999999999997766666689999997 688965 58777665


Q ss_pred             hh--hhhHHhhcc---ccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCC
Q 015066          253 KA--MADSQAQLG---IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERG  326 (414)
Q Consensus       253 ~~--l~~~~~~l~---~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~  326 (414)
                      ..  +.+......   .|+.+.|+|+++..-|.||-++ +.-|+||.||.-.        ..+.|+.++++|+.+.+ ++
T Consensus       139 ~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~--------~prlG~~l~~rVi~~re-Dg  209 (287)
T COG2996         139 IEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERFA--------EPRLGERLTARVIGVRE-DG  209 (287)
T ss_pred             chhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhcc--------cccCCceEEEEEEEEcc-CC
Confidence            33  222222222   3899999999999999999998 7999999998633        45799999999999975 99


Q ss_pred             eEEEEEeeCC
Q 015066          327 RVSLSTKKLE  336 (414)
Q Consensus       327 ri~LS~K~~~  336 (414)
                      +|.||++.+-
T Consensus       210 ~lnLSl~p~~  219 (287)
T COG2996         210 KLNLSLRPRA  219 (287)
T ss_pred             eeeccccccc
Confidence            9999999764

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.69  E-value=4.8e-17  Score=158.86  Aligned_cols=87  Identities=23%  Similarity=0.452  Sum_probs=81.0

Q ss_pred             hhcc-ccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          260 AQLG-IGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       260 ~~l~-~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      +.++ +|++|.|+|++|.+||+||+|.   |++||||+|+|||.|+.++++.+++||.|.|+|+++|+++++|.||+|++
T Consensus        12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v   91 (319)
T PTZ00248         12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRV   91 (319)
T ss_pred             hhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeec
Confidence            3555 8999999999999999999994   89999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcccCCc
Q 015066          336 EPTPGDMIRNP  346 (414)
Q Consensus       336 ~~~p~~~~~~~  346 (414)
                      .++||..+...
T Consensus        92 ~~~pw~~~~e~  102 (319)
T PTZ00248         92 SPEDIEACEEK  102 (319)
T ss_pred             ccchHHHHHHh
Confidence            99999765443

>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=99.66  E-value=3.6e-16  Score=122.18  Aligned_cols=70  Identities=27%  Similarity=0.393  Sum_probs=65.7

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCc---ccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADI---ATVLQPGDTLKVMILSHDRERGRVSLS  331 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~---~~~~~~G~~V~vkVl~id~e~~ri~LS  331 (414)
                      +++|++|.|+|+++++||+||+++ +++|++|+++++|.++.++   .+.|++||.|+|+|+++|+++++|.||
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 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            578999999999999999999998 8999999999999987775   589999999999999999999999986

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

>PRK08582 hypothetical protein; Provisional

Probab=99.65  E-value=1.1e-15  Score=133.71  Aligned_cols=85  Identities=32%  Similarity=0.629  Sum_probs=78.3

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCC
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP  339 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p  339 (414)
                      .+++|++|.|+|++|++||+||+|+ +++||||+|++++.++.++.+.|++||.|+|+|+++|. +++|.||+|++.++|
T Consensus         2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk~~~~~~   80 (139)
T PRK08582          2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIKKAKDRP   80 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEEecccCc
Confidence            3789999999999999999999998 79999999999999999999999999999999999997 599999999999999


Q ss_pred             CcccCCc
Q 015066          340 GDMIRNP  346 (414)
Q Consensus       340 ~~~~~~~  346 (414)
                      |..-+.|
T Consensus        81 ~~~~~~~   87 (139)
T PRK08582         81 KRQHDRP   87 (139)
T ss_pred             hhhcccc
Confidence            9754433

>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=99.61  E-value=5e-15  Score=115.71  Aligned_cols=71  Identities=28%  Similarity=0.361  Sum_probs=66.6

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCC
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEP  337 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~  337 (414)
                      ++++|+++.|+|++|.+||+||+++  |++||+|.+++++.      +.|++||.+.|+|+++|++++++.||+|++.+
T Consensus         1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~~   73 (74)
T cd05694           1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV   73 (74)
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            4789999999999999999999997  89999999999986      68999999999999999999999999998764

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.

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

Probab=99.59  E-value=5.6e-15  Score=115.06  Aligned_cols=70  Identities=31%  Similarity=0.529  Sum_probs=65.8

Q ss_pred             ccccEEEEEEEEEEeeceEEEEECC--EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIGG--INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST  332 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~g--v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~  332 (414)
                      ++.|+++.|+|+++.+||+||++.|  .+||+|+|++++.++.++.+.|++||+|+|+|+++|.++ ++.||+
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~   72 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL   72 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence            3589999999999999999999986  699999999999999999999999999999999999876 999987

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.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.59  E-value=2.1e-15  Score=147.49  Aligned_cols=124  Identities=17%  Similarity=0.150  Sum_probs=112.2

Q ss_pred             cCC-CCCEEEEEEEEEeCCeEEEEeC--CCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066           96 NSE-LGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (414)
Q Consensus        96 ~l~-~G~iV~G~V~~v~~~G~~Vdig--~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~  172 (414)
                      .+. +|++|.|+|+++.++|+||+|.  ++.+||||.+|+++.+..++.+. +++|+++.|+|+++|++++++.||+|+.
T Consensus        13 ~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~-vkvGd~v~vkVl~VD~ekg~IdLS~K~v   91 (319)
T PTZ00248         13 KFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKL-IRVGRHEVVVVLRVDKEKGYIDLSKKRV   91 (319)
T ss_pred             hCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHh-cCCCCEEEEEEEEEeCCCCEEEEEeeec
Confidence            455 7999999999999999999995  47999999999999999999998 9999999999999999999999999998


Q ss_pred             hhhHHHHHhhhcccCCeEEEEEEEEE-ecCcEEEE-------ECCEEEEEeccccCC
Q 015066          173 QYELAWERCRQLQSEDVVVKGKVVGA-NKGGVVAE-------VEGLRGFVPFSQISS  221 (414)
Q Consensus       173 ~~~~~~~~l~~~~~~g~iv~G~V~~v-~~~G~~V~-------i~gi~GfIp~sels~  221 (414)
                      ... +|..+.+.+..|.+++|+|..+ .++|+++.       ...+++|.|..++..
T Consensus        92 ~~~-pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af~  147 (319)
T PTZ00248         92 SPE-DIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALK  147 (319)
T ss_pred             ccc-hHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHHH
Confidence            886 9999999999999999999999 55899986       247888888877653

>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=99.59  E-value=5.9e-15  Score=115.04  Aligned_cols=69  Identities=22%  Similarity=0.359  Sum_probs=65.9

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccc--ccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR--VADIATVLQPGDTLKVMILSHDRERGRVSLSTK  333 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~--~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K  333 (414)
                      |++|.|+|+++.++|+||.++ +++|+||++++++.+  ..++.+.|++||.|+|+|+++|+++++|.||+|
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 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            789999999999999999997 899999999999864  889999999999999999999999999999997

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.

>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=99.58  E-value=4.6e-15  Score=115.30  Aligned_cols=70  Identities=27%  Similarity=0.495  Sum_probs=66.0

Q ss_pred             ccccEEEEEEEEEEee-ceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066          262 LGIGSVVIGTVQSLKP-YGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK  333 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~-~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K  333 (414)
                      +++|++|.|+|+++.+ ||+||++. |.+|++|+|+++++++.++.+.|++||.|+|+|+++|  ++++.||+|
T Consensus         1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~--~~~i~LSl~   72 (72)
T cd05704           1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKK--DGKYQLSLR   72 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEec--CCEEEEEeC
Confidence            4789999999999986 89999998 8999999999999999999999999999999999998  499999986

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.

>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=99.58  E-value=6.5e-15  Score=117.51  Aligned_cols=75  Identities=33%  Similarity=0.501  Sum_probs=71.4

Q ss_pred             HHhhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066          258 SQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST  332 (414)
Q Consensus       258 ~~~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~  332 (414)
                      ...++++|++|.|+|+++.+||+||+++ |++|++|++++++.++.++.+.|++||.|+|+|+++|.+++++.|||
T Consensus         8 ~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461           8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             hHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence            4567999999999999999999999997 89999999999999999999999999999999999999999999996

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.

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

Probab=99.58  E-value=8.6e-15  Score=113.87  Aligned_cols=73  Identities=40%  Similarity=0.783  Sum_probs=70.1

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK  333 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K  333 (414)
                      ++++|+++.|+|+++.++|+||+++ |++|+||++++++.+..++...|++||+|.|+|+++|++++++.||+|
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 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            3789999999999999999999999 999999999999999999999999999999999999999999999986

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 ....

>PRK07252 hypothetical protein; Provisional

Probab=99.57  E-value=3.1e-14  Score=121.40  Aligned_cols=77  Identities=35%  Similarity=0.670  Sum_probs=73.2

Q ss_pred             cccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCC
Q 015066          263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP  339 (414)
Q Consensus       263 ~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p  339 (414)
                      ++|++|.|+|++|.++|+||+++ ++.||+|+++++++++.++.+.|++||.|+|+|+++|++++++.||+|.++++.
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~   79 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEK   79 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence            57999999999999999999997 799999999999999999999999999999999999999999999999998744

>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=99.57  E-value=1.1e-14  Score=112.14  Aligned_cols=69  Identities=32%  Similarity=0.481  Sum_probs=66.4

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK  333 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K  333 (414)
                      |++|.|+|+++.++|+||+|+ +++||+|+++++++++.++.+.|++||.++|+|+++|++++++.||+|
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 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            789999999999999999998 799999999999999999999999999999999999999999999986

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

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

Probab=99.55  E-value=3.7e-15  Score=139.47  Aligned_cols=104  Identities=23%  Similarity=0.456  Sum_probs=86.9

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT  338 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~  338 (414)
                      +.+|++|-|+|++|.+||+||.|.   |++|++|+||++..|+.++++++++||++-|+||++|+.++.|.||||.+.++
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            568999999999999999999995   79999999999999999999999999999999999999999999999999875


Q ss_pred             CCcccCCchhhhhhHHHHHHHHHHHHH
Q 015066          339 PGDMIRNPKLVFEKAEEMAQTFRQRIA  365 (414)
Q Consensus       339 p~~~~~~~~~~~~~~~~~~~~~~~~~~  365 (414)
                      --......+....+|+...+..++++.
T Consensus        89 q~~~k~~~wk~~qka~klle~aaekl~  115 (269)
T COG1093          89 QRRKKIQEWKKEQKADKLLELAAEKLG  115 (269)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            333333333344555655555555543

>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=99.55  E-value=2e-14  Score=111.36  Aligned_cols=68  Identities=29%  Similarity=0.454  Sum_probs=64.9

Q ss_pred             cEEEE-EEEEEE-eeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066          265 GSVVI-GTVQSL-KPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST  332 (414)
Q Consensus       265 G~iv~-g~V~~i-~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~  332 (414)
                      |++|. |+|+++ .+||+||++. |++||+|+|++++.+..++.+.|++||.++|+|+++|++++++.||+
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 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            78999 999999 6999999997 89999999999999999999999999999999999999999999996

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.

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

Probab=99.55  E-value=3.2e-14  Score=111.13  Aligned_cols=73  Identities=29%  Similarity=0.531  Sum_probs=69.0

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK  334 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~  334 (414)
                      ++.|++|.|+|+++.++|+||++.   |++||+|++++++.++.++.+.|++||.|+|+|+++|.+++++.||+|+
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            468999999999999999999995   5999999999999999999999999999999999999999999999984

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

>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=99.54  E-value=3.9e-14  Score=111.88  Aligned_cols=74  Identities=32%  Similarity=0.627  Sum_probs=69.3

Q ss_pred             cEEEEEEEEEEeeceEEEEEC----CEEEEEeecccCcccc-cCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCC
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG----GINGLLHVSQISHDRV-ADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP  339 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~----gv~Glvh~sels~~~~-~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p  339 (414)
                      |+++.|+|+++.+||+||+++    +.+||+|++++++.+. .++.+.|++||.|+|+|+++|  ++++.||+|++++++
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            689999999999999999998    6899999999999986 899999999999999999999  899999999998875


Q ss_pred             C
Q 015066          340 G  340 (414)
Q Consensus       340 ~  340 (414)
                      +
T Consensus        79 ~   79 (79)
T cd05684          79 G   79 (79)
T ss_pred             C
Confidence            3

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

>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=99.54  E-value=4.3e-14  Score=109.75  Aligned_cols=72  Identities=18%  Similarity=0.371  Sum_probs=68.3

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK  333 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K  333 (414)
                      +++|++|.|+|+++.++|+||+++ +++|++|++++++++..++.+.|++||.|+|+|+++|++++++.||+|
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 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            468999999999999999999998 899999999999988888889999999999999999999999999985

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.

>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=99.54  E-value=3e-14  Score=109.49  Aligned_cols=68  Identities=32%  Similarity=0.573  Sum_probs=65.3

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST  332 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~  332 (414)
                      |++|.|+|+++.++|+||+++ +++|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+
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 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            789999999999999999997 89999999999999989999999999999999999999999999985

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.

>PHA02945 interferon resistance protein; Provisional

Probab=99.53  E-value=4.1e-14  Score=111.41  Aligned_cols=74  Identities=23%  Similarity=0.329  Sum_probs=69.0

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC---CEEEEEeeccc--CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQI--SHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sel--s~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      +.+|+++.|+|+. .+||+||.|.   |.+||+|+|++  +..++.+ ++.+ .||+|.|||+.+|+.++.|.||+|++.
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            5789999999999 9999999995   79999999955  9999999 9999 999999999999999999999999986


Q ss_pred             CC
Q 015066          337 PT  338 (414)
Q Consensus       337 ~~  338 (414)
                      ++
T Consensus        86 ~~   87 (88)
T PHA02945         86 RH   87 (88)
T ss_pred             cC
Confidence            53

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.53  E-value=2.4e-14  Score=155.71  Aligned_cols=85  Identities=27%  Similarity=0.545  Sum_probs=79.0

Q ss_pred             hhccccEEEE-EEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCC
Q 015066          260 AQLGIGSVVI-GTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEP  337 (414)
Q Consensus       260 ~~l~~G~iv~-g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~  337 (414)
                      ...++|++|. |+|++|.+||+||+|. |++||||+|+|+|+++.++.+.|++||.|+|+|+++|+ ++||.||+|++.+
T Consensus       749 ~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSlK~l~~  827 (891)
T PLN00207        749 MVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSRRALLP  827 (891)
T ss_pred             cCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEEecccc
Confidence            4678999996 6999999999999998 89999999999999999999999999999999999997 7999999999999


Q ss_pred             CCCcccCC
Q 015066          338 TPGDMIRN  345 (414)
Q Consensus       338 ~p~~~~~~  345 (414)
                      +||+....
T Consensus       828 ~Pw~~~~~  835 (891)
T PLN00207        828 EANSEKSS  835 (891)
T ss_pred             Cchhhhhh
Confidence            99985533

>PRK05807 hypothetical protein; Provisional

Probab=99.52  E-value=6.2e-14  Score=122.22  Aligned_cols=75  Identities=37%  Similarity=0.651  Sum_probs=71.8

Q ss_pred             hccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      .+++|++|.|+|++|.+||+||+|++..||||++++++.++.++.+.|++||.|+|+|+++|. +++|.||+|.+.
T Consensus         2 ~~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSlk~~~   76 (136)
T PRK05807          2 TLKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQAM   76 (136)
T ss_pred             CccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence            367899999999999999999999989999999999999999999999999999999999997 799999999987

>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=99.51  E-value=5.4e-14  Score=107.77  Aligned_cols=67  Identities=30%  Similarity=0.566  Sum_probs=64.5

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLS  331 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS  331 (414)
                      |++|.|+|+++.++|+||+|. +++|++|++++++++..++.+.|++||.|+|+|+++|+++++|.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            789999999999999999998 7999999999999999999999999999999999999999999886

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=99.50  E-value=6.8e-14  Score=107.23  Aligned_cols=67  Identities=37%  Similarity=0.743  Sum_probs=63.0

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCc-ccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH-DRVADIATVLQPGDTLKVMILSHDRERGRVSLS  331 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~-~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS  331 (414)
                      |++|.|+|+++++||+||+|+ +++||+|+++++| .+..++.+.|++||.|+|+|+++|.++++|.||
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeCC
Confidence            789999999999999999998 8999999999996 577888999999999999999999999999885

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.

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

Probab=99.50  E-value=1.3e-13  Score=106.60  Aligned_cols=72  Identities=36%  Similarity=0.634  Sum_probs=68.6

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      |++|.|+|+++.++|+||+++ +++|++|++++++.++.++.+.|++||.++|+|+++|++++++.||+|.++
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 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE   73 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEcC
Confidence            789999999999999999997 899999999999999999999999999999999999999999999999764

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

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

Probab=99.49  E-value=1.6e-13  Score=107.19  Aligned_cols=73  Identities=40%  Similarity=0.681  Sum_probs=69.1

Q ss_pred             cccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          263 GIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       263 ~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      ++|++|.|+|+++.++|+||++.  +++|++|++++++++..++.+.|++||.|+|+|+++|++++++.||+|..
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            46999999999999999999997  59999999999999988999999999999999999999999999999974

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.49  E-value=2.9e-14  Score=155.11  Aligned_cols=161  Identities=19%  Similarity=0.223  Sum_probs=133.0

Q ss_pred             CccCCCCCCccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCC-CC---CCHHHH
Q 015066           11 LRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEG-VS---FTLEEF   86 (414)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~-~~---~~~~~f   86 (414)
                      -+|.|-|...||+|||       .|+.++..|.++..+|++++    ..+++|++|.-.++.+..+++ +.   .+.+..
T Consensus       669 ~~~i~~pr~~~s~~aP-------~i~~~~i~~~ki~~vIG~GG----ktIk~I~eetg~~~Idi~ddg~V~I~a~d~~~i  737 (891)
T PLN00207        669 SKCSPPPSKRLSKYAP-------LIHIMKVKPEKVNMIIGSGG----KKVKSIIEETGVEAIDTQDDGTVKITAKDLSSL  737 (891)
T ss_pred             HHHHhhhhhhhcccCC-------eeEEEEcCHHHHHHHhcCCc----hhHHHHHHHHCCCccCcCCCeeEEEEeCCHHHH
Confidence            3688899999999999       89999999999999999999    889999999988844433333 22   233333


Q ss_pred             HH---HHHhhcccCCCCCEEE-EEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC
Q 015066           87 HS---ALEKYDFNSELGTKVK-GTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD  162 (414)
Q Consensus        87 ~~---~l~~~~~~l~~G~iV~-G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~  162 (414)
                      +.   +++.+....++|+++. |+|+++.++|+||++..+.+|++|.+++++.+..++++. +++||.|+|+|+++|+ +
T Consensus       738 ~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv-~kvGD~V~VkVi~ID~-~  815 (891)
T PLN00207        738 EKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDA-FKVGDRIDVKLIEVND-K  815 (891)
T ss_pred             HHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHh-cCCCCEEEEEEEEECC-C
Confidence            33   3455555789999996 699999999999999888999999999999888888887 9999999999999996 7


Q ss_pred             CeEEEEeeehhhhHHHHHhhhcc
Q 015066          163 DSLVLSLRMIQYELAWERCRQLQ  185 (414)
Q Consensus       163 ~~i~LS~k~~~~~~~~~~l~~~~  185 (414)
                      +++.||+|.... .+|+......
T Consensus       816 grI~LSlK~l~~-~Pw~~~~~~~  837 (891)
T PLN00207        816 GQLRLSRRALLP-EANSEKSSQK  837 (891)
T ss_pred             CcEEEEEecccc-Cchhhhhhhh
Confidence            899999998755 5898876543

>PRK08059 general stress protein 13; Validated

Probab=99.47  E-value=2.5e-13  Score=116.52  Aligned_cols=80  Identities=45%  Similarity=0.787  Sum_probs=76.2

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT  338 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~  338 (414)
                      .++++|++|.|+|+++.++|+||+++ +++|++|++++++.++.++.+.|++||.|+|+|+++|.+++++.||+|.+..+
T Consensus         3 ~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~~   82 (123)
T PRK08059          3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEA   82 (123)
T ss_pred             ccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEcccC
Confidence            45889999999999999999999998 79999999999999998999999999999999999999999999999999888


Q ss_pred             C
Q 015066          339 P  339 (414)
Q Consensus       339 p  339 (414)
                      |
T Consensus        83 ~   83 (123)
T PRK08059         83 P   83 (123)
T ss_pred             c
Confidence            7

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

Probab=99.45  E-value=3.7e-13  Score=104.18  Aligned_cols=70  Identities=36%  Similarity=0.682  Sum_probs=63.9

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcc-cccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHD-RVADIATVLQPGDTLKVMILSHDRERGRVSLS  331 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~-~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS  331 (414)
                      +++|+++.|+|+++++||+||+|. +++||+|+++++|. +..++.+.|++||.|+|+|+++|.+++++.|+
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeCC
Confidence            468999999999999999999997 89999999999875 55577788999999999999999999999875

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.

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

Probab=99.44  E-value=5.6e-13  Score=102.60  Aligned_cols=69  Identities=32%  Similarity=0.552  Sum_probs=66.3

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK  333 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K  333 (414)
                      |++|.|+|.++.++|+||+++ +.+|++|.+++++.+..++.+.|++||.++|+|+++|++++++.||+|
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            789999999999999999998 799999999999999999999999999999999999988899999986

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.

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

Probab=99.43  E-value=5e-13  Score=128.60  Aligned_cols=102  Identities=23%  Similarity=0.421  Sum_probs=82.7

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT  338 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~  338 (414)
                      +++|++|.|+|++|.++|+||+|.   |++|++|+|+++++++.++.+.|++||.|.|+|+++|+++++|.||+|.+.++
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            678999999999999999999996   79999999999999999999999999999999999999999999999999764


Q ss_pred             CCcccCCchhhhhhHHHHHHHHHHH
Q 015066          339 PGDMIRNPKLVFEKAEEMAQTFRQR  363 (414)
Q Consensus       339 p~~~~~~~~~~~~~~~~~~~~~~~~  363 (414)
                      .-......+....+++...+..+++
T Consensus        86 e~~~~~~~~~~~~~~~~il~~~a~~  110 (262)
T PRK03987         86 QRREKIQEWKNEQKADKWLELAAEK  110 (262)
T ss_pred             hHHHHHHHHHHHhhHhhHHHHHHHH
Confidence            3221112222333445555444444

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

Probab=99.41  E-value=9.3e-13  Score=100.17  Aligned_cols=68  Identities=62%  Similarity=1.024  Sum_probs=65.1

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK  333 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K  333 (414)
                      |+++.|+|+++.++|+||+++ +.+|++|.++++++++.++.+.|++||.|+|+|+++|+ ++++.||+|
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEEC
Confidence            789999999999999999998 89999999999999999999999999999999999998 899999986

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

>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=99.40  E-value=1.1e-12  Score=100.25  Aligned_cols=65  Identities=20%  Similarity=0.339  Sum_probs=59.8

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLS  331 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS  331 (414)
                      |++++|+|+++.++|+||+|. +++|++|.++++..+..  .+.|++||+|+|+|+.+|+++++|.||
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--KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            789999999999999999996 79999999999866544  778999999999999999999999886

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

>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=99.40  E-value=4.5e-13  Score=110.77  Aligned_cols=73  Identities=23%  Similarity=0.501  Sum_probs=66.8

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccc-------------------ccCcccccCCCCEEEEEEEEE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR-------------------VADIATVLQPGDTLKVMILSH  321 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~-------------------~~~~~~~~~~G~~V~vkVl~i  321 (414)
                      |++|++|.|+|+++.++|+||.|. |+.|++|++++++.+                   ..++.+.|++||.|+|+|+++
T Consensus         1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~   80 (100)
T cd05693           1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL   80 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence            578999999999999999999998 899999999999864                   335788999999999999999


Q ss_pred             eCC---CCeEEEEEee
Q 015066          322 DRE---RGRVSLSTKK  334 (414)
Q Consensus       322 d~e---~~ri~LS~K~  334 (414)
                      |++   +++|.||+|.
T Consensus        81 d~~~~~~~~i~LSlr~   96 (100)
T cd05693          81 DKSKSGKKRIELSLEP   96 (100)
T ss_pred             cCCcCCCcEEEEEecH
Confidence            997   7899999985

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

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

Probab=99.39  E-value=2e-12  Score=98.77  Aligned_cols=67  Identities=34%  Similarity=0.522  Sum_probs=62.3

Q ss_pred             cEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066          265 GSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK  333 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K  333 (414)
                      |++|.|+|+++.++|+||+++|++||+|.+++++.+..++.+  .+||.++|+|+++|+++++|.||.|
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            789999999999999999999999999999999988777766  4899999999999999999999976

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.

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

Probab=99.39  E-value=3.3e-12  Score=99.25  Aligned_cols=73  Identities=22%  Similarity=0.338  Sum_probs=68.3

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      ++.|++++|+|.+++++|+||+++++.+||||.+++++.....+.+. +.+|+.++|+|+++|.+++++.||+|
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 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEV-YKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGT-CETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccc-cCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            57999999999999999999999988999999999998877777776 99999999999999999999999986

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 ....

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

Probab=99.38  E-value=1.8e-12  Score=98.52  Aligned_cols=68  Identities=47%  Similarity=0.827  Sum_probs=64.9

Q ss_pred             ccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLS  331 (414)
Q Consensus       264 ~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS  331 (414)
                      +|+++.|+|+++.++|+||++++++|++|.+++++.++.++.+.|++||.|+|+|+++|++++++.||
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 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence            48999999999999999999999999999999999888889999999999999999999999999886

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

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

Probab=99.38  E-value=1.4e-12  Score=99.00  Aligned_cols=67  Identities=42%  Similarity=0.746  Sum_probs=63.8

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLS  331 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS  331 (414)
                      |++|.|+|++++++|+||+++ +.+|++|.+++++.++.++.+.|++||.++|+|+++|++++++.||
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            689999999999999999998 7999999999999988899999999999999999999999999886

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.

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

Probab=99.37  E-value=7.2e-13  Score=110.68  Aligned_cols=77  Identities=18%  Similarity=0.349  Sum_probs=73.4

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      .+++|++++|+|+.++++||||.+.++..|++|+||+.+.+++++.+. +.+|++|.|+|+++|+ +|++.||+|.++.
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~-L~vG~eV~vKVl~ide-~GKisLSIr~~~e   78 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDH-LKVGQEVKVKVLDIDE-NGKISLSIRKLEE   78 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHH-hcCCCEEEEEEEeecc-CCCcceehHHhhh
Confidence            578999999999999999999999999999999999999999999998 9999999999999996 9999999998765

>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=99.36  E-value=3e-12  Score=100.01  Aligned_cols=71  Identities=13%  Similarity=0.134  Sum_probs=64.6

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCcc---ccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE---EAGIVPGLKEEFVIIGENEADDSLVLS  168 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~---e~~~~vG~~v~v~Vl~id~~~~~i~LS  168 (414)
                      +++|++|.|+|.++.++|+||+++.+.+|++|.+++++.+..+++   +. |++|+.++|+|+++|++++++.||
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            478999999999999999999999899999999999998866653   45 899999999999999999998886

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.

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

Probab=99.33  E-value=5.8e-12  Score=95.85  Aligned_cols=67  Identities=43%  Similarity=0.793  Sum_probs=63.6

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST  332 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~  332 (414)
                      |+++.|+|+++.++|+||+++ +.+|++|++++++.++.++.+.|++||.|+|+|+++|+ ++++.||+
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEeeC
Confidence            689999999999999999998 79999999999999988899999999999999999998 89999985

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.

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

Probab=99.32  E-value=5e-12  Score=101.36  Aligned_cols=73  Identities=29%  Similarity=0.418  Sum_probs=66.6

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCc----ccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH----DRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~----~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      +++|++|.|+|+++.++|+||+++ +++|++|++++++    .+..++.+.|++||.++|+|+++|++ +++.||+|..
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 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTRSL   81 (86)
T ss_pred             CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeCcc
Confidence            578999999999999999999998 8999999999986    45567788899999999999999876 9999999875

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

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

Probab=99.31  E-value=7.7e-12  Score=100.99  Aligned_cols=74  Identities=31%  Similarity=0.525  Sum_probs=66.5

Q ss_pred             hccccEEEEEEEEEEeec--eEEEEEC-CEEEEEeecccCc---ccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066          261 QLGIGSVVIGTVQSLKPY--GAFIDIG-GINGLLHVSQISH---DRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK  334 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~--G~fV~l~-gv~Glvh~sels~---~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~  334 (414)
                      .+++|++|.|+|++|.+|  |+||+++ |.+||+|+|+++|   .++.++.+.+++||.|.|+|+......+--.||.+-
T Consensus         4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~~   83 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTNI   83 (88)
T ss_pred             cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEEE
Confidence            567999999999999997  9999998 8999999999999   678899999999999999999988777766777653

RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.30  E-value=8.9e-12  Score=133.27  Aligned_cols=92  Identities=29%  Similarity=0.547  Sum_probs=75.4

Q ss_pred             EEeecccceEEeehhhh--hhh-------HHh--hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccC----cccc
Q 015066          238 VEVDEEQSRLVLSNRKA--MAD-------SQA--QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQIS----HDRV  301 (414)
Q Consensus       238 l~vD~e~~ri~LS~K~~--l~~-------~~~--~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels----~~~~  301 (414)
                      ++++. ++.+.++-...  ...       ...  .+++|++|.|+|++|++||+||+|. |++||||+|+|+    +.++
T Consensus       611 Idi~d-~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv  689 (719)
T TIGR02696       611 ISIED-DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRV  689 (719)
T ss_pred             EEEec-CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCc
Confidence            45664 57776655332  111       112  4789999999999999999999997 899999999996    4689


Q ss_pred             cCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066          302 ADIATVLQPGDTLKVMILSHDRERGRVSLS  331 (414)
Q Consensus       302 ~~~~~~~~~G~~V~vkVl~id~e~~ri~LS  331 (414)
                      .++.++|++||.|+|||+++|. ++||+|+
T Consensus       690 ~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~  718 (719)
T TIGR02696       690 ENVEDVLSVGQKIQVEIADIDD-RGKLSLV  718 (719)
T ss_pred             CCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence            9999999999999999999995 7899986

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.

>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=99.28  E-value=1.4e-11  Score=98.22  Aligned_cols=73  Identities=16%  Similarity=0.166  Sum_probs=68.4

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      ++++|+++.|+|.++.++|+||+++++.+||+|.+++++.+..++.+. |.+||.++|+|+++|.+++++.||+
T Consensus        11 ~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~-~~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461          11 DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFG-FKKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             hCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHh-cCCCCEEEEEEEEEcCCCCEEEEeC
Confidence            689999999999999999999999988999999999998888777776 9999999999999999999999985

Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.27  E-value=2.1e-11  Score=94.93  Aligned_cols=70  Identities=20%  Similarity=0.254  Sum_probs=64.2

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccc--cCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK--IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~--~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      |++|+|+|.++.++|+||.++.+.+|+||.+++++..  ..++.+. |++|+.++|+|+++|++++++.||++
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 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKK-FPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHh-CCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            8999999999999999999998899999999998753  5666666 99999999999999999999999986

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.

>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=99.27  E-value=3.6e-11  Score=93.90  Aligned_cols=71  Identities=18%  Similarity=0.250  Sum_probs=63.8

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC-CCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig-~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~  173 (414)
                      +++.|++|.|+|.+++++|+||+++ ++.+||+|.+|+++.      +. +++|+.+.|+|+++|++++++.||+++..
T Consensus         1 dl~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------~~-~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~   72 (74)
T cd05694           1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------SK-LKVGQLLLCVVEKVKDDGRVVSLSADPSK   72 (74)
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------cc-cCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence            4789999999999999999999997 579999999999854      22 78999999999999999999999998754

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.

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

Probab=99.27  E-value=2.5e-11  Score=92.37  Aligned_cols=71  Identities=49%  Similarity=0.869  Sum_probs=66.8

Q ss_pred             cccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066          263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK  333 (414)
Q Consensus       263 ~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K  333 (414)
                      ++|+++.|+|.++.++|+||+++ ++.|++|.+++.+.+..++.+.|++||.++|+|++++++++++.||++
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            36999999999999999999999 899999999999988778888999999999999999998899999985

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

Probab=99.27  E-value=2.8e-11  Score=95.92  Aligned_cols=69  Identities=25%  Similarity=0.564  Sum_probs=61.8

Q ss_pred             ccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCccccc-----------CcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066          264 IGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVMILSHDRERGRVSL  330 (414)
Q Consensus       264 ~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~~-----------~~~~~~~~G~~V~vkVl~id~e~~ri~L  330 (414)
                      +|+++.|+|++++++|+||+++  |++|++|.++++++++.           +....|++||.|+|+|+++|.+++++.|
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            3889999999999999999998  69999999999876432           4557899999999999999999999999


Q ss_pred             EE
Q 015066          331 ST  332 (414)
Q Consensus       331 S~  332 (414)
                      ++
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.

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

Probab=99.27  E-value=2.4e-11  Score=92.82  Aligned_cols=65  Identities=40%  Similarity=0.776  Sum_probs=58.8

Q ss_pred             CeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC--ccccccCCeEEEEEEEeecccceEEeehh
Q 015066          188 DVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEELLGKDLPLKFVEVDEEQSRLVLSNR  252 (414)
Q Consensus       188 g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~--~~~~~vGq~V~vkVl~vD~e~~ri~LS~K  252 (414)
                      |++++|+|+++.++|++|+++|++||||.+|+++..  ++...+|+.++|+|+++|.+++++.||+|
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 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            578999999999999999999999999999999653  44556999999999999999999999975

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.

>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=99.26  E-value=2.6e-11  Score=93.20  Aligned_cols=70  Identities=24%  Similarity=0.356  Sum_probs=64.8

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      |++++|+|.++.++|+||+++++.+||+|.++++..+..++.+. +++|+.++|+|+++|++.+++.||+|
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 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEH-FRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHc-ccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            88999999999999999999988999999999998777777766 89999999999999999999999985

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=99.24  E-value=2.8e-11  Score=131.47  Aligned_cols=75  Identities=39%  Similarity=0.719  Sum_probs=71.8

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      .++++|++|.|+|++|.+||+||++. |.+||+|+|+++++++.++.+.|++||.|+|+|+++|.+ +++.||+|.+
T Consensus       617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k~~  692 (693)
T PRK11824        617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV  692 (693)
T ss_pred             ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence            46889999999999999999999998 899999999999999999999999999999999999986 9999999986

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

Probab=99.23  E-value=5.3e-11  Score=91.53  Aligned_cols=70  Identities=33%  Similarity=0.444  Sum_probs=65.3

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      |++|+|+|.++.++|++|+++.+.+|++|.+|++..+..++.+. +++|+.++|+|+++++.++++.||++
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~-~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDE-VKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHc-CCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            89999999999999999999988999999999998887777777 89999999999999988899999985

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.23  E-value=2e-11  Score=130.61  Aligned_cols=137  Identities=18%  Similarity=0.160  Sum_probs=111.9

Q ss_pred             CccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCCCC---CHHHHHHH---HHh
Q 015066           19 TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSF---TLEEFHSA---LEK   92 (414)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~~~---~~~~f~~~---l~~   92 (414)
                      ..+|+|||       -|..++..|.+..-.|++++    ..+++|+++.-..++-.++..+..   +.+..+.+   ++.
T Consensus       570 ~~~s~~aP-------~~~~~~I~~~ki~~vIG~gG----k~I~~i~~~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~  638 (719)
T TIGR02696       570 DEMSPYAP-------RIITVKIPVDKIGEVIGPKG----KMINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMINA  638 (719)
T ss_pred             cccccCCC-------eeEEEEeChHHhhheeCCCc----HhHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHH
Confidence            57999999       77889999999999999999    788999999877777655555532   33333333   333


Q ss_pred             hcc--cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccc----ccccCCccccCccCCcEEEEEEEEEeCCCCeEE
Q 015066           93 YDF--NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEAC----IHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV  166 (414)
Q Consensus        93 ~~~--~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls----~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~  166 (414)
                      +..  .+++|++++|+|+++.++|+||++..+.+||+|.+|++    +.+..++.+. +++||+|+|+|+++|+ ++++.
T Consensus       639 i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv-~kvGd~V~VKVl~ID~-~gKI~  716 (719)
T TIGR02696       639 IANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDV-LSVGQKIQVEIADIDD-RGKLS  716 (719)
T ss_pred             hhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHc-CCCCCEEEEEEEEECC-CCCee
Confidence            333  47899999999999999999999988899999999996    3567788887 9999999999999994 78888


Q ss_pred             EE
Q 015066          167 LS  168 (414)
Q Consensus       167 LS  168 (414)
                      |+
T Consensus       717 L~  718 (719)
T TIGR02696       717 LV  718 (719)
T ss_pred             ec
Confidence            75

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=99.23  E-value=3e-11  Score=131.18  Aligned_cols=147  Identities=16%  Similarity=0.179  Sum_probs=118.6

Q ss_pred             ccCCCCCCccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCC-C---CCHHHHH
Q 015066           12 RCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGV-S---FTLEEFH   87 (414)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~-~---~~~~~f~   87 (414)
                      +|-+-|-..+|+++|       -+..++..|.++.-.|+.++    ..+++|+++.-..+ +.++++. .   ...+..+
T Consensus       539 ~aI~~~r~~~~~~ap-------~~~~~~I~~~kI~~vIG~gg----~~ik~I~~~~~~~i-di~d~G~v~i~~~~~~~~~  606 (693)
T PRK11824        539 EAISEPRAELSPYAP-------RIETIKIPPDKIRDVIGPGG----KTIREITEETGAKI-DIEDDGTVKIAATDGEAAE  606 (693)
T ss_pred             HHhcCChhhhcccCc-------hheeecCCHHHHHHHhcCCc----hhHHHHHHHHCCcc-ccCCCceEEEEcccHHHHH
Confidence            345555666999998       67778889999999999999    88999999986644 4343333 1   2222222


Q ss_pred             ---HHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCe
Q 015066           88 ---SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS  164 (414)
Q Consensus        88 ---~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~  164 (414)
                         +.++.+...+++|+++.|+|+++.++|+||++..+.+|++|.+++++.+..++.+. +++||.++++|+++|+. ++
T Consensus       607 ~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v-~kvGD~V~VkV~~iD~~-gr  684 (693)
T PRK11824        607 AAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDV-LKEGDEVKVKVLEIDKR-GR  684 (693)
T ss_pred             HHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccce-eCCCCEEEEEEEEECCC-Cc
Confidence               33444446789999999999999999999999988999999999999888888877 89999999999999976 99


Q ss_pred             EEEEeeeh
Q 015066          165 LVLSLRMI  172 (414)
Q Consensus       165 i~LS~k~~  172 (414)
                      +.||+|..
T Consensus       685 I~LS~k~~  692 (693)
T PRK11824        685 IRLSRKAV  692 (693)
T ss_pred             EEEEEEec
Confidence            99999864

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=99.22  E-value=1.7e-11  Score=130.39  Aligned_cols=80  Identities=38%  Similarity=0.596  Sum_probs=76.4

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT  338 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~  338 (414)
                      .+|++|+++.|+|+++.+||+||+|+ ..+||||+|++++.++.+|.+++++||.|+|+|+++|..++||.|||+..+..
T Consensus       654 ~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~~  733 (780)
T COG2183         654 TDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDEEE  733 (780)
T ss_pred             hhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccCCc
Confidence            58999999999999999999999999 89999999999999999999999999999999999999999999999987654


Q ss_pred             C
Q 015066          339 P  339 (414)
Q Consensus       339 p  339 (414)
                      +
T Consensus       734 ~  734 (780)
T COG2183         734 G  734 (780)
T ss_pred             c
Confidence            3

>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=99.21  E-value=7.2e-11  Score=90.61  Aligned_cols=69  Identities=28%  Similarity=0.430  Sum_probs=63.6

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      |++++|+|+++.++|+||+++.+.+||+|.+++++.+..++.+. +++|+.++|+|+++|.+++++.||+
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            78999999999999999999888999999999998777666665 8999999999999999999999985

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=99.21  E-value=1.3e-10  Score=90.03  Aligned_cols=73  Identities=16%  Similarity=0.142  Sum_probs=66.4

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      +++|+++.|+|.++.++|+||+++.+.+|++|.+++++.+..++.+. |++||.++++|+++|..++++.||++
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 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYK-FKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccc-cCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence            46899999999999999999999989999999999998776666565 89999999999999998999999975

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

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

Probab=99.19  E-value=5.4e-11  Score=124.80  Aligned_cols=97  Identities=29%  Similarity=0.608  Sum_probs=83.5

Q ss_pred             EEeecccceEEeehhhhh---------hhHHhhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccc
Q 015066          238 VEVDEEQSRLVLSNRKAM---------ADSQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATV  307 (414)
Q Consensus       238 l~vD~e~~ri~LS~K~~l---------~~~~~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~  307 (414)
                      +.++ +++.+.++.....         .....++++|++|.|+|+++.+||+||.|. |-+||||+|++++.|+.+..++
T Consensus       585 Idie-ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dv  663 (692)
T COG1185         585 IDIE-DDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDV  663 (692)
T ss_pred             EEec-CCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccce
Confidence            3566 6777776655421         122368999999999999999999999997 8999999999999999999999


Q ss_pred             cCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          308 LQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       308 ~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      +++||.|+|||+.+|+ ++|+.||+|.+.
T Consensus       664 lk~Gd~v~Vkv~~iD~-~Gri~ls~~~~~  691 (692)
T COG1185         664 LKEGDEVKVKVIEIDK-QGRIRLSIKAVL  691 (692)
T ss_pred             eecCceEEEEEeeecc-cCCccceehhcc
Confidence            9999999999999995 799999999764

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

Probab=99.18  E-value=9.6e-11  Score=93.13  Aligned_cols=72  Identities=26%  Similarity=0.302  Sum_probs=67.9

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK  334 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~  334 (414)
                      +++|++|.|+|+++.+.|++|+++ +.+|++|.++++..+..++.+.|++||.+.|+|+++|.+ +++.||++.
T Consensus         4 p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~   76 (82)
T cd04454           4 PDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD   76 (82)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence            578999999999999999999998 799999999999888888899999999999999999986 899999986

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".

>PRK07252 hypothetical protein; Provisional

Probab=99.17  E-value=1.4e-10  Score=98.97  Aligned_cols=82  Identities=21%  Similarity=0.254  Sum_probs=74.5

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhhH
Q 015066           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYEL  176 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~~  176 (414)
                      +++|+++.|+|+++.++|+||+++++..|++|.+++++.+..++.+. +.+||.++|+|+++|.+.+++.||++....+.
T Consensus         1 ~kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~-~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~   79 (120)
T PRK07252          1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQL-LKVGEEVLVQVVDFDEYTGKASLSLRTLEEEK   79 (120)
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhc-cCCCCEEEEEEEEEeCCCCEEEEEEeecccCc
Confidence            36899999999999999999999888999999999998877777666 89999999999999999999999999988876


Q ss_pred             HHH
Q 015066          177 AWE  179 (414)
Q Consensus       177 ~~~  179 (414)
                      .|.
T Consensus        80 ~~~   82 (120)
T PRK07252         80 QHF   82 (120)
T ss_pred             ccc
Confidence            664

>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=99.17  E-value=1.4e-10  Score=90.00  Aligned_cols=71  Identities=20%  Similarity=0.179  Sum_probs=65.0

Q ss_pred             CCCCCEEEEEEEEEeC-CeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           97 SELGTKVKGTVFCTDN-RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~-~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      +++|+++.|+|.++.+ .|+||+++.+.+|++|.+++++.+..++.+. +++||.++|+|++++.  +++.||+|
T Consensus         1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~-~~~Gd~v~~kV~~~~~--~~i~LSl~   72 (72)
T cd05704           1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEG-FKPGKIVRCCILSKKD--GKYQLSLR   72 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHh-CCCCCEEEEEEEEecC--CEEEEEeC
Confidence            4689999999999986 8999999999999999999999988888776 8999999999999974  89999985

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

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

Probab=99.16  E-value=1.1e-10  Score=90.08  Aligned_cols=62  Identities=19%  Similarity=0.386  Sum_probs=57.5

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccc--ccCcccccCCCCEEEEEEEEEeCCCC
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR--VADIATVLQPGDTLKVMILSHDRERG  326 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~--~~~~~~~~~~G~~V~vkVl~id~e~~  326 (414)
                      |++|.|+|+++.++|+||+++ |++|++|++++++.+  ..++.+.|++||.|+|+|+++|.++.
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~   65 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT   65 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence            789999999999999999998 899999999999874  78899999999999999999997654

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=99.15  E-value=2.5e-10  Score=89.80  Aligned_cols=64  Identities=28%  Similarity=0.553  Sum_probs=58.9

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST  332 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~  332 (414)
                      .++++|+.+.|+|+++++||+||++. +.+||+|.+++.        +.+++||+++|+|.++ .+++++.||+
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 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDI-PENGNIDLIP   76 (77)
T ss_pred             hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEEEEE-CCCCcEEEEE
Confidence            46889999999999999999999998 799999999963        4699999999999999 8899999986

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=99.15  E-value=9e-11  Score=124.99  Aligned_cols=112  Identities=21%  Similarity=0.240  Sum_probs=102.2

Q ss_pred             HHHHHHHHHHHhhcccCCCCCCCCCHHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc
Q 015066           58 EELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI  137 (414)
Q Consensus        58 ~~l~~iiee~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~  137 (414)
                      ..+++|+.|+.++.++++.+   |...-|.+.+.+.. ++++|+++.|+|.++.++|+|||||-+.+|++|.+++++.++
T Consensus       621 ~Tl~dIi~eL~kp~rdpR~~---f~~~~~~~~v~~i~-dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv  696 (780)
T COG2183         621 PTLEDIILELEKPGRDPRDE---FHTPTLDEGVESIT-DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFV  696 (780)
T ss_pred             chHHHHHHHhhcCCCCCccc---ccccchhhhhhhHh-hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhc
Confidence            56899999999999999886   66666666666665 899999999999999999999999999999999999999999


Q ss_pred             CCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066          138 KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus       138 ~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      ++|.++ +++|+.|+++|+++|...+++.||++....
T Consensus       697 ~~P~~v-v~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~  732 (780)
T COG2183         697 KDPNEV-VKVGDIVKVKVIEVDTARKRIALSMRLDEE  732 (780)
T ss_pred             CChHHh-cccCCEEEEEEEEEecccCeeeeEeeccCC
Confidence            999888 999999999999999999999999997655

>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=99.15  E-value=1.9e-10  Score=89.00  Aligned_cols=69  Identities=22%  Similarity=0.233  Sum_probs=62.7

Q ss_pred             CCEEE-EEEEEE-eCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066          100 GTKVK-GTVFCT-DNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus       100 G~iV~-G~V~~v-~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      |++++ |+|+++ .++|+||++..+.+||+|.+++++....++.+. +++|+.++++|+++|+.++++.||+
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 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGP-FKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccc-cCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            78899 999999 699999999888999999999988777776665 9999999999999999999999985

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=99.15  E-value=1.6e-10  Score=88.35  Aligned_cols=68  Identities=18%  Similarity=0.191  Sum_probs=63.3

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS  168 (414)
                      |+++.|+|+++.++|+||+++++.+||+|.+++++.+..++.+. +++||.++++|+++|++++++.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKR-FKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhc-cCCCCEEEEEEEEEeCCCCEEecC
Confidence            78999999999999999999988999999999998877777776 899999999999999999999876

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

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

Probab=99.14  E-value=2.9e-10  Score=87.76  Aligned_cols=72  Identities=22%  Similarity=0.318  Sum_probs=66.6

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~  172 (414)
                      |+++.|+|+++.++|+||+++.+.+|++|.++++..+..++.+. |.+|+.++|+|+++|..++++.||++..
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~-~~~Gd~v~~~v~~~d~~~~~i~ls~k~~   72 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATER-FKVGDEVEAKITNVDRKNRKISLSIKAK   72 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHc-cCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence            78999999999999999999888999999999998877777776 8999999999999999889999999864

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.

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=99.14  E-value=1.5e-10  Score=106.68  Aligned_cols=93  Identities=24%  Similarity=0.348  Sum_probs=78.6

Q ss_pred             EEEeecccceEEeehhhhhhhHHhhccccEEEEEEEEEEeeceEEEEEC-----------CEEEEEeecccCcccccCcc
Q 015066          237 FVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIG-----------GINGLLHVSQISHDRVADIA  305 (414)
Q Consensus       237 Vl~vD~e~~ri~LS~K~~l~~~~~~l~~G~iv~g~V~~i~~~G~fV~l~-----------gv~Glvh~sels~~~~~~~~  305 (414)
                      ++++|.+++++.+.-   +......+++|++|.|+|+++.++|+||+|.           ++.|++|.+++++.+..++.
T Consensus        40 ~~~id~~~~~Isv~P---~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~  116 (189)
T PRK09521         40 KVFIDDINRKISVIP---FKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLT  116 (189)
T ss_pred             EEEEcCCCCEEEEec---CcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHH
Confidence            345677777887742   2222356789999999999999999999984           57899999999998888899


Q ss_pred             cccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          306 TVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       306 ~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      +.|++||.|+|+|++++   +++.||+|..
T Consensus       117 ~~~~~GD~V~akV~~i~---~~i~LS~k~~  143 (189)
T PRK09521        117 DAFKIGDIVRAKVISYT---DPLQLSTKGK  143 (189)
T ss_pred             hccCCCCEEEEEEEecC---CcEEEEEecC
Confidence            99999999999999998   7899999963

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

Probab=99.14  E-value=1.8e-10  Score=94.94  Aligned_cols=79  Identities=30%  Similarity=0.514  Sum_probs=69.2

Q ss_pred             EEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccC-----------cccccCCCCEEEEEEEEEeCCC-----CeEE
Q 015066          266 SVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVAD-----------IATVLQPGDTLKVMILSHDRER-----GRVS  329 (414)
Q Consensus       266 ~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~-----------~~~~~~~G~~V~vkVl~id~e~-----~ri~  329 (414)
                      ++|.|+|+++.++|+||++.+++|++|+++++++++..           ....|++||.|+|+|.++|.+.     +++.
T Consensus         1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~   80 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIG   80 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEE
Confidence            47899999999999999999999999999999876543           3578999999999999999864     5899


Q ss_pred             EEEeeCCCCCCcccC
Q 015066          330 LSTKKLEPTPGDMIR  344 (414)
Q Consensus       330 LS~K~~~~~p~~~~~  344 (414)
                      ||+|+-...||+.+.
T Consensus        81 ls~k~~~~g~~~~~~   95 (99)
T cd04460          81 LTMRQPGLGKLEWIE   95 (99)
T ss_pred             EEEecCCCCcHHHhh
Confidence            999999888887653

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.

>PRK08582 hypothetical protein; Provisional

Probab=99.10  E-value=5.7e-10  Score=97.65  Aligned_cols=82  Identities=20%  Similarity=0.321  Sum_probs=72.9

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE  175 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~  175 (414)
                      .+++|++|.|+|+.+.++|+||+|+.+.+|++|.+++++.+..++.+. +.+|+.++|+|++++. ++++.||++++.. 
T Consensus         2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~-l~vGD~VkvkV~~id~-~gkI~LSlk~~~~-   78 (139)
T PRK08582          2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDH-LKVGDEVEVKVLNVED-DGKIGLSIKKAKD-   78 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccc-cCCCCEEEEEEEEECC-CCcEEEEEEeccc-
Confidence            468999999999999999999999999999999999998888777766 8999999999999986 5899999999865 


Q ss_pred             HHHHH
Q 015066          176 LAWER  180 (414)
Q Consensus       176 ~~~~~  180 (414)
                      .+|..
T Consensus        79 ~~~~~   83 (139)
T PRK08582         79 RPKRQ   83 (139)
T ss_pred             Cchhh
Confidence            35643

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

Probab=99.10  E-value=7.1e-10  Score=86.43  Aligned_cols=73  Identities=22%  Similarity=0.236  Sum_probs=66.6

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC--CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066           98 ELGTKVKGTVFCTDNRGALVDITA--KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G~~Vdig~--k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~  171 (414)
                      +.|+++.|+|+++.++|+||++.+  +.+|++|.+++++.+..++.+. +.+||.++++|+++|...+++.||+++
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 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKL-VKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHe-eCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence            579999999999999999999963  4899999999998888887776 899999999999999888999999874

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c

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

Probab=99.10  E-value=2.8e-10  Score=84.77  Aligned_cols=64  Identities=41%  Similarity=0.765  Sum_probs=60.0

Q ss_pred             EEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066          268 VIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLS  331 (414)
Q Consensus       268 v~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS  331 (414)
                      +.|+|+++.++|+||+++ +.+|++|.+++++.+..++.+.|++||.|+|+|+++|++++++.||
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            579999999999999998 8999999999999888888899999999999999999999999876

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.

>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=99.09  E-value=4.6e-10  Score=85.62  Aligned_cols=66  Identities=17%  Similarity=0.092  Sum_probs=58.1

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS  168 (414)
                      |++|+|+|.++.++|++|++.+..+||+|.+|++.....  .+. |++|++++|+|+++|++++++.||
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~--~~~-~~~G~~i~~kVi~id~~~~~i~LS   66 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS--KST-YKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc--ccC-cCCCCEEEEEEEEEeCCCCEEecC
Confidence            799999999999999999997779999999999754333  333 899999999999999999998886

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.

>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=99.07  E-value=9.5e-10  Score=85.71  Aligned_cols=74  Identities=19%  Similarity=0.304  Sum_probs=66.6

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066           98 ELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~  172 (414)
                      ++|+++.|+|.++.++|+||++.+ +.+|++|.+++++.+..++.+. |++||.++++|++++.+.+++.||+|..
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 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKL-FRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHe-ecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            469999999999999999999984 7999999999998776666665 8999999999999999999999999864

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.

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

Probab=99.04  E-value=7.9e-09  Score=97.75  Aligned_cols=148  Identities=19%  Similarity=0.162  Sum_probs=115.1

Q ss_pred             cCCCCCEEEEEEEEEe-CCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066           96 NSELGTKVKGTVFCTD-NRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~-~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      .+.+|+.=.++|+.++ +.|+|||+|-..+.++|.+|+.....-+     +++|+++-|.+.- | .++++..+++.-..
T Consensus        70 ~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~~~w-----pq~Gd~l~v~l~~-D-kk~Ri~g~~a~~~~  142 (287)
T COG2996          70 KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLKSLW-----PQKGDKLLVYLYV-D-KKGRIWGTLAIEKI  142 (287)
T ss_pred             eEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccccccC-----CCCCCEEEEEEEE-c-cCCcEEEEecchhH
Confidence            5678999999999999 7899999999899999999986432222     4689999888754 3 56788877754332


Q ss_pred             hHHHHHhhhccc--CCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeeh
Q 015066          175 ELAWERCRQLQS--EDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSN  251 (414)
Q Consensus       175 ~~~~~~l~~~~~--~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~  251 (414)
                        -|........  .++.+.|+|.+....|.||-++ ++.||||.|+.-...    .+|+.++++|+.+.+ +++|.||.
T Consensus       143 --l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~p----rlG~~l~~rVi~~re-Dg~lnLSl  215 (287)
T COG2996         143 --LENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAEP----RLGERLTARVIGVRE-DGKLNLSL  215 (287)
T ss_pred             --HHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhcccc----cCCceEEEEEEEEcc-CCeeeccc
Confidence              1222222222  2568999999999999999886 999999999976543    389999999999986 89999999


Q ss_pred             hhhhhh
Q 015066          252 RKAMAD  257 (414)
Q Consensus       252 K~~l~~  257 (414)
                      ++...+
T Consensus       216 ~p~~~E  221 (287)
T COG2996         216 RPRAHE  221 (287)
T ss_pred             ccccHH
Confidence            986433

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

Probab=99.03  E-value=1.7e-09  Score=84.10  Aligned_cols=70  Identities=24%  Similarity=0.305  Sum_probs=62.5

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066           98 ELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      +.|+++.|+|+++.++|+||++.+ +.+|++|.+++++....++.+. +++||+++++|+++|.++ ++.||+
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~-~~~Gd~v~vkv~~vd~~~-ki~ls~   72 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEV-VDVGEKVWVKVIGREMKD-KMKLSL   72 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhE-ECCCCEEEEEEEEECCCC-cEEEEe
Confidence            589999999999999999999954 3799999999998887777776 899999999999999765 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.

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

Probab=99.03  E-value=1.4e-09  Score=82.45  Aligned_cols=69  Identities=22%  Similarity=0.355  Sum_probs=63.1

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      |+++.|+|.++.++|+||+++.+.+||+|.++++..+..++.+. +.+|+.++++|++++. ++++.||+|
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDV-LKEGDKVKVKVLSIDA-RGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHc-cCCCCEEEEEEEEECC-CCcEEEEEC
Confidence            78999999999999999999988999999999998777777665 8999999999999998 899999975

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.

>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=99.03  E-value=7.9e-10  Score=91.41  Aligned_cols=76  Identities=14%  Similarity=0.164  Sum_probs=66.6

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC-------------------CccccCccCCcEEEEEEEE
Q 015066           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-------------------HVEEAGIVPGLKEEFVIIG  157 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~-------------------~~~e~~~~vG~~v~v~Vl~  157 (414)
                      +++|++|.|+|.++.+.|++|+++++.+||+|.+++++.+..                   ++.+. |++||.+.|+|++
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 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDL-FSVGQLVRCKVVS   79 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHh-ccCCCEEEEEEEE
Confidence            478999999999999999999999899999999999876522                   24455 8999999999999


Q ss_pred             EeCC---CCeEEEEeeehh
Q 015066          158 ENEA---DDSLVLSLRMIQ  173 (414)
Q Consensus       158 id~~---~~~i~LS~k~~~  173 (414)
                      +++.   ++++.||+|+..
T Consensus        80 ~d~~~~~~~~i~LSlr~~~   98 (100)
T cd05693          80 LDKSKSGKKRIELSLEPEL   98 (100)
T ss_pred             ccCCcCCCcEEEEEecHHH
Confidence            9987   789999998754

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.

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

Probab=99.02  E-value=1.5e-09  Score=86.22  Aligned_cols=75  Identities=21%  Similarity=0.198  Sum_probs=66.9

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~  172 (414)
                      ..++|++|.|+|+++.+++++|+++.+.+|++|.++++.....+..+. +++|+.+.|+|+++++. +++.||++..
T Consensus         3 ~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~-~~~GD~i~~~V~~~~~~-~~i~LS~~~~   77 (82)
T cd04454           3 LPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKS-LQPGDLILAKVISLGDD-MNVLLTTADN   77 (82)
T ss_pred             CCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhc-CCCCCEEEEEEEEeCCC-CCEEEEECCC
Confidence            458999999999999999999999999999999999987666666665 89999999999999876 8999999763

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=99.02  E-value=1.2e-09  Score=87.47  Aligned_cols=75  Identities=21%  Similarity=0.166  Sum_probs=64.5

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccc----cccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI----HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~----~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~  171 (414)
                      .+++|++|.|+|+++.++|++|+++.+.+|++|.++++.    ....+..+. +++|+.+.|+|++++++ +++.||++.
T Consensus         3 ~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~-l~vGd~i~~~V~~~~~~-~~i~LS~~~   80 (86)
T cd05789           3 IPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSY-LDEGDLIVAEVQSVDSD-GSVSLHTRS   80 (86)
T ss_pred             cCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhh-CCCCCEEEEEEEEECCC-CCEEEEeCc
Confidence            468999999999999999999999999999999999974    233344444 89999999999999865 899999987


Q ss_pred             h
Q 015066          172 I  172 (414)
Q Consensus       172 ~  172 (414)
                      .
T Consensus        81 ~   81 (86)
T cd05789          81 L   81 (86)
T ss_pred             c
Confidence            5

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".

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=99.00  E-value=5.2e-10  Score=121.36  Aligned_cols=141  Identities=15%  Similarity=0.157  Sum_probs=113.9

Q ss_pred             cCCCCCCccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCCCC---CHHHHH--
Q 015066           13 CPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSF---TLEEFH--   87 (414)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~~~---~~~~f~--   87 (414)
                      |-+-+...+|+|||       -+..++..|.+..-+|++++    +.+++|+++.-..++-..++.+..   ..+...  
T Consensus       537 ~l~~~~~~~~~~~p-------~~~~~~I~~~kI~~vIG~gG----k~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a  605 (684)
T TIGR03591       537 VISEPRAELSPYAP-------RIETIKINPDKIRDVIGPGG----KVIREITEETGAKIDIEDDGTVKIAASDGEAAEAA  605 (684)
T ss_pred             HHhhhhccccccCC-------eEEEEecCHHHHHhhcCCCc----HHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHH
Confidence            34445667999999       77888999999999999999    788999999877776544444422   222233  


Q ss_pred             -HHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEE
Q 015066           88 -SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV  166 (414)
Q Consensus        88 -~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~  166 (414)
                       +.++.+...+++|+++.|+|+++.++|+||++..+.+||+|.+++++.+..++.+. +++||.+.++|+++|. .+++.
T Consensus       606 ~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~-~kvGD~V~VkVi~id~-~gki~  683 (684)
T TIGR03591       606 IKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDV-LKEGDEVKVKVLEIDK-QGRIK  683 (684)
T ss_pred             HHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhc-cCCCCEEEEEEEEECC-CCCcc
Confidence             33344445679999999999999999999999888999999999999888888887 8999999999999986 56654

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=99.00  E-value=1.2e-09  Score=118.54  Aligned_cols=70  Identities=39%  Similarity=0.750  Sum_probs=65.8

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSL  330 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~L  330 (414)
                      ..+++|++|.|+|++|.+||+||++. |.+||+|+|++++.++.++.+.|++||.|+|+|+++|. ++++.|
T Consensus       614 ~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L  684 (684)
T TIGR03591       614 AEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL  684 (684)
T ss_pred             cccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence            46789999999999999999999997 89999999999999999999999999999999999997 788765

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).

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

Probab=98.99  E-value=2.9e-09  Score=80.83  Aligned_cols=72  Identities=28%  Similarity=0.422  Sum_probs=64.4

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      +.|+++.|+|.++.++|++|+++.+..|++|.+++...+..++.+. +++|+.+.++|++++..++++.+|++
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~-~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEV-LKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHe-ecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            4699999999999999999999988999999999987765555555 89999999999999988899999975

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.99  E-value=1.5e-09  Score=112.52  Aligned_cols=116  Identities=13%  Similarity=0.262  Sum_probs=90.9

Q ss_pred             EEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehhhhhhh---------HHhhcc--ccEEEEEEEEEEeece
Q 015066          211 RGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMAD---------SQAQLG--IGSVVIGTVQSLKPYG  279 (414)
Q Consensus       211 ~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~~---------~~~~l~--~G~iv~g~V~~i~~~G  279 (414)
                      .++|+.++.-.. ++...+|+.+.+.|...+. .+....+.|+.+..         ..+.++  .|++|+|+|.++.++|
T Consensus        72 ~~eI~L~eAk~~-~~~~~vGD~ie~~I~~~~f-gRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~g  149 (470)
T PRK09202         72 TKEISLEEARKI-DPDAEVGDYIEEEIESVDF-GRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGN  149 (470)
T ss_pred             cceeeHHHHhhh-CccccCCCeEEEEEccccC-ChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCC
Confidence            366777665432 4555699999999988873 22333334444321         235676  8999999999999999


Q ss_pred             EEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCC--eEEEEEee
Q 015066          280 AFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERG--RVSLSTKK  334 (414)
Q Consensus       280 ~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~--ri~LS~K~  334 (414)
                      +||+++|++|++|.++++      |.+.|++||+|+|+|++++++++  +|.||.+.
T Consensus       150 iiVDLggvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~  200 (470)
T PRK09202        150 IIVDLGRAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILSRTH  200 (470)
T ss_pred             EEEEECCeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence            999999999999999985      67889999999999999999877  89999874

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

Probab=98.99  E-value=7.7e-10  Score=112.93  Aligned_cols=81  Identities=28%  Similarity=0.551  Sum_probs=75.5

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT  338 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~  338 (414)
                      .++..|.+|+|+|+++.+||+||+|. +..||+|+||++.+++.+|++.+.+||.|.||.+..|+ ++.+.||-|.+.|+
T Consensus       664 ~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~-~g~~~ls~ralLp~  742 (760)
T KOG1067|consen  664 QDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP-RGGIMLSSRALLPD  742 (760)
T ss_pred             cceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecC-ccceeehhhhhcCC
Confidence            47889999999999999999999998 89999999999999999999999999999999999997 77788888889888


Q ss_pred             CCc
Q 015066          339 PGD  341 (414)
Q Consensus       339 p~~  341 (414)
                      |.-
T Consensus       743 p~~  745 (760)
T KOG1067|consen  743 PAT  745 (760)
T ss_pred             ccc
Confidence            754

>PRK05807 hypothetical protein; Provisional

Probab=98.99  E-value=3e-09  Score=92.77  Aligned_cols=75  Identities=20%  Similarity=0.312  Sum_probs=68.3

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~  173 (414)
                      .+++|++|+|+|+.+.++|+||++. +..|++|.+++++.+..++.+. +.+|+.++|+|++++. ++++.||++.+.
T Consensus         2 ~~~vG~vv~G~Vt~i~~~GafV~L~-~~~Glvhiseis~~~v~~~~~~-~kvGd~V~VkV~~id~-~gkI~LSlk~~~   76 (136)
T PRK05807          2 TLKAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTYVKDIREH-LKEQDKVKVKVISIDD-NGKISLSIKQAM   76 (136)
T ss_pred             CccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEhhhcccccccCcccc-CCCCCEEEEEEEEECC-CCcEEEEEEecc
Confidence            3678999999999999999999995 5899999999999888887776 8999999999999987 799999999865

>PRK08059 general stress protein 13; Validated

Probab=98.98  E-value=3.3e-09  Score=91.03  Aligned_cols=78  Identities=19%  Similarity=0.300  Sum_probs=71.1

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      .+++|+++.|+|+++.++|+||+++.+.+|++|.++++..+..++.+. +.+|+.++|+|+++|.+++++.||++....
T Consensus         4 ~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~-~~vGD~I~vkI~~id~~~~~i~lslk~~~~   81 (123)
T PRK08059          4 QYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDF-LSVGDEVKVKVLSVDEEKGKISLSIRATEE   81 (123)
T ss_pred             cCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHc-CCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence            478999999999999999999999988999999999988777666665 899999999999999999999999998755

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

Probab=98.96  E-value=6.4e-10  Score=116.83  Aligned_cols=144  Identities=15%  Similarity=0.188  Sum_probs=120.3

Q ss_pred             CCCCccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCCCCCHHH------HHHH
Q 015066           16 ISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEE------FHSA   89 (414)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~~~~~~~------f~~~   89 (414)
                      -|.+-||+|||       =|.-++..+.+..-.|++++    +.+++|+++.-..+...+++.+..+..+      -.+.
T Consensus       541 ~pr~els~~aP-------ri~t~~i~~dKI~dvIG~gG----k~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~  609 (692)
T COG1185         541 EPRKELSPYAP-------RIETIKIDPDKIRDVIGPGG----KTIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKER  609 (692)
T ss_pred             hhhhhhhccCC-------ceEEEccCHHHHhhccCCcc----cchhhhhhhhCcEEEecCCCcEEEEecchHHHHHHHHH
Confidence            34455999999       67788999999999999999    7788999998888876655555333322      1233


Q ss_pred             HHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066           90 LEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus        90 l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      ++.....+++|+++.|+|+++.++|+||.+..+.+|++|.++++.....++++. +++||.+.++|+.+| ..|++.||+
T Consensus       610 I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dv-lk~Gd~v~Vkv~~iD-~~Gri~ls~  687 (692)
T COG1185         610 IEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDV-LKEGDEVKVKVIEID-KQGRIRLSI  687 (692)
T ss_pred             HHHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccce-eecCceEEEEEeeec-ccCCcccee
Confidence            455567899999999999999999999999999999999999999988888887 899999999999998 578999999


Q ss_pred             eeh
Q 015066          170 RMI  172 (414)
Q Consensus       170 k~~  172 (414)
                      +..
T Consensus       688 ~~~  690 (692)
T COG1185         688 KAV  690 (692)
T ss_pred             hhc
Confidence            764

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

Probab=98.95  E-value=2.9e-09  Score=81.33  Aligned_cols=68  Identities=18%  Similarity=0.317  Sum_probs=60.3

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccc-cccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI-HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~-~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS  168 (414)
                      |+++.|+|.++.++|+||++..+.+|++|.+++++ ....++.+. |++||.++++|+++|.+++++.||
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~-~~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEI-YKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhE-ECCCCEEEEEEEEEECCcCEEeCC
Confidence            78999999999999999999988999999999984 445566555 899999999999999999988775

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=98.95  E-value=2.2e-09  Score=111.25  Aligned_cols=122  Identities=14%  Similarity=0.109  Sum_probs=90.1

Q ss_pred             eeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhhHHH-----HHhhhccc--CCeEEEEEE
Q 015066          123 SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAW-----ERCRQLQS--EDVVVKGKV  195 (414)
Q Consensus       123 ~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~~~~-----~~l~~~~~--~g~iv~G~V  195 (414)
                      ..+.++.+++...   ++   .+.+|+.+++.|...+  -+++.++..+......|     +.+.+.+.  .|++++|+|
T Consensus        71 ~~~eI~L~eAk~~---~~---~~~vGD~ie~~I~~~~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V  142 (470)
T PRK09202         71 PTKEISLEEARKI---DP---DAEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVV  142 (470)
T ss_pred             CcceeeHHHHhhh---Cc---cccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEE
Confidence            3466776666322   22   2689999999998765  44444443332222333     35555565  789999999


Q ss_pred             EEEecCcEEEEECCEEEEEeccccCCCCccccccCCeEEEEEEEeecccc--eEEeehhhh
Q 015066          196 VGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQS--RLVLSNRKA  254 (414)
Q Consensus       196 ~~v~~~G~~V~i~gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~--ri~LS~K~~  254 (414)
                      .+++++|++|++||+.||||.+++.....  ..+|++++|+|++++++++  +|.||++..
T Consensus       143 ~ri~~~giiVDLggvea~LP~sE~ip~E~--~~~GdrIka~I~~Vd~~~kg~qIilSRt~p  201 (470)
T PRK09202        143 KRVERGNIIVDLGRAEAILPRKEQIPREN--FRPGDRVRAYVYEVRKEARGPQIILSRTHP  201 (470)
T ss_pred             EEEecCCEEEEECCeEEEecHHHcCCCcc--CCCCCEEEEEEEEEecCCCCCeEEEEeCcH
Confidence            99999999999999999999999973322  2389999999999999877  899999865

>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=98.94  E-value=3.7e-09  Score=80.01  Aligned_cols=68  Identities=24%  Similarity=0.316  Sum_probs=61.9

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS  168 (414)
                      |+++.|+|.++.++|+||+++.+.+|++|.+++++.+..++.+. +++|+.++|+|+++|.+++++.||
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~-~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDV-VSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHh-cCCCCEEEEEEEEEECCCCEEecC
Confidence            78999999999999999999988999999999988776666655 899999999999999888988876

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

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

Probab=98.92  E-value=5.5e-09  Score=79.21  Aligned_cols=68  Identities=24%  Similarity=0.331  Sum_probs=61.4

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066           99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (414)
Q Consensus        99 ~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS  168 (414)
                      +|+++.|+|.++.++|+||+++ +.+|++|.+++++.+..++.+. |++|+.++|+|++++.+++++.||
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-GVDGLLHISDMSWGRVKHPSEV-VNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCccccCHhHE-ECCCCEEEEEEEEEECCCCEEecC
Confidence            4899999999999999999998 5999999999987777666666 899999999999999988998876

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.

>PHA02945 interferon resistance protein; Provisional

Probab=98.91  E-value=8.8e-09  Score=81.43  Aligned_cols=73  Identities=15%  Similarity=0.232  Sum_probs=65.5

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEcCccc--cccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066           97 SELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEA--CIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdig--~k~~g~lp~sEl--s~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~  172 (414)
                      .++|+++-|+|.. .++|+||++.  ++.+||||.+|.  +..++++ .+. + +|+++-|+|+++|+.+|.+-||+|+.
T Consensus         9 P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~-l-~GqkvV~KVirVd~~kg~IDlSlK~V   84 (88)
T PHA02945          9 PNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDK-L-VGKTVKVKVIRVDYTKGYIDVNYKRM   84 (88)
T ss_pred             CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeE-e-cCCEEEEEEEEECCCCCEEEeEeeEc
Confidence            3789999999999 9999999993  469999999965  9888888 776 6 99999999999999999999999975


Q ss_pred             h
Q 015066          173 Q  173 (414)
Q Consensus       173 ~  173 (414)
                      .
T Consensus        85 ~   85 (88)
T PHA02945         85 C   85 (88)
T ss_pred             c
Confidence            3

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

Probab=98.90  E-value=8.8e-09  Score=78.73  Aligned_cols=63  Identities=22%  Similarity=0.427  Sum_probs=55.5

Q ss_pred             cccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEEE
Q 015066          263 GIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRER--GRVSLS  331 (414)
Q Consensus       263 ~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~--~ri~LS  331 (414)
                      ..|++|+|+|.++.++|+||++++.+|++|.++++.      .+.|++||.|+|.|++++.++  ..|.||
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS   66 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTSKGPQIILS   66 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence            469999999999999999999999999999999863      457899999999999999654  467777

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.

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

Probab=98.88  E-value=9.1e-09  Score=78.06  Aligned_cols=68  Identities=21%  Similarity=0.312  Sum_probs=61.7

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      |+++.|+|.++.++|+||+++.+..||+|.++++..+..++.+. +.+|+.+.++|+++|+ .+++.||+
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDV-LKVGDEVKVKVIEVDD-RGRISLSR   68 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHc-cCCCCEEEEEEEEECC-CCcEEeeC
Confidence            78999999999999999999988999999999988777666665 8999999999999998 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.

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

Probab=98.87  E-value=9.5e-09  Score=99.07  Aligned_cols=88  Identities=20%  Similarity=0.279  Sum_probs=77.0

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCC--CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066           97 SELGTKVKGTVFCTDNRGALVDITA--KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdig~--k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      .++|++|.|+|.++.++|+||++..  +.+||+|.+|++..+..++.+. +++|+.+.|+|+++|..++++.||++....
T Consensus         6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~-~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~   84 (262)
T PRK03987          6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDH-VKEGQKVVCKVIRVDPRKGHIDLSLKRVNE   84 (262)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHh-CCCCCEEEEEEEEEecccCeEEEEEEeccc
Confidence            5789999999999999999999964  6899999999998888887776 899999999999999999999999998877


Q ss_pred             hHHHHHhhhcc
Q 015066          175 ELAWERCRQLQ  185 (414)
Q Consensus       175 ~~~~~~l~~~~  185 (414)
                      ...|+.+.+..
T Consensus        85 ~e~~~~~~~~~   95 (262)
T PRK03987         85 HQRREKIQEWK   95 (262)
T ss_pred             chHHHHHHHHH
Confidence            66666555443

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

Probab=98.86  E-value=1.4e-08  Score=78.42  Aligned_cols=71  Identities=18%  Similarity=0.240  Sum_probs=60.6

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccc-ccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH-KIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~-~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS  168 (414)
                      +.+|+++.|+|.++.++|+||++..+.+|++|.+++.+. ...++.+. +++||.++|+|+++|.+++++.||
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~-~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKV-VSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccE-eCCCCEEEEEEEEeeCCcCEEeCC
Confidence            468999999999999999999998889999999999753 22344444 899999999999999888888764

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.

>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=98.86  E-value=1.8e-08  Score=79.33  Aligned_cols=72  Identities=15%  Similarity=0.271  Sum_probs=63.6

Q ss_pred             CCEEEEEEEEEeCCeEEEEeC---CCeeEEEcCcccccccc-CCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066          100 GTKVKGTVFCTDNRGALVDIT---AKSSAYLPTQEACIHKI-KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig---~k~~g~lp~sEls~~~~-~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      |+++.|+|.++.++|+||+++   .+.+|++|.+++++.+. .++.+. |++|+.++++|+++|  .+++.+|++....
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~-~~~Gd~v~v~v~~vd--~~~i~~s~k~~~~   76 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDV-VKRGQKVKVKVISIQ--NGKISLSMKDVDQ   76 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhhe-eCCCCEEEEEEEEEe--CCEEEEEEEeccc
Confidence            789999999999999999998   35899999999988765 666666 899999999999998  7999999987543

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.

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

Probab=98.85  E-value=1.6e-09  Score=110.59  Aligned_cols=151  Identities=13%  Similarity=0.083  Sum_probs=119.0

Q ss_pred             CccCCCCCCccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCC---CCCHHHHH
Q 015066           11 LRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGV---SFTLEEFH   87 (414)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~---~~~~~~f~   87 (414)
                      -||.|.|..++++|.|       ++..++++|.+.+..|++++    ..+|.|..|.- .+....++.+   ..+...++
T Consensus       581 ~k~i~~Pr~~~~~y~P-------~~~tlkv~~sk~~~lIGp~G----~~~kki~~EtG-ai~~vDe~t~~i~A~~~~am~  648 (760)
T KOG1067|consen  581 EKNINSPRGSDKEYSP-------VLETLKVSPSKRATLIGPGG----VLKKKIEVETG-AISQVDEGTFSIFAPTQAAME  648 (760)
T ss_pred             HhhcCCcccCccccCc-------eeeEEeecchhhheeecCcc----ceeeeEeeecc-ceeeecCceEEEEecCHHHHH
Confidence            4899999999999999       99999999999999999999    45566666644 3333222222   23333333


Q ss_pred             HH---HHhhc-----ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEe
Q 015066           88 SA---LEKYD-----FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN  159 (414)
Q Consensus        88 ~~---l~~~~-----~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id  159 (414)
                      ++   ++.+.     .+++.|-+.+++|+++.+.|+||.+.....|++|.+||+..++.++++. +.+||+|+++.++.|
T Consensus       649 ~Ak~~I~~i~~~~~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~-levGq~I~vk~ie~d  727 (760)
T KOG1067|consen  649 EAKEFIDGIIKDDQVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDL-LEVGQEIQVKYIERD  727 (760)
T ss_pred             HHHHHHHHHhcCccccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHH-HhhcceeEEEEEeec
Confidence            33   33222     3678899999999999999999999999999999999999999999999 999999999999998


Q ss_pred             CCCCeEEEEeeehhhh
Q 015066          160 EADDSLVLSLRMIQYE  175 (414)
Q Consensus       160 ~~~~~i~LS~k~~~~~  175 (414)
                      + .+.+.+|.|+.+..
T Consensus       728 ~-~g~~~ls~ralLp~  742 (760)
T KOG1067|consen  728 P-RGGIMLSSRALLPD  742 (760)
T ss_pred             C-ccceeehhhhhcCC
Confidence            6 45567777766653

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

Probab=98.84  E-value=1.8e-08  Score=92.14  Aligned_cols=82  Identities=28%  Similarity=0.515  Sum_probs=69.8

Q ss_pred             ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCccccc-----------CcccccCCCCEEEEEEEEEe-----CCC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVMILSHD-----RER  325 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~-----------~~~~~~~~G~~V~vkVl~id-----~e~  325 (414)
                      ..+|+++.|+|++++++|+||+++.++|++|.+++.+++..           +....|+.||.|+++|+++|     ++.
T Consensus        79 p~~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~  158 (179)
T TIGR00448        79 PELGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEG  158 (179)
T ss_pred             ccCCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCc
Confidence            44799999999999999999999889999999999866432           23467999999999999998     667


Q ss_pred             CeEEEEEeeCCCCCCccc
Q 015066          326 GRVSLSTKKLEPTPGDMI  343 (414)
Q Consensus       326 ~ri~LS~K~~~~~p~~~~  343 (414)
                      .+|.||||+--.-|.+.+
T Consensus       159 ~~I~lt~k~~~LG~~~w~  176 (179)
T TIGR00448       159 SKIGLTMRQPLLGKLEWI  176 (179)
T ss_pred             ceEEEEeccCcCCccccc
Confidence            899999998776666554

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

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

Probab=98.84  E-value=1.7e-08  Score=77.09  Aligned_cols=64  Identities=25%  Similarity=0.336  Sum_probs=55.0

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC--CeEEEEe
Q 015066           98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD--DSLVLSL  169 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~--~~i~LS~  169 (414)
                      ..|++|+|+|.+++++|+||++++ .+||||.+|++.      .+. +++|+++++.|+++++.+  +++.||+
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~~------~~~-~~~Gd~v~v~v~~v~~~~~~~~i~lSr   67 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQIP------GES-YRPGDRIKAYVLEVRKTSKGPQIILSR   67 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCCC------CCc-CCCCCEEEEEEEEEecCCCCCEEEEeC
Confidence            479999999999999999999986 999999999862      233 789999999999998654  4788885

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.84  E-value=9.5e-09  Score=97.83  Aligned_cols=75  Identities=28%  Similarity=0.325  Sum_probs=68.0

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccc----cCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV----ADIATVLQPGDTLKVMILSHDRERGRVSLSTKK  334 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~----~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~  334 (414)
                      -.+++||+|.|+|+++.++|+||+++ +..|++|++++++.++    .++.+.|++||.|.|+|++++++ +++.||+|.
T Consensus        59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~-~~~~LS~k~  137 (235)
T PRK04163         59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRT-RDVVLTLKG  137 (235)
T ss_pred             ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCC-CcEEEEEcC
Confidence            34689999999999999999999999 7999999999999887    78899999999999999999864 459999986


Q ss_pred             C
Q 015066          335 L  335 (414)
Q Consensus       335 ~  335 (414)
                      -
T Consensus       138 ~  138 (235)
T PRK04163        138 K  138 (235)
T ss_pred             C
Confidence            4

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

Probab=98.81  E-value=2.5e-08  Score=80.54  Aligned_cols=74  Identities=18%  Similarity=0.161  Sum_probs=63.3

Q ss_pred             cCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEcCccccc---cccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           96 NSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACI---HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~--G~~Vdig~k~~g~lp~sEls~---~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      .++.|+++.|+|+++.++  |+||+++.+.+||||.+|+++   ....++.+. +++|+.+.|+|+......+...||.+
T Consensus         4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~-~~~Gd~v~VqV~~~~~~~K~~~lt~~   82 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKL-LKEGQEILVQVVKEPIGTKGPRLTTN   82 (88)
T ss_pred             cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHc-CCCCCEEEEEEEEecCCCCCceEEEE
Confidence            567999999999999996  999999988999999999987   445566665 89999999999998766677777765

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

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

Probab=98.79  E-value=1.1e-08  Score=96.37  Aligned_cols=77  Identities=21%  Similarity=0.271  Sum_probs=72.1

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEe--CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066           97 SELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdi--g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      .++|++|-|+|.++.++|+||.+  .++.+||+|.||++..+++++.++ +++|+++-|+|+++|+..|.+-||+|+...
T Consensus         9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~-vkegqkvV~kVlrVd~~rg~IDLSlkrV~~   87 (269)
T COG1093           9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDY-VKEGQKVVAKVLRVDPKRGHIDLSLKRVTE   87 (269)
T ss_pred             CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHH-hhcCCeEEEEEEEEcCCCCeEeeehhhCCH
Confidence            57899999999999999999999  456999999999999999999998 999999999999999999999999998754

>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=98.70  E-value=6.6e-08  Score=74.40  Aligned_cols=63  Identities=19%  Similarity=0.127  Sum_probs=55.8

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccc--cCCccccCccCCcEEEEEEEEEeCCCC
Q 015066          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK--IKHVEEAGIVPGLKEEFVIIGENEADD  163 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~--~~~~~e~~~~vG~~v~v~Vl~id~~~~  163 (414)
                      |++|.|+|+++.++|++|+++.+.+|++|.+++++.+  ..++.+. |++|+.++++|++++..+.
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~-~~~Gd~i~~kVl~~d~~~~   65 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSK-FKIGQKIKARVIGGHDAKT   65 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHh-CCCCCEEEEEEEEEeCccc
Confidence            8999999999999999999999999999999998764  5566565 8999999999999986543

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.

>TIGR02063 RNase_R ribonuclease R

Probab=98.69  E-value=5.7e-08  Score=106.47  Aligned_cols=72  Identities=25%  Similarity=0.548  Sum_probs=63.8

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCcccc-----------cCcccccCCCCEEEEEEEEEeCCCCe
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVMILSHDRERGR  327 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~-----------~~~~~~~~~G~~V~vkVl~id~e~~r  327 (414)
                      .-++|+++.|+|++|++||+||++.  |++||+|+++++++++           .+....|++||.|+|+|.++|.++++
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            4467999999999999999999997  6999999999986643           33456799999999999999999999


Q ss_pred             EEEEE
Q 015066          328 VSLST  332 (414)
Q Consensus       328 i~LS~  332 (414)
                      |.|++
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.

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

Probab=98.67  E-value=6.2e-08  Score=71.96  Aligned_cols=65  Identities=18%  Similarity=0.240  Sum_probs=57.5

Q ss_pred             EEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEE
Q 015066          103 VKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (414)
Q Consensus       103 V~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS  168 (414)
                      +.|+|.++.++|++|+++.+.+|++|.++++..+..++.+. +.+|+.+.|+|+++|+.++++.||
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            47999999999999999988999999999987766555555 899999999999999888888875

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.

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

Probab=98.64  E-value=8.9e-09  Score=96.50  Aligned_cols=104  Identities=19%  Similarity=0.397  Sum_probs=83.3

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCC
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEP  337 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~  337 (414)
                      -+.++++|-+.|.+|.+.|+||.|-   +++|++-.||||..|+.+++...++|..=-|.|+.+|+++|.|.||.+.+.+
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            3668999999999999999999984   7999999999999999999999999999999999999999999999999987


Q ss_pred             CCCcccCCchhhhhhHHHHHHHHHHHH
Q 015066          338 TPGDMIRNPKLVFEKAEEMAQTFRQRI  364 (414)
Q Consensus       338 ~p~~~~~~~~~~~~~~~~~~~~~~~~~  364 (414)
                      +--..+++......-+.......++++
T Consensus        93 ed~~kC~Er~~ksK~v~sIlrhvAe~~  119 (304)
T KOG2916|consen   93 EDKEKCEERFAKSKLVYSILRHVAEKL  119 (304)
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHh
Confidence            543333332222222334444444443

>TIGR01953 NusA transcription termination factor NusA

Probab=98.60  E-value=1.4e-07  Score=94.29  Aligned_cols=106  Identities=19%  Similarity=0.224  Sum_probs=78.4

Q ss_pred             ccCCcEEEEEEEEEeCCCCeEEEEe-eehh----hhHHHHHhhhcc--cCCeEEEEEEEEEecCc-EEEEECCEEEEEec
Q 015066          145 IVPGLKEEFVIIGENEADDSLVLSL-RMIQ----YELAWERCRQLQ--SEDVVVKGKVVGANKGG-VVAEVEGLRGFVPF  216 (414)
Q Consensus       145 ~~vG~~v~v~Vl~id~~~~~i~LS~-k~~~----~~~~~~~l~~~~--~~g~iv~G~V~~v~~~G-~~V~i~gi~GfIp~  216 (414)
                      +.+|+.+++.+...+  -++..++. |+..    .+..++.+.+.+  ..|++++|+|.+++++| ++|++|++.||||.
T Consensus        84 ~~vGD~I~~~I~~~~--fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP~  161 (341)
T TIGR01953        84 VQIGDEVKKEIPPEN--FGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGILPK  161 (341)
T ss_pred             cccCCEEEEEecccC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEECCeEEEecH
Confidence            789999998885432  34444333 3321    233455555555  37899999999999988 69999999999999


Q ss_pred             cccCCCCccccccCCeEEEEEEEeeccc--ceEEeehhhh
Q 015066          217 SQISSKSTAEELLGKDLPLKFVEVDEEQ--SRLVLSNRKA  254 (414)
Q Consensus       217 sels~~~~~~~~vGq~V~vkVl~vD~e~--~ri~LS~K~~  254 (414)
                      ++......  ..+|+++++.|++++.+.  ..+.||++..
T Consensus       162 ~E~ip~E~--~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~  199 (341)
T TIGR01953       162 KEQIPGEK--FRIGDRIKAYVYEVRKTAKGPQIILSRTHP  199 (341)
T ss_pred             HHcCCCcC--CCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence            99885432  237999999999999654  4699999875

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.

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

Probab=98.59  E-value=1.5e-07  Score=76.53  Aligned_cols=73  Identities=25%  Similarity=0.403  Sum_probs=64.3

Q ss_pred             ccccEEEEEEEEEEeeceEEEEE--------C-CEEEEEeecccCccccc--CcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDI--------G-GINGLLHVSQISHDRVA--DIATVLQPGDTLKVMILSHDRERGRVSL  330 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l--------~-gv~Glvh~sels~~~~~--~~~~~~~~G~~V~vkVl~id~e~~ri~L  330 (414)
                      +++|++|.|+|+++....++|++        . ...|++|++++......  ++.+.|++||.|+|||++++. ...+.|
T Consensus         4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~-~~~~~L   82 (92)
T cd05791           4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD-ASSYYL   82 (92)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC-CCCcEE
Confidence            57999999999999999999999        4 48999999999877666  688999999999999999974 467999


Q ss_pred             EEeeC
Q 015066          331 STKKL  335 (414)
Q Consensus       331 S~K~~  335 (414)
                      |++.-
T Consensus        83 st~~~   87 (92)
T cd05791          83 STAEN   87 (92)
T ss_pred             EecCC
Confidence            99863

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

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

Probab=98.59  E-value=1.6e-07  Score=84.58  Aligned_cols=76  Identities=32%  Similarity=0.527  Sum_probs=63.9

Q ss_pred             ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccc----------cC-cccccCCCCEEEEEEEEEeCCC-----
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV----------AD-IATVLQPGDTLKVMILSHDRER-----  325 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~----------~~-~~~~~~~G~~V~vkVl~id~e~-----  325 (414)
                      +..|++|.|.|+++..||+||+++-++||+|+|++.++++          .. -...+++||.|.+||+++....     
T Consensus        79 P~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~  158 (183)
T COG1095          79 PFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRE  158 (183)
T ss_pred             eccccEEEEEEEEEeecceEEEeccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcccc
Confidence            4469999999999999999999999999999999988732          12 2337999999999999987655     


Q ss_pred             CeEEEEEeeCCC
Q 015066          326 GRVSLSTKKLEP  337 (414)
Q Consensus       326 ~ri~LS~K~~~~  337 (414)
                      .+|.|+||+.-.
T Consensus       159 ~~I~lTmrq~~L  170 (183)
T COG1095         159 SKIGLTMRQPGL  170 (183)
T ss_pred             ceEEEEeccccC
Confidence            589999998643

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=98.58  E-value=1.5e-07  Score=73.67  Aligned_cols=70  Identities=19%  Similarity=0.338  Sum_probs=65.4

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC--CEEEEEe-ecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLH-VSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST  332 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh-~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~  332 (414)
                      -+++|+++. .|..+.+.|++|.|-  |++|++. .+|++.+|+.++.+.+ +|-.+.|+|+.+|+++|.|.||.
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            367899999 889999999999985  8999999 9999999999999999 99999999999999999999985

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

Probab=98.57  E-value=2.7e-07  Score=84.85  Aligned_cols=75  Identities=31%  Similarity=0.559  Sum_probs=64.4

Q ss_pred             ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCccccc-----------CcccccCCCCEEEEEEEEEeCCCC----
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVMILSHDRERG----  326 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~-----------~~~~~~~~G~~V~vkVl~id~e~~----  326 (414)
                      +.+|+++.|+|+++.++|+||+++.++|++|.+++.+++..           +....+++||.|+++|.+++.+.+    
T Consensus        79 P~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~  158 (187)
T PRK08563         79 PELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPRG  158 (187)
T ss_pred             ccCCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCCC
Confidence            55799999999999999999999989999999999876432           345679999999999999997543    


Q ss_pred             -eEEEEEeeCC
Q 015066          327 -RVSLSTKKLE  336 (414)
Q Consensus       327 -ri~LS~K~~~  336 (414)
                       +|.||+|+--
T Consensus       159 ~~I~ls~~~~~  169 (187)
T PRK08563        159 SKIGLTMRQPG  169 (187)
T ss_pred             CEEEEEecCCC
Confidence             8999999754

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

Probab=98.55  E-value=4.8e-07  Score=71.42  Aligned_cols=70  Identities=10%  Similarity=0.145  Sum_probs=58.5

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccC-----------CccccCccCCcEEEEEEEEEeCCCCeEE
Q 015066           99 LGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADDSLV  166 (414)
Q Consensus        99 ~G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~-----------~~~e~~~~vG~~v~v~Vl~id~~~~~i~  166 (414)
                      .|+++.|+|+++.++|+||+++. +.+|++|.+++++.+..           ..... +++|+.++++|+++|.+.+++.
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            48999999999999999999987 69999999999754211           12233 7899999999999998889998


Q ss_pred             EEe
Q 015066          167 LSL  169 (414)
Q Consensus       167 LS~  169 (414)
                      +++
T Consensus        80 ~~l   82 (83)
T cd04471          80 FEL   82 (83)
T ss_pred             EEE
Confidence            875

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=98.55  E-value=3e-07  Score=101.53  Aligned_cols=73  Identities=23%  Similarity=0.447  Sum_probs=64.2

Q ss_pred             cccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCccccc-----------CcccccCCCCEEEEEEEEEeCCCCeEE
Q 015066          263 GIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVMILSHDRERGRVS  329 (414)
Q Consensus       263 ~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~~-----------~~~~~~~~G~~V~vkVl~id~e~~ri~  329 (414)
                      ++|+++.|+|++|++||+||+|.  +++||||++++.++++.           +....|++||.|+|+|.++|.++++|.
T Consensus       642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~  721 (813)
T PRK11642        642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKID  721 (813)
T ss_pred             cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEE
Confidence            68999999999999999999997  49999999999876322           234679999999999999999999999


Q ss_pred             EEEeeC
Q 015066          330 LSTKKL  335 (414)
Q Consensus       330 LS~K~~  335 (414)
                      |++-..
T Consensus       722 f~l~~~  727 (813)
T PRK11642        722 FSLISS  727 (813)
T ss_pred             EEEecc
Confidence            998543

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

Probab=98.54  E-value=7.6e-07  Score=69.91  Aligned_cols=64  Identities=16%  Similarity=0.166  Sum_probs=57.6

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      +++.|+.+.|+|.++.++|+||++..+.+|++|.+++.        +. +++|+.++++|.++ .+++++.+|.
T Consensus        13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~-~~iGd~v~v~I~~i-~e~~~i~l~~   76 (77)
T cd04473          13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RD-YEVGDEVIVQVTDI-PENGNIDLIP   76 (77)
T ss_pred             hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------Cc-CCCCCEEEEEEEEE-CCCCcEEEEE
Confidence            57899999999999999999999998899999999863        22 78999999999999 7889998875

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

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

Probab=98.52  E-value=3.6e-07  Score=99.23  Aligned_cols=70  Identities=24%  Similarity=0.515  Sum_probs=62.5

Q ss_pred             cccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCcccc-----------cCcccccCCCCEEEEEEEEEeCCCCeEE
Q 015066          263 GIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVMILSHDRERGRVS  329 (414)
Q Consensus       263 ~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~-----------~~~~~~~~~G~~V~vkVl~id~e~~ri~  329 (414)
                      ++|+.++|+|+++++||+||+|.  +++||||++++.++++           .+....|++||+|+|+|.++|.++++|.
T Consensus       571 ~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~  650 (654)
T TIGR00358       571 KVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSII  650 (654)
T ss_pred             CCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEE
Confidence            57999999999999999999997  7999999999987641           2344679999999999999999999999


Q ss_pred             EEE
Q 015066          330 LST  332 (414)
Q Consensus       330 LS~  332 (414)
                      +++
T Consensus       651 f~l  653 (654)
T TIGR00358       651 FEL  653 (654)
T ss_pred             EEE
Confidence            986

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.44  E-value=5.5e-07  Score=90.55  Aligned_cols=103  Identities=16%  Similarity=0.266  Sum_probs=77.9

Q ss_pred             ccccccCCeEEEEEEEeecccceEEeehhhhhhh---------HHhhc--cccEEEEEEEEEEeeceEEEEECCEEEEEe
Q 015066          224 TAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMAD---------SQAQL--GIGSVVIGTVQSLKPYGAFIDIGGINGLLH  292 (414)
Q Consensus       224 ~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~~---------~~~~l--~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh  292 (414)
                      +++..+|+.+...+...+..+..+ .+.|+.+..         .++.|  +.|++++|+|.++.++|+||++++++|++|
T Consensus        84 ~~~~~vGD~i~~~I~~~~fgR~aa-q~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP  162 (362)
T PRK12327         84 NPAYELGDVIEIEVTPKDFGRIAA-QTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLGKIEAVLP  162 (362)
T ss_pred             CccccCCCEEEEecCcCCCChHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeCCeEEEec
Confidence            455568999999876665433222 333433221         23566  899999999999999999999999999999


Q ss_pred             ecccCcccccCcccccCCCCEEEEEEEEEeCCCC--eEEEEEe
Q 015066          293 VSQISHDRVADIATVLQPGDTLKVMILSHDRERG--RVSLSTK  333 (414)
Q Consensus       293 ~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~--ri~LS~K  333 (414)
                      .+++.      +.+.|++||+++|.|++++.+++  .|.||..
T Consensus       163 ~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt  199 (362)
T PRK12327        163 PAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT  199 (362)
T ss_pred             HHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence            98874      36779999999999999996654  4666654

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=98.44  E-value=4.6e-07  Score=83.50  Aligned_cols=78  Identities=23%  Similarity=0.202  Sum_probs=65.7

Q ss_pred             HHhhcccCCCCCEEEEEEEEEeCCeEEEEeCC----------CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEe
Q 015066           90 LEKYDFNSELGTKVKGTVFCTDNRGALVDITA----------KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN  159 (414)
Q Consensus        90 l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~----------k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id  159 (414)
                      |..+.+.+++|++|.|+|+++.++|++|+|+.          ..+|++|.+++++....+..+. |++||.+.|+|++++
T Consensus        55 ~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~-~~~GD~V~akV~~i~  133 (189)
T PRK09521         55 FKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDA-FKIGDIVRAKVISYT  133 (189)
T ss_pred             CcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhc-cCCCCEEEEEEEecC
Confidence            33344577899999999999999999999953          4789999999987766666665 899999999999987


Q ss_pred             CCCCeEEEEeee
Q 015066          160 EADDSLVLSLRM  171 (414)
Q Consensus       160 ~~~~~i~LS~k~  171 (414)
                         +++.||++.
T Consensus       134 ---~~i~LS~k~  142 (189)
T PRK09521        134 ---DPLQLSTKG  142 (189)
T ss_pred             ---CcEEEEEec
Confidence               789999974

>TIGR01953 NusA transcription termination factor NusA

Probab=98.44  E-value=9.3e-07  Score=88.36  Aligned_cols=104  Identities=13%  Similarity=0.293  Sum_probs=77.8

Q ss_pred             ccccccCCeEEEEEEEeecccceEEeehhhhhh----h-----HHhhc--cccEEEEEEEEEEeece-EEEEECCEEEEE
Q 015066          224 TAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMA----D-----SQAQL--GIGSVVIGTVQSLKPYG-AFIDIGGINGLL  291 (414)
Q Consensus       224 ~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~----~-----~~~~l--~~G~iv~g~V~~i~~~G-~fV~l~gv~Glv  291 (414)
                      +++..+|+.+.+.+..-+. .+....+.|+.+.    +     .++.+  +.|++|+|+|.++.+.| +||++++++|++
T Consensus        81 d~~~~vGD~I~~~I~~~~f-gR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~L  159 (341)
T TIGR01953        81 DPDVQIGDEVKKEIPPENF-GRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGIL  159 (341)
T ss_pred             ccccccCCEEEEEecccCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEECCeEEEe
Confidence            4555689999988754432 2333344444321    1     12455  59999999999999988 699999999999


Q ss_pred             eecccCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEEEEee
Q 015066          292 HVSQISHDRVADIATVLQPGDTLKVMILSHDRER--GRVSLSTKK  334 (414)
Q Consensus       292 h~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~--~ri~LS~K~  334 (414)
                      |.++..      +.+.|++||+++|.|++++.+.  ..|.||.+.
T Consensus       160 P~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~  198 (341)
T TIGR01953       160 PKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTH  198 (341)
T ss_pred             cHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence            999986      3456999999999999999553  579999874

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=98.32  E-value=2.5e-06  Score=81.28  Aligned_cols=75  Identities=23%  Similarity=0.238  Sum_probs=64.8

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc----CCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI----KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~----~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      +..++||+|.|+|+++..++++|+|+....|+||.++++..+.    .++.+. |.+||.+.|+|+++++ ++.+.||++
T Consensus        59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~-~~~GDlV~akV~~i~~-~~~~~LS~k  136 (235)
T PRK04163         59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKY-LDIGDYIIAKVKDVDR-TRDVVLTLK  136 (235)
T ss_pred             ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhh-CCCCCEEEEEEEEECC-CCcEEEEEc
Confidence            4568999999999999999999999988999999999987654    555555 8999999999999985 445999986


Q ss_pred             e
Q 015066          171 M  171 (414)
Q Consensus       171 ~  171 (414)
                      .
T Consensus       137 ~  137 (235)
T PRK04163        137 G  137 (235)
T ss_pred             C
Confidence            4

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.30  E-value=9.1e-06  Score=81.83  Aligned_cols=78  Identities=19%  Similarity=0.222  Sum_probs=62.6

Q ss_pred             HHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCC--e
Q 015066           87 HSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD--S  164 (414)
Q Consensus        87 ~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~--~  164 (414)
                      +..|++|  .-+.|++|+|+|.+++++|++|++|+ .+||||.+++..      .+. |++|++++|+|++++...+  +
T Consensus       124 e~v~~ef--~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~ip------~e~-~~~Gd~Ika~V~~V~~~~kgp~  193 (362)
T PRK12327        124 EIIYNEF--SEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQIP------GET-YKHGDRIKVYVVKVEKTTKGPQ  193 (362)
T ss_pred             HHHHHHH--HHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcCC------CCC-CCCCCEEEEEEEEEecCCCCCe
Confidence            3445544  34899999999999999999999986 999999988742      343 8999999999999985543  6


Q ss_pred             EEEEeeehhh
Q 015066          165 LVLSLRMIQY  174 (414)
Q Consensus       165 i~LS~k~~~~  174 (414)
                      +.||+.....
T Consensus       194 IivSRt~p~~  203 (362)
T PRK12327        194 IFVSRTHPGL  203 (362)
T ss_pred             EEEEeCCHHH
Confidence            8888876554

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

Probab=98.25  E-value=3.9e-06  Score=69.09  Aligned_cols=66  Identities=24%  Similarity=0.341  Sum_probs=55.3

Q ss_pred             eEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC---cc-----------cc-ccCCeEEEEEEEeeccc-----ceEE
Q 015066          189 VVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS---TA-----------EE-LLGKDLPLKFVEVDEEQ-----SRLV  248 (414)
Q Consensus       189 ~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~---~~-----------~~-~vGq~V~vkVl~vD~e~-----~ri~  248 (414)
                      +++.|+|++++++|+||+++++.||+|.+++++..   +.           .. .+|+.++++|.++|.+.     .++.
T Consensus         1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~   80 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIG   80 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEE
Confidence            37899999999999999998899999999998642   11           11 37999999999999874     4799


Q ss_pred             eehhhh
Q 015066          249 LSNRKA  254 (414)
Q Consensus       249 LS~K~~  254 (414)
                      ||++..
T Consensus        81 ls~k~~   86 (99)
T cd04460          81 LTMRQP   86 (99)
T ss_pred             EEEecC
Confidence            999875

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.

>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.03  E-value=1.8e-05  Score=60.97  Aligned_cols=69  Identities=19%  Similarity=0.212  Sum_probs=56.0

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccc-cCccCCcEE-EEEEEEEeCCCCeEEEEee
Q 015066          100 GTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEE-AGIVPGLKE-EFVIIGENEADDSLVLSLR  170 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e-~~~~vG~~v-~v~Vl~id~~~~~i~LS~k  170 (414)
                      |++|+|+|+..++++++|++.+ +..|++|..++++...++... ..+.+|+++ ++.|+  +...+.+.+|.|
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 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence            7899999999999999999976 899999999999843332221 226799999 89998  667788888865

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.

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

Probab=97.98  E-value=4.2e-05  Score=61.71  Aligned_cols=64  Identities=20%  Similarity=0.294  Sum_probs=52.5

Q ss_pred             ccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCc-----------ccccCCCCEEEEEEEEEeCCCCe
Q 015066          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADI-----------ATVLQPGDTLKVMILSHDRERGR  327 (414)
Q Consensus       264 ~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~-----------~~~~~~G~~V~vkVl~id~e~~r  327 (414)
                      +|+++.|+|+++.++|+||+++.+++|+|.+.+..+..-++           ...++.|+.|.+||+++..+.+.
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~   75 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDATD   75 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccCc
Confidence            48999999999999999999999999999999865432222           34588999999999998765443

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.

>TIGR02063 RNase_R ribonuclease R

Probab=97.96  E-value=4.8e-05  Score=83.66  Aligned_cols=73  Identities=8%  Similarity=0.156  Sum_probs=61.2

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCcccccccc-----------CCccccCccCCcEEEEEEEEEeCCCC
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKI-----------KHVEEAGIVPGLKEEFVIIGENEADD  163 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~-----------~~~~e~~~~vG~~v~v~Vl~id~~~~  163 (414)
                      .-++|++++|+|+++.++|+||.+.+ +.+|++|.+++++.+.           ...... +++||+++|+|+++|..++
T Consensus       624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~-~~lGd~V~Vkv~~vd~~~~  702 (709)
T TIGR02063       624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKV-FRLGDRVKVRVVKADLDTG  702 (709)
T ss_pred             hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcE-ECCCCEEEEEEEEEecccC
Confidence            45789999999999999999999986 6999999999975432           111223 8899999999999999999


Q ss_pred             eEEEEe
Q 015066          164 SLVLSL  169 (414)
Q Consensus       164 ~i~LS~  169 (414)
                      ++.+++
T Consensus       703 ~I~~~l  708 (709)
T TIGR02063       703 KIDFEL  708 (709)
T ss_pred             eEEEEE
Confidence            999885

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.

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

Probab=97.95  E-value=3.5e-05  Score=62.68  Aligned_cols=74  Identities=19%  Similarity=0.147  Sum_probs=61.2

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEe--------CCCeeEEEcCccccccccC--CccccCccCCcEEEEEEEEEeCCCCeE
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDI--------TAKSSAYLPTQEACIHKIK--HVEEAGIVPGLKEEFVIIGENEADDSL  165 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdi--------g~k~~g~lp~sEls~~~~~--~~~e~~~~vG~~v~v~Vl~id~~~~~i  165 (414)
                      -.++|++|.|+|+++....+.|+|        .....|++|.+++...+..  +..+. |.+||.+.++|++.++ ...+
T Consensus         3 ~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~-f~~GDiV~AkVis~~~-~~~~   80 (92)
T cd05791           3 LPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKC-FRPGDIVRAKVISLGD-ASSY   80 (92)
T ss_pred             CCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhh-cCCCCEEEEEEEEcCC-CCCc
Confidence            358999999999999999999999        7777899999998755444  34444 8999999999999874 3568


Q ss_pred             EEEeee
Q 015066          166 VLSLRM  171 (414)
Q Consensus       166 ~LS~k~  171 (414)
                      .||.+.
T Consensus        81 ~Lst~~   86 (92)
T cd05791          81 YLSTAE   86 (92)
T ss_pred             EEEecC
Confidence            899875

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".

>PRK05054 exoribonuclease II; Provisional

Probab=97.92  E-value=3.5e-05  Score=83.65  Aligned_cols=68  Identities=15%  Similarity=0.179  Sum_probs=57.3

Q ss_pred             cEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCccc--c--c-C-------cccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDR--V--A-D-------IATVLQPGDTLKVMILSHDRERGRVSL  330 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~--~--~-~-------~~~~~~~G~~V~vkVl~id~e~~ri~L  330 (414)
                      |+.+.|.|+++++||+||+|.  |++||||++.+.+.+  +  . +       -...|+.||+|+|+|.++|.++++|.+
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            459999999999999999997  799999999986531  1  0 1       124699999999999999999999988


Q ss_pred             EE
Q 015066          331 ST  332 (414)
Q Consensus       331 S~  332 (414)
                      ++
T Consensus       642 ~~  643 (644)
T PRK05054        642 RP  643 (644)
T ss_pred             EE
Confidence            75

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

Probab=97.90  E-value=7e-05  Score=68.42  Aligned_cols=77  Identities=18%  Similarity=0.169  Sum_probs=61.9

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC-Ccc---------ccCccCCcEEEEEEEEEe-----C
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-HVE---------EAGIVPGLKEEFVIIGEN-----E  160 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~-~~~---------e~~~~vG~~v~v~Vl~id-----~  160 (414)
                      ....|+++.|+|+++++.|+||+++. .+|+++.+++...+.. +..         ...+..|+.++++|++++     +
T Consensus        78 ~p~~gEvv~G~V~~v~~~GifV~lg~-~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~  156 (179)
T TIGR00448        78 KPELGEIVEGEVIEIVEFGAFVSLGP-FDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP  156 (179)
T ss_pred             eccCCCEEEEEEEEEEeeEEEEEeCC-ceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC
Confidence            45689999999999999999999975 9999999998754321 111         123789999999999998     5


Q ss_pred             CCCeEEEEeeehh
Q 015066          161 ADDSLVLSLRMIQ  173 (414)
Q Consensus       161 ~~~~i~LS~k~~~  173 (414)
                      +..++.+|+|..-
T Consensus       157 ~~~~I~lt~k~~~  169 (179)
T TIGR00448       157 EGSKIGLTMRQPL  169 (179)
T ss_pred             CcceEEEEeccCc
Confidence            5678999998754

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

>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=97.89  E-value=5.4e-05  Score=58.30  Aligned_cols=63  Identities=17%  Similarity=0.375  Sum_probs=51.9

Q ss_pred             CeEEEEEEEEEecCcEEEEEC--CEEEEEeccccCCCCc--c---cc-ccCCeE-EEEEEEeecccceEEeehh
Q 015066          188 DVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKST--A---EE-LLGKDL-PLKFVEVDEEQSRLVLSNR  252 (414)
Q Consensus       188 g~iv~G~V~~v~~~G~~V~i~--gi~GfIp~sels~~~~--~---~~-~vGq~V-~vkVl~vD~e~~ri~LS~K  252 (414)
                      |++++|+|...++.+++|+++  |++||+|..|+++...  .   .. .+||++ ++-|+  |...+.+.+|.|
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 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCL--SNYKGRIILTKK   72 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEE--eccccEEEEecC
Confidence            468999999999999999995  8999999999998421  1   11 279999 88888  877888888865

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

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.87  E-value=0.00018  Score=72.33  Aligned_cols=76  Identities=25%  Similarity=0.316  Sum_probs=61.6

Q ss_pred             HHHhhcccCCCCCEEEEEEEEEeC-CeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCC---e
Q 015066           89 ALEKYDFNSELGTKVKGTVFCTDN-RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD---S  164 (414)
Q Consensus        89 ~l~~~~~~l~~G~iV~G~V~~v~~-~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~---~  164 (414)
                      .+++|  .-+.|++|+|+|.+++. ++++|++| +.+|+||.+|..      +.+. |.+|+.++|+|..++...+   +
T Consensus       130 i~~ey--~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eqi------p~E~-~~~Gdrik~~i~~V~~~~k~gp~  199 (374)
T PRK12328        130 IFEKY--KKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNRI------KGEK-FKVGDVVKAVLKRVKIDKNNGIL  199 (374)
T ss_pred             HHHHH--HHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHcC------CCCc-CCCCCEEEEEEEEEecCCCCCCE
Confidence            34444  45799999999999997 56999998 599999999874      3344 8999999999999987655   7


Q ss_pred             EEEEeeehhh
Q 015066          165 LVLSLRMIQY  174 (414)
Q Consensus       165 i~LS~k~~~~  174 (414)
                      +.||+.....
T Consensus       200 IilSRt~p~~  209 (374)
T PRK12328        200 IELSRTSPKF  209 (374)
T ss_pred             EEEEcCCHHH
Confidence            8899876654

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

Probab=97.83  E-value=8.2e-05  Score=67.26  Aligned_cols=87  Identities=24%  Similarity=0.351  Sum_probs=69.8

Q ss_pred             cceEEeehhhhhhhHHhhccccEEEEEEEEEEeeceEEEEECC-----------EEEEEeecccCcccccCcccccCCCC
Q 015066          244 QSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGG-----------INGLLHVSQISHDRVADIATVLQPGD  312 (414)
Q Consensus       244 ~~ri~LS~K~~l~~~~~~l~~G~iv~g~V~~i~~~G~fV~l~g-----------v~Glvh~sels~~~~~~~~~~~~~G~  312 (414)
                      .++...|.+.... ...-++.|++|-|.|+++....+.|++-+           ..|-+|+|+++...+++.++.|++||
T Consensus        45 ~~n~~~~V~p~~~-~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GD  123 (188)
T COG1096          45 DKNRVISVKPGKK-TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGD  123 (188)
T ss_pred             ccceEEEeccCCC-CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEeccccccccccccccccc
Confidence            3444445443322 33568899999999999999999999842           56789999999999999999999999


Q ss_pred             EEEEEEEEEeCCCCeEEEEEee
Q 015066          313 TLKVMILSHDRERGRVSLSTKK  334 (414)
Q Consensus       313 ~V~vkVl~id~e~~ri~LS~K~  334 (414)
                      .|+|+|++.-   ..+.||++.
T Consensus       124 ivrA~Vis~~---~~~~Lst~~  142 (188)
T COG1096         124 IVRARVISTG---DPIQLSTKG  142 (188)
T ss_pred             EEEEEEEecC---CCeEEEecC
Confidence            9999999984   567788774

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.80  E-value=4.6e-05  Score=78.28  Aligned_cols=62  Identities=32%  Similarity=0.580  Sum_probs=53.2

Q ss_pred             hhccccEEEEEEEEEEeec--eEEEEEC-CEEEEEeecccCcc------------cccCcccccCCCCEEEEEEEEE
Q 015066          260 AQLGIGSVVIGTVQSLKPY--GAFIDIG-GINGLLHVSQISHD------------RVADIATVLQPGDTLKVMILSH  321 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~--G~fV~l~-gv~Glvh~sels~~------------~~~~~~~~~~~G~~V~vkVl~i  321 (414)
                      ....+|++|.|+|.++.++  ||||+++ +-.||+|++++.+.            +..++.+.+++||.|.|.|.+-
T Consensus        21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke   97 (414)
T TIGR00757        21 SRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKE   97 (414)
T ss_pred             CcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeC
Confidence            3456899999999999999  9999999 79999999998653            2345667899999999999983

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.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=97.80  E-value=0.00011  Score=55.12  Aligned_cols=61  Identities=18%  Similarity=0.192  Sum_probs=37.8

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        99 ~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      .|++.+.+|.+.++.|+|++.+...+-+||.+|+..       .  +.+|+.+++.|+.  +.++++..|++
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~-------~--~~~Gd~v~VFvY~--D~~~rl~AT~k   61 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPE-------P--LKVGDEVEVFVYL--DKEGRLVATTK   61 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG---------------TTSEEEEEEEE---TTS-EEEE--
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCC-------C--CCCCCEEEEEEEE--CCCCCEEEecC
Confidence            489999999999999999999888999999998842       1  6899999999976  46778888864

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

Probab=97.80  E-value=7.1e-05  Score=67.63  Aligned_cols=85  Identities=21%  Similarity=0.237  Sum_probs=65.1

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC----------CccccCccCCcEEEEEEEEEeCCC--
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK----------HVEEAGIVPGLKEEFVIIGENEAD--  162 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~----------~~~e~~~~vG~~v~v~Vl~id~~~--  162 (414)
                      +....|++|.|.|+++.+.|+||.+|. .+||+|.+++.+.+..          .-+...+.+|+.|+++|+..+...  
T Consensus        77 fkP~~gEVV~GeVv~~~~~G~fV~igp-~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~  155 (183)
T COG1095          77 FKPFRGEVVEGEVVEVVEFGAFVRIGP-LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR  155 (183)
T ss_pred             EEeccccEEEEEEEEEeecceEEEecc-ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCc
Confidence            356789999999999999999999996 8999999999877322          111222778999999999886544  


Q ss_pred             ---CeEEEEeeehhh-hHHHHH
Q 015066          163 ---DSLVLSLRMIQY-ELAWER  180 (414)
Q Consensus       163 ---~~i~LS~k~~~~-~~~~~~  180 (414)
                         .++.+|+|+.-. ...|-.
T Consensus       156 ~~~~~I~lTmrq~~LGklew~~  177 (183)
T COG1095         156 PRESKIGLTMRQPGLGKLEWIE  177 (183)
T ss_pred             cccceEEEEeccccCCcchhhh
Confidence               578889887643 344643

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=97.72  E-value=0.00013  Score=57.28  Aligned_cols=70  Identities=7%  Similarity=0.098  Sum_probs=61.7

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEe-CCCeeEEEc-CccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066           97 SELGTKVKGTVFCTDNRGALVDI-TAKSSAYLP-TQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdi-g~k~~g~lp-~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      .++|+.+. .|+.+.+.|+||.+ ..+.+|+|. .+|++-.++++..+. + +|..+.++|+++|..+|.+-||.
T Consensus        14 P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kl-l-VGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         14 PNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKK-L-VGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             CCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhh-h-cCCeeEEEEEEECCCCCEEEeEc
Confidence            47899998 89999999999998 345899888 999998888888776 5 99999999999999999999884

>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=97.69  E-value=9.1e-05  Score=58.81  Aligned_cols=60  Identities=20%  Similarity=0.430  Sum_probs=41.8

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-------------------CEEEEEeecccCccccc--CcccccCCCCEEEEEEEE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-------------------GINGLLHVSQISHDRVA--DIATVLQPGDTLKVMILS  320 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-------------------gv~Glvh~sels~~~~~--~~~~~~~~G~~V~vkVl~  320 (414)
                      +++|++|.|+|+++++.-+++++-                   ...|++|.+++......  .+.+.|++||.|+|+|++
T Consensus         2 P~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViS   81 (82)
T PF10447_consen    2 PKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVIS   81 (82)
T ss_dssp             --TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEE
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEee
Confidence            468999999999999988888762                   26899999998765444  368889999999999998


Q ss_pred             E
Q 015066          321 H  321 (414)
Q Consensus       321 i  321 (414)
                      +
T Consensus        82 l   82 (82)
T PF10447_consen   82 L   82 (82)
T ss_dssp             E
T ss_pred             C
Confidence            5

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.

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

Probab=97.66  E-value=0.00028  Score=76.85  Aligned_cols=73  Identities=14%  Similarity=0.158  Sum_probs=60.6

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC-CCeeEEEcCcccccccc-----------CCccccCccCCcEEEEEEEEEeCCCC
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEACIHKI-----------KHVEEAGIVPGLKEEFVIIGENEADD  163 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig-~k~~g~lp~sEls~~~~-----------~~~~e~~~~vG~~v~v~Vl~id~~~~  163 (414)
                      .-+.|+.++|+|+++.++|+||.+. .+.+|++|.+++.+.+.           ++.... +++|++|+++|+++|..++
T Consensus       569 ~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~-~~lGD~V~Vki~~vd~~~~  647 (654)
T TIGR00358       569 LDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKV-YRIGDRVTVKLTEVNMETR  647 (654)
T ss_pred             hhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcE-ECCCCEEEEEEEEEecccC
Confidence            3467999999999999999999997 67999999999976431           111122 8899999999999999999


Q ss_pred             eEEEEe
Q 015066          164 SLVLSL  169 (414)
Q Consensus       164 ~i~LS~  169 (414)
                      ++.+++
T Consensus       648 ~I~f~l  653 (654)
T TIGR00358       648 SIIFEL  653 (654)
T ss_pred             eEEEEE
Confidence            998875

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.

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

Probab=97.59  E-value=0.0004  Score=63.79  Aligned_cols=77  Identities=21%  Similarity=0.206  Sum_probs=61.3

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC-----------CccccCccCCcEEEEEEEEEeCCCC
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADD  163 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~-----------~~~e~~~~vG~~v~v~Vl~id~~~~  163 (414)
                      +....|+++.|+|+++++.|++|+++. .+|+++.+++...+..           +.... +.+|+.++++|++++...+
T Consensus        77 f~P~~GEVv~g~V~~v~~~Gi~V~lg~-~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~-i~~Gd~VrvrV~~v~~~~~  154 (187)
T PRK08563         77 FKPELQEVVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYISYDPKNGRLIGKESKRV-LKVGDVVRARIVAVSLKER  154 (187)
T ss_pred             EeccCCCEEEEEEEEEEccEEEEEEeC-ceEEEEcHHcCCCceEEccccceEEEccCCeE-EcCCCEEEEEEEEEEcccC
Confidence            356789999999999999999999985 9999999998754321           11222 7889999999999986543


Q ss_pred             -----eEEEEeeehh
Q 015066          164 -----SLVLSLRMIQ  173 (414)
Q Consensus       164 -----~i~LS~k~~~  173 (414)
                           .+.+|++..-
T Consensus       155 ~~~~~~I~ls~~~~~  169 (187)
T PRK08563        155 RPRGSKIGLTMRQPG  169 (187)
T ss_pred             CCCCCEEEEEecCCC
Confidence                 7888998653

>PRK11642 exoribonuclease R; Provisional

Probab=97.57  E-value=0.00045  Score=76.79  Aligned_cols=72  Identities=14%  Similarity=0.127  Sum_probs=60.8

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCC-eeEEEcCccccccccC-----------CccccCccCCcEEEEEEEEEeCCCCeE
Q 015066           98 ELGTKVKGTVFCTDNRGALVDITAK-SSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADDSL  165 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G~~Vdig~k-~~g~lp~sEls~~~~~-----------~~~e~~~~vG~~v~v~Vl~id~~~~~i  165 (414)
                      ++|++++|+|++++++|+||.+... .+|++|.+++.+.+..           .... .|.+|+.|+|+|+.+|..++++
T Consensus       642 ~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~-~~~lGD~V~VkV~~vD~~~rkI  720 (813)
T PRK11642        642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQ-TYRLGDRVEVRVEAVNMDERKI  720 (813)
T ss_pred             cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCc-EECCCCEEEEEEEEeecCCCeE
Confidence            7899999999999999999999764 9999999999764211           1112 2889999999999999999999


Q ss_pred             EEEee
Q 015066          166 VLSLR  170 (414)
Q Consensus       166 ~LS~k  170 (414)
                      .+++-
T Consensus       721 ~f~l~  725 (813)
T PRK11642        721 DFSLI  725 (813)
T ss_pred             EEEEe
Confidence            99985

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

Probab=97.55  E-value=0.00039  Score=63.38  Aligned_cols=74  Identities=14%  Similarity=0.132  Sum_probs=57.7

Q ss_pred             ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcc-cc-----------cCcccccCCCCEEEEEEEEEeCCC--Ce
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHD-RV-----------ADIATVLQPGDTLKVMILSHDRER--GR  327 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~-~~-----------~~~~~~~~~G~~V~vkVl~id~e~--~r  327 (414)
                      +-.|+++.|.|+++.++|+||+++-+++++|.++|... .+           .+-...++.|+.|++||.++..+.  .+
T Consensus        79 Pf~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~  158 (176)
T PTZ00162         79 PFKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLF  158 (176)
T ss_pred             cCCCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcE
Confidence            55799999999999999999999878899999999643 11           112346899999999998876443  34


Q ss_pred             EEEEEeeC
Q 015066          328 VSLSTKKL  335 (414)
Q Consensus       328 i~LS~K~~  335 (414)
                      +..|||+-
T Consensus       159 ~i~T~~~~  166 (176)
T PTZ00162        159 AIATINSD  166 (176)
T ss_pred             EEEEecCC
Confidence            66677753

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=97.44  E-value=0.00038  Score=76.59  Aligned_cols=73  Identities=25%  Similarity=0.506  Sum_probs=62.3

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCcccc-----------cCcccccCCCCEEEEEEEEEeCCCCe
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVMILSHDRERGR  327 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~-----------~~~~~~~~~G~~V~vkVl~id~e~~r  327 (414)
                      .-.+|+.+.|+|+++..||+||.+.  +++|++|++.+..+++           ......|+.||.|+|+|.+++...++
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            4568999999999999999999997  5899999999985422           23345799999999999999999999


Q ss_pred             EEEEEe
Q 015066          328 VSLSTK  333 (414)
Q Consensus       328 i~LS~K  333 (414)
                      +.+++-
T Consensus       699 i~~~~v  704 (706)
T COG0557         699 IDFELV  704 (706)
T ss_pred             eEEEec
Confidence            988763

>TIGR02062 RNase_B exoribonuclease II

Probab=97.44  E-value=0.00034  Score=75.95  Aligned_cols=67  Identities=13%  Similarity=0.225  Sum_probs=55.3

Q ss_pred             cEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCc--ccc-----c---Cc--ccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISH--DRV-----A---DI--ATVLQPGDTLKVMILSHDRERGRVSL  330 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~--~~~-----~---~~--~~~~~~G~~V~vkVl~id~e~~ri~L  330 (414)
                      |+.+.|.|+.+.++|+||++.  |++|+||.+.+..  +.+     .   .+  ...|+.||.|+|+|.++|.++++|.+
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            458999999999999999995  7999999999865  211     1   11  12699999999999999999999876


Q ss_pred             E
Q 015066          331 S  331 (414)
Q Consensus       331 S  331 (414)
                      .
T Consensus       638 ~  638 (639)
T TIGR02062       638 R  638 (639)
T ss_pred             e
Confidence            4

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.

>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=0.00053  Score=64.58  Aligned_cols=76  Identities=30%  Similarity=0.465  Sum_probs=66.6

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEECC-EEEEEeecccCcccc----cCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRV----ADIATVLQPGDTLKVMILSHDRERGRVSLSTKK  334 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~g-v~Glvh~sels~~~~----~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~  334 (414)
                      -.+++||+|-|.|..+...+-.|++++ ..+++|.|++-+..+    .+.+..|++||.|.|+|..+|+ .+...|++|+
T Consensus        60 YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~-~~~~~L~~k~  138 (239)
T COG1097          60 YIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDR-DGEVELTLKD  138 (239)
T ss_pred             ccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccC-CCceEEEeec
Confidence            457899999999999999999999995 999999999966543    4678889999999999999996 7889999976


Q ss_pred             CC
Q 015066          335 LE  336 (414)
Q Consensus       335 ~~  336 (414)
                      .-
T Consensus       139 ~~  140 (239)
T COG1097         139 EG  140 (239)
T ss_pred             CC
Confidence            43

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=97.38  E-value=0.0015  Score=66.88  Aligned_cols=72  Identities=13%  Similarity=0.132  Sum_probs=58.9

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC---C--CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC---CeEEE
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDIT---A--KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD---DSLVL  167 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig---~--k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~---~~i~L  167 (414)
                      .-+.|++|+|+|.+++.++++|+++   +  +.+|+||.+|..      +.+. |++|+.++|+|.+++...   -++.|
T Consensus       149 ~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~-y~~Gdrika~i~~V~~~~~kGpqIil  221 (449)
T PRK12329        149 QDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDN-YRANATFKVFLKEVSEGPRRGPQLFV  221 (449)
T ss_pred             HHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCc-CCCCCEEEEEEEEeecCCCCCCEEEE
Confidence            4579999999999999999999993   3  489999998874      3344 899999999999997652   26899


Q ss_pred             Eeeehhh
Q 015066          168 SLRMIQY  174 (414)
Q Consensus       168 S~k~~~~  174 (414)
                      |+.....
T Consensus       222 SRt~p~l  228 (449)
T PRK12329        222 SRANAGL  228 (449)
T ss_pred             EcCCHHH
Confidence            9876554

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

Probab=97.35  E-value=0.00015  Score=75.40  Aligned_cols=72  Identities=22%  Similarity=0.475  Sum_probs=64.0

Q ss_pred             HhhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          259 QAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       259 ~~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      ..+++.|.+|.|+|+++..||+||+++ -+.||+|.++++..      ..|.+|+.+-|.|..+.++++.|++....++
T Consensus       117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~  189 (715)
T COG1107         117 MEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLD  189 (715)
T ss_pred             hhhcccceeeeccccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCc
Confidence            467999999999999999999999999 79999999998763      2578999999999999998898888777665

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

Probab=97.35  E-value=0.0012  Score=52.92  Aligned_cols=72  Identities=21%  Similarity=0.140  Sum_probs=59.8

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      +++||+|-|+|+.+...+.+|+|+ -..|++|.+.+... ..+.+..|++||.|-|+|.++|++ ....||+.+.
T Consensus         4 P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~-~~~eLtc~~~   76 (86)
T cd05790           4 PAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRD-MEPELSCVDS   76 (86)
T ss_pred             CCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEEEecCCC-CCeEEEEeCC
Confidence            578999999999999999999998 48999999887433 233456799999999999999974 5688888763

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".

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

Probab=97.29  E-value=0.002  Score=51.98  Aligned_cols=62  Identities=16%  Similarity=0.158  Sum_probs=45.9

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCc----------cccCccCCcEEEEEEEEEeCC
Q 015066           99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV----------EEAGIVPGLKEEFVIIGENEA  161 (414)
Q Consensus        99 ~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~----------~e~~~~vG~~v~v~Vl~id~~  161 (414)
                      .|+++.|+|.++++.|+||.+|. .++|++...+..+...++          .+..+..|+.|+|+|+.+..+
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gp-l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~   72 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGP-LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVD   72 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcC-ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEc
Confidence            48999999999999999999986 778887777754432222          122256788888888877544

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.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.28  E-value=0.0006  Score=70.15  Aligned_cols=62  Identities=21%  Similarity=0.234  Sum_probs=50.4

Q ss_pred             cCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEcCcccccc------------ccCCccccCccCCcEEEEEEEEE
Q 015066           96 NSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACIH------------KIKHVEEAGIVPGLKEEFVIIGE  158 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~--G~~Vdig~k~~g~lp~sEls~~------------~~~~~~e~~~~vG~~v~v~Vl~i  158 (414)
                      ...+|+++.|+|.++.++  ||||+||.+..||+|.+++...            ...+..+. +++|+.+-|.|...
T Consensus        22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~-l~~G~~IlVQV~Ke   97 (414)
T TIGR00757        22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISEL-LRPGQSVLVQVVKE   97 (414)
T ss_pred             cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHh-CcCCCEEEEEEeeC
Confidence            456899999999999997  9999999999999999998542            11223334 78899999999874

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.

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

Probab=97.27  E-value=0.00079  Score=74.80  Aligned_cols=117  Identities=16%  Similarity=0.084  Sum_probs=90.1

Q ss_pred             HHHHHHHHHHHhhcccCCCCCCCCCHHHHHHHHHhhc-ccCCCCCEEEEEEEEEeCCe---EEEEeCCCeeEEEcCcccc
Q 015066           58 EELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYD-FNSELGTKVKGTVFCTDNRG---ALVDITAKSSAYLPTQEAC  133 (414)
Q Consensus        58 ~~l~~iiee~~~~~~~~~~~~~~~~~~~f~~~l~~~~-~~l~~G~iV~G~V~~v~~~G---~~Vdig~k~~g~lp~sEls  133 (414)
                      ..|.+|..|+...-.+-+......+.++.=.++..-. ..+..|.+|.++|.+++..-   +-|.+..+.+||||..+++
T Consensus       943 ~tl~dI~~ELsdgykd~R~~f~~l~~eeiF~mLTget~et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~S 1022 (1299)
T KOG1856|consen  943 NTLYDIRLELSDGYKDLRNPFHELTGEEIFDMLTGETPETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLS 1022 (1299)
T ss_pred             chHHHHHHHhhcchhhhccccCCCCHHHHHHHHhCCChhHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccC
Confidence            4566666666555545455444566665555665444 35899999999999998855   5568888899999999999


Q ss_pred             ccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhh
Q 015066          134 IHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE  175 (414)
Q Consensus       134 ~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~  175 (414)
                      +..+.+|.+. +++|+.+.|+|++++.+.=.+.||++.+...
T Consensus      1023 d~~v~~p~~~-v~vgq~v~~kvi~id~e~f~v~Ls~r~sdlk 1063 (1299)
T KOG1856|consen 1023 DRDVRRPENR-VKVGQTVYCKVIKIDKERFSVELSCRTSDLK 1063 (1299)
T ss_pred             hhhccCHHHh-hccCceEEEEeeeeeHhhhhhhhhhhhHHhh
Confidence            9888888887 8899999999999997766788899887653

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.24  E-value=0.0018  Score=65.16  Aligned_cols=67  Identities=16%  Similarity=0.244  Sum_probs=55.4

Q ss_pred             cCCeEEEEEEEEEec-CcEEEEECCEEEEEeccccCCCCccccccCCeEEEEEEEeecccc---eEEeehhhh
Q 015066          186 SEDVVVKGKVVGANK-GGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQS---RLVLSNRKA  254 (414)
Q Consensus       186 ~~g~iv~G~V~~v~~-~G~~V~i~gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~---ri~LS~K~~  254 (414)
                      ..|++++|+|.++.. ++++|++|+..|+||.++......  ...|+.++|.|.+|+...+   .+.||+...
T Consensus       137 ~~Geiv~g~V~r~~~~~~i~vdlg~~ea~LP~~eqip~E~--~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p  207 (374)
T PRK12328        137 KVGKIVFGTVVRVDNEENTFIEIDEIRAVLPMKNRIKGEK--FKVGDVVKAVLKRVKIDKNNGILIELSRTSP  207 (374)
T ss_pred             hcCcEEEEEEEEEecCCCEEEEcCCeEEEeCHHHcCCCCc--CCCCCEEEEEEEEEecCCCCCCEEEEEcCCH
Confidence            358899999999986 569999999999999998774422  2279999999999998766   689998754

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

Probab=97.23  E-value=0.0025  Score=51.07  Aligned_cols=73  Identities=19%  Similarity=0.005  Sum_probs=58.5

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~  171 (414)
                      ..++||.|-|+|+.+...++.|||+....|++|..++... .+..... +.+|+.|-++|..+++. ....||+..
T Consensus         3 ~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~-L~~GDlV~ArV~~~~~~-~~~eLtc~~   75 (86)
T cd05790           3 VPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPN-LNVGDLVYARVVKANRD-MEPELSCVD   75 (86)
T ss_pred             cCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-ccccccc-CCCCCEEEEEEEecCCC-CCeEEEEeC
Confidence            4689999999999999999999999988999999876432 2222222 88999999999998754 557888764

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".

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=97.11  E-value=0.0023  Score=47.89  Aligned_cols=59  Identities=27%  Similarity=0.411  Sum_probs=35.5

Q ss_pred             CeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehh
Q 015066          188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNR  252 (414)
Q Consensus       188 g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K  252 (414)
                      |++.+.+|+..++.|+|++.+ +-+.|||.+++.....    +|++|.| ++..|.+ +|+..|++
T Consensus         2 G~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~~~----~Gd~v~V-FvY~D~~-~rl~AT~k   61 (61)
T PF13509_consen    2 GQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEPLK----VGDEVEV-FVYLDKE-GRLVATTK   61 (61)
T ss_dssp             -------EEEE-SSEEEEEETT-EEEEEEGGG----------TTSEEEE-EEEE-TT-S-EEEE--
T ss_pred             CCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCCCC----CCCEEEE-EEEECCC-CCEEEecC
Confidence            568889999999999999998 5999999999874432    8999999 5688864 57777754

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

Probab=97.11  E-value=0.00046  Score=76.58  Aligned_cols=77  Identities=21%  Similarity=0.307  Sum_probs=67.9

Q ss_pred             hhccccEEEEEEEEEEeece---EEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          260 AQLGIGSVVIGTVQSLKPYG---AFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G---~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      +.+.+|.+|.++|++++..-   +-|.+. |+.|+||.+++|+..+.+|...+++||+|.|||+++|.++=-+.||.|..
T Consensus       981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~s 1060 (1299)
T KOG1856|consen  981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred             hHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence            46889999999999998643   346677 99999999999999999999999999999999999998887888898876


Q ss_pred             C
Q 015066          336 E  336 (414)
Q Consensus       336 ~  336 (414)
                      +
T Consensus      1061 d 1061 (1299)
T KOG1856|consen 1061 D 1061 (1299)
T ss_pred             H
Confidence            4

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

Probab=97.07  E-value=0.0006  Score=64.55  Aligned_cols=77  Identities=19%  Similarity=0.227  Sum_probs=70.8

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEe--CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066           97 SELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdi--g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      .+++++|-+.|.++..-|+||.+  .++.+|++-.+|||-.+++++... .++|..--|.|+.+|.++|.+-||.++...
T Consensus        14 Pev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~kl-irVGr~E~vvVlrVDkekGYIDLSkrrVs~   92 (304)
T KOG2916|consen   14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKL-IRVGRNEPVVVLRVDKEKGYIDLSKRRVSP   92 (304)
T ss_pred             CCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHH-HhcCCcceEEEEEEcCCCCceechhccCCH
Confidence            57899999999999999999998  567999999999999999888887 899999999999999999999999998754

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

Probab=97.06  E-value=0.0023  Score=58.38  Aligned_cols=68  Identities=21%  Similarity=0.264  Sum_probs=50.1

Q ss_pred             CCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--Ccc----c-------cc---cCCeEEEEEEEeeccc--ceEE
Q 015066          187 EDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STA----E-------EL---LGKDLPLKFVEVDEEQ--SRLV  248 (414)
Q Consensus       187 ~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~----~-------~~---vGq~V~vkVl~vD~e~--~ri~  248 (414)
                      .|+++.|.|+++++.|+||.+|-+++|||.+++.+.  ++.    .       ..   .|+.|++||+.+..+.  -.+.
T Consensus        81 ~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~i  160 (176)
T PTZ00162         81 KDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAI  160 (176)
T ss_pred             CCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEEE
Confidence            468999999999999999999989999999999843  111    0       11   4888888887765433  3355


Q ss_pred             eehhhh
Q 015066          249 LSNRKA  254 (414)
Q Consensus       249 LS~K~~  254 (414)
                      .|+|+.
T Consensus       161 ~T~~~~  166 (176)
T PTZ00162        161 ATINSD  166 (176)
T ss_pred             EEecCC
Confidence            566543

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

Probab=96.84  E-value=0.0065  Score=57.32  Aligned_cols=74  Identities=22%  Similarity=0.253  Sum_probs=61.1

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc----CCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI----KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~----~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      |..++||.|-|.|+.+...++.|||++...|++|.+++.....    .+.... +.+||.+-++|..+| .++.+.|++|
T Consensus        60 YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~-l~vGD~v~AkV~~vd-~~~~~~L~~k  137 (239)
T COG1097          60 YIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPF-LNVGDLVYAKVVDVD-RDGEVELTLK  137 (239)
T ss_pred             ccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccc-cccCCEEEEEEEEcc-CCCceEEEee
Confidence            4678999999999999999999999999999999999833221    233333 789999999999998 5677888884

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

Probab=96.78  E-value=0.0092  Score=62.53  Aligned_cols=149  Identities=14%  Similarity=0.157  Sum_probs=102.7

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      ++++.|....|+|.++.+.|+||+++..+.|+++.++++..       ..+.+|+++-+.+..+.+.++.+-+....+..
T Consensus       118 ~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~-------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~~  190 (715)
T COG1107         118 EDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD-------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLDR  190 (715)
T ss_pred             hhcccceeeeccccchhhhcceeecChhhhccccccccCCC-------CCCCCCCeEEEEeeccCCCCCccceeecCCcc
Confidence            47899999999999999999999999999999999998741       12789999999999998887876665544431


Q ss_pred             ------hH-----HHHHhhhcccCCeEEEEEEEEEe-cCc-EEEEECCEEEEEeccccCCC---CccccccCCeEEEEEE
Q 015066          175 ------EL-----AWERCRQLQSEDVVVKGKVVGAN-KGG-VVAEVEGLRGFVPFSQISSK---STAEELLGKDLPLKFV  238 (414)
Q Consensus       175 ------~~-----~~~~l~~~~~~g~iv~G~V~~v~-~~G-~~V~i~gi~GfIp~sels~~---~~~~~~vGq~V~vkVl  238 (414)
                            ++     ....+.+..-.-..++|.|+.+. ..| -+..+-.=.|+++..-+...   ..|.-.+|+.|.+ +=
T Consensus       191 Y~~~~~~ke~~r~~i~~id~~ig~tV~I~GeV~qikqT~GPTVFtltDetg~i~aAAFe~aGvRAyP~IevGdiV~V-iG  269 (715)
T COG1107         191 YREVQVEKELPRTLIDDLDEMIGKTVRIEGEVTQIKQTSGPTVFTLTDETGAIWAAAFEEAGVRAYPEIEVGDIVEV-IG  269 (715)
T ss_pred             chhhhhhhhcccccHHHHHhhcCceEEEEEEEEEEEEcCCCEEEEEecCCCceehhhhccCCcccCCCCCCCceEEE-EE
Confidence                  11     12223332212236789999983 334 33455555677776655532   2344458999887 45


Q ss_pred             EeecccceEEeeh
Q 015066          239 EVDEEQSRLVLSN  251 (414)
Q Consensus       239 ~vD~e~~ri~LS~  251 (414)
                      .++...+++.+-.
T Consensus       270 ~V~~r~g~lQiE~  282 (715)
T COG1107         270 EVTRRDGRLQIEI  282 (715)
T ss_pred             EEeecCCcEEEee
Confidence            6676777776543

>PRK10811 rne ribonuclease E; Reviewed

Probab=96.64  E-value=0.0042  Score=68.73  Aligned_cols=65  Identities=25%  Similarity=0.456  Sum_probs=52.1

Q ss_pred             ccccEEEEEEEEEEee--ceEEEEEC-CEEEEEeecccCccccc---------CcccccCCCCEEEEEEEEEeCCCC
Q 015066          262 LGIGSVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISHDRVA---------DIATVLQPGDTLKVMILSHDRERG  326 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~--~G~fV~l~-gv~Glvh~sels~~~~~---------~~~~~~~~G~~V~vkVl~id~e~~  326 (414)
                      -.+|.||.|+|.+|.+  .++||+|+ |..||+|++++....+.         +..+.++.||.|-|.|.+-...++
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtK  112 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNK  112 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCCC
Confidence            3589999999999997  58999999 89999999998643322         235579999999999998654333

>PRK05054 exoribonuclease II; Provisional

Probab=96.48  E-value=0.014  Score=63.52  Aligned_cols=63  Identities=19%  Similarity=0.341  Sum_probs=52.2

Q ss_pred             CeEEEEEEEEEecCcEEEEEC--CEEEEEeccccCCC---C----c--------c-ccccCCeEEEEEEEeecccceEEe
Q 015066          188 DVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSK---S----T--------A-EELLGKDLPLKFVEVDEEQSRLVL  249 (414)
Q Consensus       188 g~iv~G~V~~v~~~G~~V~i~--gi~GfIp~sels~~---~----~--------~-~~~vGq~V~vkVl~vD~e~~ri~L  249 (414)
                      |+.+.|.|++++.+|+||.+.  ++.||||.+.+.+.   +    +        . ...+||.|+|+|.++|.++++|.+
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            469999999999999999995  89999999998642   1    1        0 112799999999999999998876


Q ss_pred             e
Q 015066          250 S  250 (414)
Q Consensus       250 S  250 (414)
                      +
T Consensus       642 ~  642 (644)
T PRK05054        642 R  642 (644)
T ss_pred             E
Confidence            5

>PRK11712 ribonuclease G; Provisional

Probab=96.40  E-value=0.0075  Score=63.31  Aligned_cols=63  Identities=29%  Similarity=0.496  Sum_probs=50.5

Q ss_pred             hhccccEEEEEEEEEEee--ceEEEEEC-CEEEEEeecccCcc------------cccCcccccCCCCEEEEEEEEEe
Q 015066          260 AQLGIGSVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISHD------------RVADIATVLQPGDTLKVMILSHD  322 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~--~G~fV~l~-gv~Glvh~sels~~------------~~~~~~~~~~~G~~V~vkVl~id  322 (414)
                      ....+|.||.|+|.+|.|  .+|||+++ +-.||+|.+++...            ...++.+.++.||.|-|.|.+--
T Consensus        34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~  111 (489)
T PRK11712         34 KRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDP  111 (489)
T ss_pred             cccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCC
Confidence            345689999999999998  48999999 89999999987321            11234566999999999999853

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.33  E-value=0.025  Score=58.10  Aligned_cols=67  Identities=19%  Similarity=0.245  Sum_probs=53.9

Q ss_pred             cCCeEEEEEEEEEecCcEEEEE----C--CEEEEEeccccCCCCccccccCCeEEEEEEEeeccc---ceEEeehhhh
Q 015066          186 SEDVVVKGKVVGANKGGVVAEV----E--GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQ---SRLVLSNRKA  254 (414)
Q Consensus       186 ~~g~iv~G~V~~v~~~G~~V~i----~--gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~---~ri~LS~K~~  254 (414)
                      ..|++++|+|.++.+++++|++    |  ++.|+||.++......  ...|+.++|.|.+|+...   -.|.||+...
T Consensus       151 ~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~E~--y~~Gdrika~i~~V~~~~~kGpqIilSRt~p  226 (449)
T PRK12329        151 LEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPNDN--YRANATFKVFLKEVSEGPRRGPQLFVSRANA  226 (449)
T ss_pred             hcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCCCc--CCCCCEEEEEEEEeecCCCCCCEEEEEcCCH
Confidence            3588999999999999999998    4  3999999998764422  127999999999998763   2589998654

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

Probab=96.21  E-value=0.02  Score=45.52  Aligned_cols=60  Identities=18%  Similarity=0.176  Sum_probs=38.4

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeC------------------CCeeEEEcCccccccccCC--ccccCccCCcEEEEEEEE
Q 015066           98 ELGTKVKGTVFCTDNRGALVDIT------------------AKSSAYLPTQEACIHKIKH--VEEAGIVPGLKEEFVIIG  157 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G~~Vdig------------------~k~~g~lp~sEls~~~~~~--~~e~~~~vG~~v~v~Vl~  157 (414)
                      ++|++|.|+|+++....++++|-                  ....|.|+.+++.......  +.+- |++||.|.++|++
T Consensus         3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~-FrpGDIVrA~ViS   81 (82)
T PF10447_consen    3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDC-FRPGDIVRARVIS   81 (82)
T ss_dssp             -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT---SSSEEEEEEEE
T ss_pred             CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhc-cCCCCEEEEEEee
Confidence            68999999999999999988872                  1246788888776544333  2333 8999999999987


Q ss_pred             E
Q 015066          158 E  158 (414)
Q Consensus       158 i  158 (414)
                      +
T Consensus        82 l   82 (82)
T PF10447_consen   82 L   82 (82)
T ss_dssp             E
T ss_pred             C
Confidence            4

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.

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

Probab=96.20  E-value=0.029  Score=45.96  Aligned_cols=67  Identities=21%  Similarity=0.227  Sum_probs=51.8

Q ss_pred             HHHHHHHHhhcc---cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEE
Q 015066           84 EEFHSALEKYDF---NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE  158 (414)
Q Consensus        84 ~~f~~~l~~~~~---~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~i  158 (414)
                      +.|++++...-.   --..|.+|.|+|..+..+-+|+|+|+|-.++|+..+...       +. +..|.+|.+++...
T Consensus         5 ~sFaslLR~S~fi~lG~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~-------~~-y~~G~rV~lrLkdl   74 (104)
T PF10246_consen    5 ESFASLLRNSPFIQLGDPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNG-------EK-YVRGSRVRLRLKDL   74 (104)
T ss_pred             ccHHHHhcCChhhhcCCccCCEEEEEEEEEecCceEEEeCCceeEEEecccccc-------cc-cccCCEEEEEECCH
Confidence            568887754331   225899999999999999999999999999999765421       22 77899998888554

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 [].

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

Probab=95.93  E-value=0.034  Score=50.57  Aligned_cols=72  Identities=21%  Similarity=0.170  Sum_probs=60.9

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCC----------CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeE
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITA----------KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL  165 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~----------k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i  165 (414)
                      -++.|++|-|.|+++....+.|.+-+          -..|-+|.++....+.++.++. |.+||.++++|++.-   ..+
T Consensus        61 ~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~-f~~GDivrA~Vis~~---~~~  136 (188)
T COG1096          61 LPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDA-FRIGDIVRARVISTG---DPI  136 (188)
T ss_pred             CCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccc-cccccEEEEEEEecC---CCe
Confidence            46889999999999999999988721          1467899999999888888887 999999999999964   568


Q ss_pred             EEEeee
Q 015066          166 VLSLRM  171 (414)
Q Consensus       166 ~LS~k~  171 (414)
                      .||.+.
T Consensus       137 ~Lst~~  142 (188)
T COG1096         137 QLSTKG  142 (188)
T ss_pred             EEEecC
Confidence            888864

>PRK10811 rne ribonuclease E; Reviewed

Probab=95.81  E-value=0.022  Score=63.22  Aligned_cols=60  Identities=20%  Similarity=0.279  Sum_probs=47.6

Q ss_pred             CCCCEEEEEEEEEeC--CeEEEEeCCCeeEEEcCccccccccC---------CccccCccCCcEEEEEEEEE
Q 015066           98 ELGTKVKGTVFCTDN--RGALVDITAKSSAYLPTQEACIHKIK---------HVEEAGIVPGLKEEFVIIGE  158 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~--~G~~Vdig~k~~g~lp~sEls~~~~~---------~~~e~~~~vG~~v~v~Vl~i  158 (414)
                      .+|.|+.|+|.++.+  +++||+||.+..||||.++.......         +..+. +++|+.|-|.|...
T Consensus        37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~-Lk~GqeILVQV~KE  107 (1068)
T PRK10811         37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDV-LREGQEVIVQIDKE  107 (1068)
T ss_pred             CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccc-cCCCCEEEEEEeec
Confidence            589999999999998  69999999999999999988532211         11222 67899999998774

>PRK11712 ribonuclease G; Provisional

Probab=95.79  E-value=0.021  Score=60.04  Aligned_cols=62  Identities=21%  Similarity=0.331  Sum_probs=47.6

Q ss_pred             cCCCCCEEEEEEEEEeC--CeEEEEeCCCeeEEEcCccccccc------------cCCccccCccCCcEEEEEEEEE
Q 015066           96 NSELGTKVKGTVFCTDN--RGALVDITAKSSAYLPTQEACIHK------------IKHVEEAGIVPGLKEEFVIIGE  158 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~--~G~~Vdig~k~~g~lp~sEls~~~------------~~~~~e~~~~vG~~v~v~Vl~i  158 (414)
                      ...+|.++.|+|.++.+  ++||||||.+..||+|.+++....            .....+. +++|+.+-|.|+..
T Consensus        35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~-l~~Gq~iLVQV~Ke  110 (489)
T PRK11712         35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISEL-VRQGQDIMVQVVKD  110 (489)
T ss_pred             ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHh-ccCCCEEEEEEEeC
Confidence            44689999999999999  689999999999999999873100            0112233 77899999888764

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

Probab=95.20  E-value=0.13  Score=46.17  Aligned_cols=72  Identities=19%  Similarity=0.296  Sum_probs=55.8

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC---------CEEEEEeecccCcc--cccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG---------GINGLLHVSQISHD--RVADIATVLQPGDTLKVMILSHDRERGRVSL  330 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~---------gv~Glvh~sels~~--~~~~~~~~~~~G~~V~vkVl~id~e~~ri~L  330 (414)
                      +.+|+||+++|.++..--+-|+|-         -..|++|..++...  --..+.+.|++||.|.|+|++.+ .+....|
T Consensus        66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~-~~~~y~L  144 (193)
T KOG3409|consen   66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLG-DGSNYLL  144 (193)
T ss_pred             CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecC-CCCcEEE
Confidence            568999999999998877777762         28999999988653  12356677999999999999964 4667777


Q ss_pred             EEee
Q 015066          331 STKK  334 (414)
Q Consensus       331 S~K~  334 (414)
                      |.-+
T Consensus       145 TtAe  148 (193)
T KOG3409|consen  145 TTAE  148 (193)
T ss_pred             EEec
Confidence            7654

>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=94.99  E-value=0.13  Score=44.05  Aligned_cols=62  Identities=15%  Similarity=0.099  Sum_probs=44.7

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC------------CccccCccCCcEEEEEEEEEeC
Q 015066           99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK------------HVEEAGIVPGLKEEFVIIGENE  160 (414)
Q Consensus        99 ~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~------------~~~e~~~~vG~~v~v~Vl~id~  160 (414)
                      +|+++.|+|.+.+..|+.|.++.-.+-|||.+.|.....-            .-.+.-+..|+.|+|+|.++.-
T Consensus         3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f   76 (122)
T PF08292_consen    3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF   76 (122)
T ss_dssp             TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred             CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence            6999999999999999999999888999999988631100            1112225679999999988753

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=94.86  E-value=0.1  Score=57.59  Aligned_cols=84  Identities=10%  Similarity=0.059  Sum_probs=63.0

Q ss_pred             HHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCC-eeEEEcCccccccccCC-c---------cccCccCCcEEEEE
Q 015066           86 FHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAK-SSAYLPTQEACIHKIKH-V---------EEAGIVPGLKEEFV  154 (414)
Q Consensus        86 f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k-~~g~lp~sEls~~~~~~-~---------~e~~~~vG~~v~v~  154 (414)
                      +...|......-.+|+...|+|.++..+|+||.+... .+|+++.+.+...+... .         ....+..|+.++++
T Consensus       609 ~~~~~~~~~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~  688 (706)
T COG0557         609 VIDLLKAEYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVK  688 (706)
T ss_pred             HHHHHHHHHHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEE
Confidence            3344433333567999999999999999999999765 89999999998532211 1         11127789999999


Q ss_pred             EEEEeCCCCeEEEEe
Q 015066          155 IIGENEADDSLVLSL  169 (414)
Q Consensus       155 Vl~id~~~~~i~LS~  169 (414)
                      |.+++...+++.+++
T Consensus       689 v~~v~~~~~~i~~~~  703 (706)
T COG0557         689 VTSVDLDERKIDFEL  703 (706)
T ss_pred             EEEEcccccceEEEe
Confidence            999998888888765

>TIGR02062 RNase_B exoribonuclease II

Probab=94.58  E-value=0.2  Score=54.64  Aligned_cols=71  Identities=13%  Similarity=0.149  Sum_probs=54.1

Q ss_pred             CCC--CEEEEEEEEEeCCeEEEEe-CCCeeEEEcCccccc--ccc---CCc------cccCccCCcEEEEEEEEEeCCCC
Q 015066           98 ELG--TKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACI--HKI---KHV------EEAGIVPGLKEEFVIIGENEADD  163 (414)
Q Consensus        98 ~~G--~iV~G~V~~v~~~G~~Vdi-g~k~~g~lp~sEls~--~~~---~~~------~e~~~~vG~~v~v~Vl~id~~~~  163 (414)
                      ++|  +...|.|+.+..+|+||.+ ..+.+|++|.+.+.+  ...   .+-      ....|..|++|+++|.++|...+
T Consensus       554 ~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~  633 (639)
T TIGR02062       554 KAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETR  633 (639)
T ss_pred             ccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccC
Confidence            454  5899999999999999999 566999999998864  111   000      11137889999999999998888


Q ss_pred             eEEEE
Q 015066          164 SLVLS  168 (414)
Q Consensus       164 ~i~LS  168 (414)
                      ++.+.
T Consensus       634 ~i~~~  638 (639)
T TIGR02062       634 SIIAR  638 (639)
T ss_pred             cEeee
Confidence            87653

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.

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

Probab=93.97  E-value=0.33  Score=43.13  Aligned_cols=64  Identities=20%  Similarity=0.301  Sum_probs=46.3

Q ss_pred             ccEEEEEEEEEEeeceEEEEECCEEEEEeecccCc----ccccC-c------ccccCCCCEEEEEEEEEeCCCCe
Q 015066          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISH----DRVAD-I------ATVLQPGDTLKVMILSHDRERGR  327 (414)
Q Consensus       264 ~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~----~~~~~-~------~~~~~~G~~V~vkVl~id~e~~r  327 (414)
                      .|+++.|+|+.+...|+|++.+-++-++..-.+..    ..-+| |      .+..++|..|.++|+...-+...
T Consensus        81 KGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~~  155 (170)
T KOG3298|consen   81 KGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDETE  155 (170)
T ss_pred             CCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEeeee
Confidence            69999999999999999999997776665433321    11222 1      12688999999999987654444

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

Probab=93.71  E-value=0.095  Score=55.27  Aligned_cols=73  Identities=29%  Similarity=0.456  Sum_probs=57.2

Q ss_pred             hhccccEEEEEEEEEEeec--eEEEEEC-CEEEEEeecccCcccccCc-----ccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066          260 AQLGIGSVVIGTVQSLKPY--GAFIDIG-GINGLLHVSQISHDRVADI-----ATVLQPGDTLKVMILSHDRERGRVSLS  331 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~--G~fV~l~-gv~Glvh~sels~~~~~~~-----~~~~~~G~~V~vkVl~id~e~~ri~LS  331 (414)
                      ....+|.+|.|+|++|.|.  .+||+++ +-.||+|.+++.+ +...+     +..++.||.+-|.|+.-....+--.||
T Consensus        33 ~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT  111 (487)
T COG1530          33 KEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARLT  111 (487)
T ss_pred             cEeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecCccccccce
Confidence            4556899999999999984  7899999 7999999999988 43333     458999999999999876544433444


Q ss_pred             Ee
Q 015066          332 TK  333 (414)
Q Consensus       332 ~K  333 (414)
                      ..
T Consensus       112 ~~  113 (487)
T COG1530         112 TD  113 (487)
T ss_pred             eE
Confidence            33

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=93.17  E-value=0.53  Score=37.62  Aligned_cols=63  Identities=21%  Similarity=0.361  Sum_probs=51.4

Q ss_pred             EEEEEEEEEeeceEE-EEEC-CEEEEEeecc-cCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066          267 VVIGTVQSLKPYGAF-IDIG-GINGLLHVSQ-ISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK  334 (414)
Q Consensus       267 iv~g~V~~i~~~G~f-V~l~-gv~Glvh~se-ls~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~  334 (414)
                      .+.|+|+.+.+.+.| |+|+ |..-+.|+|- |...+     -.+.+||.|+|-+--+|.++++|..-.|.
T Consensus         8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~r-----IrIl~GD~V~VE~spYDltkGRIiyR~~~   73 (87)
T PRK12442          8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHR-----IRILAGDRVTLELSPYDLTKGRINFRHKD   73 (87)
T ss_pred             EEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeee-----EEecCCCEEEEEECcccCCceeEEEEecC
Confidence            478999999999888 6887 8888888874 32222     24679999999999999999999998884

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

Probab=93.02  E-value=0.58  Score=41.64  Aligned_cols=63  Identities=17%  Similarity=0.207  Sum_probs=41.2

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccc----ccCC-c-----cccCccCCcEEEEEEEEEe
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH----KIKH-V-----EEAGIVPGLKEEFVIIGEN  159 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~----~~~~-~-----~e~~~~vG~~v~v~Vl~id  159 (414)
                      ..-.|++|.|+|+++.+.|+|+++|. .+-|+...-...+    +-.+ |     .+....+|.+|+++|+...
T Consensus        78 kpfKGEVvdgvV~~Vnk~G~F~~~GP-l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr  150 (170)
T KOG3298|consen   78 KPFKGEVVDGVVTKVNKMGVFARSGP-LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR  150 (170)
T ss_pred             eecCCcEEEEEEEEEeeeeEEEeccc-eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence            34579999999999999999999986 5555543322211    1111 0     0102567888888887764

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

Probab=92.90  E-value=0.48  Score=42.57  Aligned_cols=73  Identities=19%  Similarity=0.147  Sum_probs=52.2

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEe---CC-----CeeEEEcCccccccccCCcc-ccCccCCcEEEEEEEEEeCCCCeEEE
Q 015066           97 SELGTKVKGTVFCTDNRGALVDI---TA-----KSSAYLPTQEACIHKIKHVE-EAGIVPGLKEEFVIIGENEADDSLVL  167 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdi---g~-----k~~g~lp~sEls~~~~~~~~-e~~~~vG~~v~v~Vl~id~~~~~i~L  167 (414)
                      ...|++|+++|.+++...+.|+|   ++     ..+|+|+..++-......++ -.+|.+|+.|.++|++... .....|
T Consensus        66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~-~~~y~L  144 (193)
T KOG3409|consen   66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGD-GSNYLL  144 (193)
T ss_pred             CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCC-CCcEEE
Confidence            46899999999999999888877   22     35799998887532221111 1238899999999999654 445666


Q ss_pred             Eee
Q 015066          168 SLR  170 (414)
Q Consensus       168 S~k  170 (414)
                      |.-
T Consensus       145 TtA  147 (193)
T KOG3409|consen  145 TTA  147 (193)
T ss_pred             EEe
Confidence            653

>TIGR00008 infA translation initiation factor IF-1

Probab=92.60  E-value=0.58  Score=35.79  Aligned_cols=58  Identities=31%  Similarity=0.493  Sum_probs=46.5

Q ss_pred             EEEEEEEEEeeceEE-EEEC-CEEEEEeecc-cCcccccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 015066          267 VVIGTVQSLKPYGAF-IDIG-GINGLLHVSQ-ISHDRVADIATVLQPGDTLKVMILSHDRERGRVS  329 (414)
Q Consensus       267 iv~g~V~~i~~~G~f-V~l~-gv~Glvh~se-ls~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~  329 (414)
                      .+.|.|+...+.+.| |++. |..-++|++- |...     .-.+.+||.|.|-+-..|.++++|.
T Consensus         6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~-----rI~I~~GD~V~Ve~spyd~tkgrIi   66 (68)
T TIGR00008         6 EMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMH-----YIRILPGDKVKVELSPYDLTRGRIT   66 (68)
T ss_pred             EEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhc-----cEEECCCCEEEEEECcccCCcEeEE
Confidence            478999999999888 6887 8999999874 3222     2247899999999999999888875

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).

>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=92.28  E-value=0.71  Score=39.53  Aligned_cols=56  Identities=18%  Similarity=0.233  Sum_probs=42.2

Q ss_pred             CCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCC--Cc---------c---ccc---cCCeEEEEEEEeec
Q 015066          187 EDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--ST---------A---EEL---LGKDLPLKFVEVDE  242 (414)
Q Consensus       187 ~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~--~~---------~---~~~---vGq~V~vkVl~vD~  242 (414)
                      .|+++.|+|++.++.|+.|.++ --+-|||.+.|...  ++         .   .++   .|++|++||.++..
T Consensus         3 ~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f   76 (122)
T PF08292_consen    3 VGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF   76 (122)
T ss_dssp             TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred             CCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence            3789999999999999999998 56789999999843  11         1   111   59999999998865

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

>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]

Probab=91.63  E-value=1.3  Score=38.47  Aligned_cols=69  Identities=17%  Similarity=0.196  Sum_probs=53.8

Q ss_pred             HHHHHHHHHhhc---ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEe
Q 015066           83 LEEFHSALEKYD---FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN  159 (414)
Q Consensus        83 ~~~f~~~l~~~~---~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id  159 (414)
                      .+.|++++....   ..-..|..|.|+|..+..+-+|+|+|+|..+.|..-++.      .++  |..|.+|..+++..+
T Consensus        63 nqsFASlLRnSkl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n------~e~--Y~~GaRVrlRl~DlE  134 (173)
T KOG4078|consen   63 NQSFASLLRNSKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALN------GEA--YQKGARVRLRLIDLE  134 (173)
T ss_pred             hhhHHHHHhcCccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcC------HHH--hhcCceEEEEEcChh
Confidence            568999885433   234679999999999999999999999999999876663      222  677888888886643

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

Probab=89.41  E-value=0.55  Score=49.63  Aligned_cols=73  Identities=21%  Similarity=0.214  Sum_probs=52.5

Q ss_pred             cCCCCCEEEEEEEEEeC--CeEEEEeCCCeeEEEcCccccccccCCccc----cCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066           96 NSELGTKVKGTVFCTDN--RGALVDITAKSSAYLPTQEACIHKIKHVEE----AGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~--~G~~Vdig~k~~g~lp~sEls~~~~~~~~e----~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      ...+|.++.|+|.++.+  ..+|||||....||+|.++...+ .+.+.+    ..++.|+.+-+.|+......+-..||.
T Consensus        34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~~-~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~Kga~lT~  112 (487)
T COG1530          34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVPY-FRAVLEEKIKVRLRGGQATLVQVVKEPRGTKGARLTT  112 (487)
T ss_pred             EeeecCceEEEecccCccchhheeeccCCccceEEecccchh-hhhcccccceeeecCCceEEEEEEeecCcccccccee
Confidence            34689999999999999  47999999999999999999873 222222    226778888777776543333333333

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

Probab=88.85  E-value=2  Score=35.41  Aligned_cols=53  Identities=17%  Similarity=0.345  Sum_probs=44.1

Q ss_pred             cccEEEEEEEEEEeeceEEEEECC-EEEEEeecccCcccccCcccccCCCCEEEEEEEEEe
Q 015066          263 GIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD  322 (414)
Q Consensus       263 ~~G~iv~g~V~~i~~~G~fV~l~g-v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id  322 (414)
                      ..|.+|.|+|..+.+.-+||++++ ..+.|.......       +.|.+|.+|.+++....
T Consensus        22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~-------~~y~~G~rV~lrLkdlE   75 (104)
T PF10246_consen   22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNG-------EKYVRGSRVRLRLKDLE   75 (104)
T ss_pred             ccCCEEEEEEEEEecCceEEEeCCceeEEEecccccc-------cccccCCEEEEEECCHh
Confidence            479999999999999999999996 999998665432       35889999999887654

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 [].

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=88.38  E-value=2.2  Score=34.14  Aligned_cols=64  Identities=17%  Similarity=0.163  Sum_probs=46.6

Q ss_pred             eEEEEEEEEEecCcEE-EEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehh
Q 015066          189 VVVKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNR  252 (414)
Q Consensus       189 ~iv~G~V~~v~~~G~~-V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K  252 (414)
                      -.++|+|+....++.| |.+. |..-+.++|==.......-+.|+.|.+.+-.+|..+++|+.-.+
T Consensus         7 ie~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~   72 (87)
T PRK12442          7 IELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHK   72 (87)
T ss_pred             EEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEEEec
Confidence            4688999999888877 6875 65555544432222233445799999999999999999987665

>TIGR00008 infA translation initiation factor IF-1

Probab=86.62  E-value=4  Score=31.23  Aligned_cols=60  Identities=18%  Similarity=0.246  Sum_probs=42.3

Q ss_pred             eEEEEEEEEEecCcEE-EEEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEE
Q 015066          189 VVVKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLV  248 (414)
Q Consensus       189 ~iv~G~V~~v~~~G~~-V~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~  248 (414)
                      -.+.|+|+....++.| |.+. |..-+.+.+-=.......-..|+.|.+.+-.+|.++++|+
T Consensus         5 ie~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd~tkgrIi   66 (68)
T TIGR00008         5 IEMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRIT   66 (68)
T ss_pred             EEEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECcccCCcEeEE
Confidence            3678999999888877 6875 6555554443222223333469999999999998888875

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).

>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=85.95  E-value=2.4  Score=31.48  Aligned_cols=64  Identities=27%  Similarity=0.347  Sum_probs=40.8

Q ss_pred             cEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST  332 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~  332 (414)
                      |+..+-.|..++..|-..--+ .+.|+.    +...|+..-...+-+||++++-|+.+|.-+-.+..|+
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 GDQLKLVVQDVTEDGSVMFSGGQVSGLT----VLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL   65 (65)
T ss_pred             CceEEEEEeeeccCCcEEEecCCcCCcE----EEEEEEEecceecCCCceeEEEEEEEeeEEeEEEEeC
Confidence            455666677766555443333 366652    2223444445568899999999999997666666664

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.

>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=83.99  E-value=14  Score=27.37  Aligned_cols=50  Identities=14%  Similarity=0.214  Sum_probs=35.0

Q ss_pred             EEEEEEEEeC--CeEEEEe-CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066          103 VKGTVFCTDN--RGALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG  157 (414)
Q Consensus       103 V~G~V~~v~~--~G~~Vdi-g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~  157 (414)
                      .+|+|...++  +.-|+.- ++..+-|+|.+++......     .+..|+.|+|.+..
T Consensus         1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~-----~l~~G~~V~F~~~~   53 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFR-----SLKEGDRVEFEVEE   53 (66)
T ss_dssp             EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSST-----S--TTSEEEEEEEE
T ss_pred             CeEEEEEEECCCCceEEEEcccceeEEeccccccccccc-----cCCCCCEEEEEEEE
Confidence            4799999987  3345544 4445899999998754311     26789999999977

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 ....

>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]

Probab=82.55  E-value=8.8  Score=29.94  Aligned_cols=64  Identities=28%  Similarity=0.430  Sum_probs=48.5

Q ss_pred             EEEEEEEEEEeeceEE-EEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066          266 SVVIGTVQSLKPYGAF-IDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTK  333 (414)
Q Consensus       266 ~iv~g~V~~i~~~G~f-V~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K  333 (414)
                      -.+.|+|....+.+-| |.+. |..-+.|++-=-..    -.--+.+||.|.|..-..|.++++|..-.+
T Consensus         7 ~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~----~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~   72 (75)
T COG0361           7 IEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRK----NRIRILPGDVVLVELSPYDLTKGRIVYRYK   72 (75)
T ss_pred             cEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchh----eeEEeCCCCEEEEEecccccccccEEEEec
Confidence            4588999999988876 8887 88889898742211    122368999999999999988888766554

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

Probab=82.45  E-value=5.7  Score=37.03  Aligned_cols=63  Identities=17%  Similarity=0.055  Sum_probs=49.4

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEe
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN  159 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id  159 (414)
                      |-..+||.|-|.|+.....+..|||++-..|.+|.--+.....++-.  ++++|+.+-++|...+
T Consensus        61 YiP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrP--nl~vGdliyakv~~a~  123 (230)
T KOG1004|consen   61 YIPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRP--NLQVGDLIYAKVVDAN  123 (230)
T ss_pred             ecCCCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCC--ccccccEEEEEEEecC
Confidence            46789999999999999999999999877888887655433222222  2789999999998765

>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=81.01  E-value=19  Score=26.73  Aligned_cols=48  Identities=29%  Similarity=0.515  Sum_probs=35.4

Q ss_pred             EEEEEEEEee---ceEEEEEC--CEEEEEeecccCcccccCcccccCCCCEEEEEEEE
Q 015066          268 VIGTVQSLKP---YGAFIDIG--GINGLLHVSQISHDRVADIATVLQPGDTLKVMILS  320 (414)
Q Consensus       268 v~g~V~~i~~---~G~fV~l~--gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~  320 (414)
                      .+|+|+...+   || ||.-.  +-+-++|++++....    ...+..|+.|...+..
T Consensus         1 ~~G~V~~~~~~kgyG-FI~~~~~~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~   53 (66)
T PF00313_consen    1 MTGTVKWFDDEKGYG-FITSDDGGEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE   53 (66)
T ss_dssp             EEEEEEEEETTTTEE-EEEETTSSSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred             CeEEEEEEECCCCce-EEEEcccceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence            3799999885   44 55555  369999999997654    3467899999998887

During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	414
2k4k_A	130	Solution Structure Of Gsp13 From Bacillus Subtilis		7e-11
2oce_A	780	Crystal Structure Of Tex Family Protein Pa5201 From		4e-08
3bzc_A	785	Crystal Structure Of The Tex Protein From Pseudomon		4e-08
4aim_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		5e-08
4aid_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		7e-08
4am3_A	717	Crystal Structure Of C. Crescentus Pnpase Bound To		7e-08
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		7e-08
1sro_A	76	S1 Rna Binding Domain, Nmr, 20 Structures Length =		2e-07
1q8k_A	308	Solution Structure Of Alpha Subunit Of Human Eif2 L		2e-05
2aho_B	266	Structure Of The Archaeal Initiation Factor Eif2 Al		8e-05
2eqs_A	103	Solution Structure Of The S1 Rna Binding Domain Of		2e-04
3aev_A	275	Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex		3e-04
2khj_A	109	Nmr Structure Of The Domain 6 Of The E. Coli Riboso		3e-04
1yz6_A	274	Crystal Structure Of Intact Alpha Subunit Of Aif2 F		3e-04

>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis Length = 130

Iteration: 1
 Score = 65.1 bits (157), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 32/89 (35%), Positives = 52/89 (58%), Gaps = 1/89 (1%)
Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKVMI 318
           A+  +GSV  G V  L+ YGAF+ +     GL+H+S+++H  V DI   L  GD ++V +
Sbjct: 3   AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKV 62
Query: 319 LSHDRERGRVSLSTKKLEPTPGDMIRNPK 347
           L+ D E+G++SLS +  +  P      P+
Sbjct: 63  LAVDEEKGKISLSIRATQAAPEKKESKPR 91

>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From Pseudomonas Aeruginosa Length = 780

Iteration: 1
 Score = 55.8 bits (133), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 52/88 (59%), Gaps = 2/88 (2%)
Query: 257 DSQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLK 315
           +S   L  G V+ G V ++  +GAF+DIG   +GL+H+S +S   V D   V++ GD +K
Sbjct: 648 ESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVK 707
Query: 316 VMILSHDRERGRVSLSTKKLEPTPGDMI 343
           V ++  D  R RV LS  ++  TPG+ +
Sbjct: 708 VKVMEVDIPRNRVGLSM-RMSDTPGEKV 734

>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas Aeruginosa, Crystal Form I Length = 785

Iteration: 1
 Score = 55.8 bits (133), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 33/88 (37%), Positives = 52/88 (59%), Gaps = 2/88 (2%)
Query: 257 DSQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLK 315
           +S   L  G V+ G V ++  +GAF+DIG   +GL+H+S +S   V D   V++ GD +K
Sbjct: 647 ESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVK 706
Query: 316 VMILSHDRERGRVSLSTKKLEPTPGDMI 343
           V ++  D  R RV LS  ++  TPG+ +
Sbjct: 707 VKVMEVDIPRNRVGLSM-RMSDTPGEKV 733

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 34/91 (37%), Positives = 55/91 (60%), Gaps = 2/91 (2%)
Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           IG +  G V  +  +GAF++  G  +GL+HVSQIS++RVA  + VL+ G  +KV +L  D
Sbjct: 637 IGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD 696
Query: 323 RERGRVSLSTKKLEPTPGDMIRNPKLVFEKA 353
            +RG+  LS K ++   G+ +   +   E+A
Sbjct: 697 -DRGKTKLSMKVVDQETGEDLSKKEAAAEEA 726

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 33/91 (36%), Positives = 55/91 (60%), Gaps = 2/91 (2%)
Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           +G +  G V  +  +GAF++  G  +GL+HVSQIS++RVA  + VL+ G  +KV +L  D
Sbjct: 637 VGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD 696
Query: 323 RERGRVSLSTKKLEPTPGDMIRNPKLVFEKA 353
            +RG+  LS K ++   G+ +   +   E+A
Sbjct: 697 -DRGKTKLSMKVVDQETGEDLSKKEAAAEEA 726

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 33/91 (36%), Positives = 55/91 (60%), Gaps = 2/91 (2%)
Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           +G +  G V  +  +GAF++  G  +GL+HVSQIS++RVA  + VL+ G  +KV +L  D
Sbjct: 628 VGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD 687
Query: 323 RERGRVSLSTKKLEPTPGDMIRNPKLVFEKA 353
            +RG+  LS K ++   G+ +   +   E+A
Sbjct: 688 -DRGKTKLSMKVVDQETGEDLSKKEAAAEEA 717

>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase Length = 723

Iteration: 1
 Score = 55.1 bits (131), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 35/104 (33%), Positives = 58/104 (55%), Gaps = 5/104 (4%)
Query: 232 DLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGG-INGL 290
           D  +K    D E+++  +   + + +  A++ +G V  G V  +  +GAF+ IGG   GL
Sbjct: 598 DGTVKIAATDGEKAKHAI---RRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGL 654
Query: 291 LHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK 334
           +H+SQI+  RV  +   LQ G  + V +L  DR+ GR+ LS K+
Sbjct: 655 VHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQ-GRIRLSIKE 697

>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures Length = 76

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/76 (40%), Positives = 46/76 (60%), Gaps = 2/76 (2%)
Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKVMI 318
           A++ +G V  G V  +  +GAF+ IGG   GL+H+SQI+  RV  +   LQ G  + V +
Sbjct: 1   AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKV 60
Query: 319 LSHDRERGRVSLSTKK 334
           L  DR+ GR+ LS K+
Sbjct: 61  LEVDRQ-GRIRLSIKE 75

>pdb|1Q8K|A Chain A, Solution Structure Of Alpha Subunit Of Human Eif2 Length = 308

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 46/77 (59%), Gaps = 3/77 (3%)
Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
           +  VV+  V+S++  GA++ +     I G++H+S++S  R+  I  +++ G    V ++ 
Sbjct: 13  VEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIR 72
Query: 321 HDRERGRVSLSTKKLEP 337
            D+E+G + LS +++ P
Sbjct: 73  VDKEKGYIDLSKRRVSP 89

>pdb|2AHO|B Chain B, Structure Of The Archaeal Initiation Factor Eif2 Alpha- Gamma Heterodimer From Sulfolobus Solfataricus Complexed With Gdpnp Length = 266

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 265 GSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSH 321
           G ++I TV+ +  YG+++ +   GG+   L  S++S   V +I  VL+    + V ++  
Sbjct: 12  GEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRV 71
Query: 322 DRERGRVSLSTKKL 335
           DR +G V +S KK+
Sbjct: 72  DRRKGTVDVSLKKV 85

>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 = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 50/88 (56%), Gaps = 8/88 (9%)
Query: 264 IGSVVIGTVQSLKPYGAFIDIGGIN----GLLHVSQISHD-RVADIATVLQPGDTLKVMI 318
           IG +  G V S+  +G F+ + G+     GL+H+S++  + RVA++A V+  G  +KV +
Sbjct: 12  IGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKV 71
Query: 319 LSHDRERGRVSLSTKKLEPTPGDMIRNP 346
           LS      + SLS K ++   G+ + NP
Sbjct: 72  LSFTGT--KTSLSMKDVDQETGEDL-NP 96

>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From Pyrococcus Horikoshii Ot3 Length = 275

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 265 GSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSH 321
           G  V+ TV+ +  YGAF+++    G    +H+S+++   V +I   L+ G  +   ++  
Sbjct: 12  GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRV 71
Query: 322 DRERGRVSLSTKKL 335
           D  +G + LS +++
Sbjct: 72  DPRKGHIDLSLRRV 85

>pdb|2KHJ|A Chain A, Nmr Structure Of The Domain 6 Of The E. Coli Ribosomal Protein S1 Length = 109

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR 323
           G++V G V ++   GA +++  G+ G L  S+ S DRV D   VL  GD ++      DR
Sbjct: 32  GAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDR 91
Query: 324 ERGRVSLSTK 333
           +   +SLS +
Sbjct: 92  KNRAISLSVR 101

>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From Pyrococcus Abyssi Length = 274

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 265 GSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSH 321
           G  V+ TV+ +  YGAF+++    G    +H+S+++   V +I   L+ G  +   ++  
Sbjct: 11  GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRV 70
Query: 322 DRERGRVSLSTKKL 335
           D  +G + LS +++
Sbjct: 71  DPRKGHIDLSLRRV 84

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	414
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	2e-26
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	4e-10
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	4e-23
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	1e-22
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	1e-21
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	2e-06
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	1e-21
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	3e-08
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	2e-20
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	2e-19
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	4e-19
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	3e-06
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	4e-18
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	3e-17
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	7e-17
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	2e-16
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	2e-16
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	2e-14
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	7e-14
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	1e-13
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	4e-13
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	1e-12
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	2e-09
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	8e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	5e-06
2bh8_A	101	1B11; transcription, molecular evolution, unique a	3e-04
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	3e-04
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	4e-04

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

 Score =  102 bits (255), Expect = 2e-26
 Identities = 32/89 (35%), Positives = 52/89 (58%), Gaps = 1/89 (1%)

Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMI 318
           A+  +GSV  G V  L+ YGAF+ +     GL+H+S+++H  V DI   L  GD ++V +
Sbjct: 3   AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKV 62

Query: 319 LSHDRERGRVSLSTKKLEPTPGDMIRNPK 347
           L+ D E+G++SLS +  +  P      P+
Sbjct: 63  LAVDEEKGKISLSIRATQAAPEKKESKPR 91

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

 Score = 56.3 bits (136), Expect = 4e-10
 Identities = 26/116 (22%), Positives = 43/116 (37%), Gaps = 8/116 (6%)

Query: 190 VVKGKVVG-ANKGGVVAEVEGLRGFVPFSQISSK--STAEELL--GKDLPLKFVEVDEEQ 244
           V  GKV G    G  VA  E  +G V  S+++        E L  G ++ +K + VDEE+
Sbjct: 10  VYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEK 69

Query: 245 SRLVLSNRKAMAD--SQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQIS 297
            ++ LS R   A    +             +       F  +   +   + +S   
Sbjct: 70  GKISLSIRATQAAPEKKESKPRKPKAAQVSEEASTPQGFNTLKDKLEEWIEMSNRK 125

>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 = 92.9 bits (231), Expect = 4e-23
 Identities = 26/96 (27%), Positives = 46/96 (47%), Gaps = 4/96 (4%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGIN--GLLHVSQISHDRVADIATVLQPGDTLKVMILSH 321
           + ++  G V  +  YGAFI I G    GL+H + +S  RV   + ++  GD + V ++  
Sbjct: 22  LYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGR 81

Query: 322 D--RERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEE 355
           +   +R +VSLS K +    G  +    ++ E    
Sbjct: 82  EMKNDRIKVSLSMKVVNQGTGKDLDPNNVIIESGPS 117

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 91.1 bits (227), Expect = 1e-22
 Identities = 25/106 (23%), Positives = 41/106 (38%), Gaps = 5/106 (4%)

Query: 239 EVDEEQSRLVLSNRKAMAD----SQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHV 293
                            +       A    G++V G V ++   GA +++  G+ G L  
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRA 61

Query: 294 SQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP 339
           S+ S DRV D   VL  GD ++      DR+   +SLS +  +   
Sbjct: 62  SEASRDRVEDATLVLSVGDEVEAKFTGVDRKNRAISLSVRAKDEAD 107

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 Length = 182

 Score = 90.6 bits (225), Expect = 1e-21
 Identities = 20/79 (25%), Positives = 45/79 (56%), Gaps = 3/79 (3%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
           +  VV+  V+S+   GA++ +     I G++ +S++S  R+  I  +++ G    V+++ 
Sbjct: 15  VEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIR 74

Query: 321 HDRERGRVSLSTKKLEPTP 339
            D+E+G + LS +++ P  
Sbjct: 75  VDKEKGYIDLSKRRVSPEE 93

>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 = 46.7 bits (111), Expect = 2e-06
 Identities = 18/119 (15%), Positives = 45/119 (37%), Gaps = 11/119 (9%)

Query: 187 EDVVVKGKVVGANKGGV---VAEVEGLRGFVPFSQISSK--STAEELL--GKDLPLKFVE 239
            + VV   V    + G    + E   + G +  S++S +   +  +L+  G++  +  + 
Sbjct: 15  VEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIR 74

Query: 240 VDEEQSRLVLSNRKAMADSQAQLG----IGSVVIGTVQSLKPYGAFIDIGGINGLLHVS 294
           VD+E+  + LS R+   +   +          V   ++ +     +     +  L   +
Sbjct: 75  VDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRT 133

>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 = 90.2 bits (224), Expect = 1e-21
 Identities = 19/79 (24%), Positives = 42/79 (53%), Gaps = 3/79 (3%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
           I  +V+  VQ +   GA++ +     I G++ +S++S  R+  I  +++ G     ++L 
Sbjct: 15  IDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLR 74

Query: 321 HDRERGRVSLSTKKLEPTP 339
            D+E+G + LS +++    
Sbjct: 75  VDKEKGYIDLSKRRVSSED 93

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A Length = 175

 Score = 52.1 bits (125), Expect = 3e-08
 Identities = 27/156 (17%), Positives = 54/156 (34%), Gaps = 8/156 (5%)

Query: 187 EDVVVKGKVVG-ANKGGVV--AEVEGLRGFVPFSQISSK--STAEELL--GKDLPLKFVE 239
            D +V   V   A  G  V   E + + G +  S++S +   + ++L+  GK+     + 
Sbjct: 15  IDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLR 74

Query: 240 VDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQIS-H 298
           VD+E+  + LS R+  ++   +         TV S+  Y A      +  L         
Sbjct: 75  VDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLS 134

Query: 299 DRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK 334
            +        +     + +    +     V    K 
Sbjct: 135 RKFGHAYEAFKLSIIDETVWEGIEPPSKDVLDELKN 170

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115

 Score = 85.4 bits (212), Expect = 2e-20
 Identities = 28/114 (24%), Positives = 48/114 (42%), Gaps = 7/114 (6%)

Query: 238 VEVDEEQSRLVLSNRKAMAD----SQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLH 292
           +                          +   G+ + G V +L  YG F++I  G+ GL+H
Sbjct: 1   MGSSHHHHHHSSG-LVPRGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVH 59

Query: 293 VSQISHD-RVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRN 345
           VS++    +    + V+  GD ++VM+L  D ER R+SL  K+ +  P      
Sbjct: 60  VSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRRISLGLKQCKANPWQQFAE 113

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80

 Score = 81.2 bits (201), Expect = 2e-19
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
            G    G V  ++ YGAFI++   + GLL    +   R+ +    L  GD + V  +   
Sbjct: 5   PGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRLEN----LNVGDEIIVQAIDVR 60

Query: 323 RERGRVSLSTKKLE 336
            E+  +      LE
Sbjct: 61  PEKREIDFKYIPLE 74

>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 = 86.6 bits (214), Expect = 4e-19
 Identities = 21/79 (26%), Positives = 46/79 (58%), Gaps = 3/79 (3%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
           +  VV+  V+S++  GA++ +     I G++H+S++S  R+  I  +++ G    V ++ 
Sbjct: 13  VEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIR 72

Query: 321 HDRERGRVSLSTKKLEPTP 339
            D+E+G + LS +++ P  
Sbjct: 73  VDKEKGYIDLSKRRVSPEE 91

>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 = 47.7 bits (113), Expect = 3e-06
 Identities = 25/173 (14%), Positives = 60/173 (34%), Gaps = 20/173 (11%)

Query: 187 EDVVVKGKVVGANKGGV---VAEVEGLRGFVPFSQISS---KSTAEEL-LGKDLPLKFVE 239
            + VV   V    + G    + E   + G +  S++S    +S  + + +G++  +K + 
Sbjct: 13  VEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIR 72

Query: 240 VDEEQSRLVLSNRKAMADSQAQLG----IGSVVIGTVQSLKPYGAFIDIGGINGLLH-VS 294
           VD+E+  + LS R+   +   +          V   ++ +     +     +  L    +
Sbjct: 73  VDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTA 132

Query: 295 QISHDRVADIATVL--------QPGDTLKVMILSHDRERGRVSLSTKKLEPTP 339
            +  D+                     L  + L+ D     ++   ++L P  
Sbjct: 133 WVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQA 185

>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 = 82.7 bits (204), Expect = 4e-18
 Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 3/83 (3%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
            G ++I TV+ +  YG+++ +   GG+   L  S++S   V +I  VL+    + V ++ 
Sbjct: 11  EGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIR 70

Query: 321 HDRERGRVSLSTKKLEPTPGDMI 343
            DR +G V +S KK+        
Sbjct: 71  VDRRKGTVDVSLKKVTDDERRKK 93

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 82.9 bits (206), Expect = 3e-17
 Identities = 33/91 (36%), Positives = 54/91 (59%), Gaps = 2/91 (2%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           +G +  G V  +  +GAF++  G  +GL+HVSQIS++RVA  + VL+ G  +KV +L  D
Sbjct: 637 VGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD 696

Query: 323 RERGRVSLSTKKLEPTPGDMIRNPKLVFEKA 353
             RG+  LS K ++   G+ +   +   E+A
Sbjct: 697 D-RGKTKLSMKVVDQETGEDLSKKEAAAEEA 726

>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 = 74.7 bits (184), Expect = 7e-17
 Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 7/83 (8%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGIN----GLLHVSQISHD-RVADIATVLQPGDTLKVMI 318
           IG +  G V S+  +G F+ + G+     GL+H+S++  + RVA++A V+  G  +KV +
Sbjct: 12  IGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKV 71

Query: 319 LSHDRERGRVSLSTKKLEPTPGD 341
           LS      + SLS K ++   G+
Sbjct: 72  LSFT--GTKTSLSMKDVDQETGE 92

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

 Score = 80.6 bits (200), Expect = 2e-16
 Identities = 32/93 (34%), Positives = 46/93 (49%), Gaps = 2/93 (2%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           +G V  G V  +  +GAF+ I GG  GL+H+SQI+  RV  +   LQ G  + V +L  D
Sbjct: 627 VGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVD 686

Query: 323 RERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEE 355
           R +GR+ LS K+                E+ E 
Sbjct: 687 R-QGRIRLSIKEATEQSQPAAAPEAPAAEQGEH 718

>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 = 78.1 bits (192), Expect = 2e-16
 Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 3/77 (3%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
            G  V+ TV+ +  YGAF+++    G    +H+S+++   V +I   L+ G  +   ++ 
Sbjct: 11  EGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIR 70

Query: 321 HDRERGRVSLSTKKLEP 337
            D  +G + LS +++  
Sbjct: 71  VDPRKGHIDLSLRRVTQ 87

>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 = 74.5 bits (184), Expect = 2e-14
 Identities = 33/115 (28%), Positives = 53/115 (46%), Gaps = 1/115 (0%)

Query: 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
           L  G V+ G V ++  +GAF+DIG   +GL+H+S +S   V D   V++ GD +KV ++ 
Sbjct: 652 LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVME 711

Query: 321 HDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARADM 375
            D  R RV LS +  +     +          + +  Q       Q+   A   M
Sbjct: 712 VDIPRNRVGLSMRMSDTPGEKVEGQRGGRPTGSGQPRQERGAPRGQSAPPANNAM 766

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

 Score = 72.6 bits (178), Expect = 7e-14
 Identities = 10/114 (8%), Positives = 32/114 (28%), Gaps = 2/114 (1%)

Query: 262  LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVAD-IATVLQPGDTLKVMIL 319
               GS++   V+              +  +++  + +  ++      + + G T    ++
Sbjct: 903  FFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVI 962

Query: 320  SHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMARA 373
              D       +S    +     +  +        +   +       +   MA A
Sbjct: 963  YIDYANITAEVSLLDHDVKQQYVPISYSKDPSIWDLKQELEDAEEERKLMMAEA 1016

>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 = 71.8 bits (177), Expect = 1e-13
 Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 6/89 (6%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQIS----HDRVADIATVLQPGDTLKVMI 318
           +G  ++G+V     +GAF+ +  G +GLLH+SQI       RV ++  VL  G  ++V I
Sbjct: 667 VGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEI 726

Query: 319 LSHDRERGRVSLSTKKLEPTPGDMIRNPK 347
              D  RG++SL             +   
Sbjct: 727 AEIDS-RGKLSLIPVIEGEEAASDEKKDD 754

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

 Score = 70.7 bits (173), Expect = 4e-13
 Identities = 15/118 (12%), Positives = 39/118 (33%), Gaps = 6/118 (5%)

Query: 258  SQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVAD-IATVLQPGDTLK 315
            S+     GS++   V+              +  +++  + +  ++      + + G T  
Sbjct: 896  SEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYP 955

Query: 316  VMILSHDRERGRVSLSTKKLE----PTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEA 369
              ++  D       +S    +      P    ++P +   K E       +++  AEA
Sbjct: 956  AKVIYIDYANITAEVSLLDHDVKQQYVPISYSKDPSIWDLKQELEDAEEERKLMMAEA 1013

>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 = 66.9 bits (163), Expect = 1e-12
 Identities = 39/256 (15%), Positives = 72/256 (28%), Gaps = 45/256 (17%)

Query: 96  NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVI 155
           N+ L + + G +   ++R   V            Q   + K +     G           
Sbjct: 3   NTNLASFIVGLIIDENDRFYFVQKD--------GQTYALAKEEGQHTVG-----DTVKGF 49

Query: 156 IGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKG-GVVAEVEGLRG-- 212
              +     L L+   +               D    G+V    K  GV  +  GL    
Sbjct: 50  AYTDM-KQKLRLTTLEVTATQ-----------DQFGWGRVTEVRKDLGVFVDT-GLPDKE 96

Query: 213 -FVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNR----KAMADSQAQLGIGSV 267
             V    +          G  L ++ +EVD++     L       + +A           
Sbjct: 97  IVVSLDILPELKELWPKKGDQLYIR-LEVDKKDRIWGLLAYQEDFQRLARPAYNNMQNQN 155

Query: 268 VIGTVQSLKPYGAFIDI--GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRER 325
               V  LK  G F+ +    + G +H S+   +         + G  L   ++      
Sbjct: 156 WPAIVYRLKLSGTFVYLPENNMLGFIHPSERYAE--------PRLGQVLDARVIGFREVD 207

Query: 326 GRVSLSTKKLEPTPGD 341
             ++LS K       +
Sbjct: 208 RTLNLSLKPRSFEMLE 223

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5 Length = 119

 Score = 54.3 bits (130), Expect = 2e-09
 Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 3/84 (3%)

Query: 258 SQAQLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHD-RVADIATVLQPGDTL 314
           S   L  G ++ GTV SL+ +G  +DIG  G    L + +     R  +    L+ G  L
Sbjct: 15  SAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYL 74

Query: 315 KVMILSHDRERGRVSLSTKKLEPT 338
             ++       G VSLS    E +
Sbjct: 75  NCIVEKVKGNGGVVSLSVGHSEVS 98

>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 Length = 209

 Score = 51.6 bits (123), Expect = 8e-08
 Identities = 19/110 (17%), Positives = 39/110 (35%), Gaps = 11/110 (10%)

Query: 238 VEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGIN--------- 288
           +    E   L + +     +SQ    +G++V   V S+    A + I  +          
Sbjct: 55  LMKSSENGALPVVSVVRETESQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFR 114

Query: 289 GLLHVSQISHDRV--ADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE 336
           G +    +        +I    +PGD +   ++S    +    L+T + E
Sbjct: 115 GTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAENE 164

>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 = 53.3 bits (127), Expect = 9e-08
 Identities = 43/375 (11%), Positives = 104/375 (27%), Gaps = 109/375 (29%)

Query: 14  PPISHTRLSRRKSITQIQQKLLNSRKNKTIV---------SAVAISNAETREREELNQLF 64
              +   +SR +   +++Q LL  R  K ++         + VA+        +   ++ 
Sbjct: 124 QVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVC--LSYKVQCKMD 181

Query: 65  EEAY----ERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDIT 120
            + +    + C +   E V   L++    ++                    N  +  D +
Sbjct: 182 FKIFWLNLKNCNSP--ETVLEMLQKLLYQIDP-------------------NWTSRSDHS 220

Query: 121 AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWE- 179
             S+  L        +++                ++     ++ L L L  +Q   AW  
Sbjct: 221 --SNIKLRIHSI-QAELRR---------------LLKSKPYENCL-LVLLNVQNAKAWNA 261

Query: 180 ---RCRQL-QSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPL 235
               C+ L  +    V    + A     ++               +    + LL     L
Sbjct: 262 FNLSCKILLTTRFKQVT-DFLSAATTTHISLDHHSMTL-------TPDEVKSLL-----L 308

Query: 236 KFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFI--DIGGINGLLHV 293
           K+++   +               +  L      +  +         I   +   +   HV
Sbjct: 309 KYLDCRPQDLP-----------REV-LTTNPRRLSII------AESIRDGLATWDNWKHV 350

Query: 294 SQISHDRVADIA-TVLQPGDTLKV----MILSHDRERGRVSLSTKKLEPTPGDMIRNPKL 348
           +      + + +  VL+P +  K+     +           + T  L     D+I+    
Sbjct: 351 NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS-----AHIPTILLSLIWFDVIK---- 401

Query: 349 VFEKAEEMAQTFRQR 363
                  +     + 
Sbjct: 402 --SDVMVVVNKLHKY 414

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 42.9 bits (100), Expect = 2e-04
 Identities = 63/390 (16%), Positives = 122/390 (31%), Gaps = 90/390 (23%)

Query: 2   ATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREEL- 60
           A     F  L C  +  TR    K +T      L++     I            E + L 
Sbjct: 256 AKAWNAF-NLSCKILLTTR---FKQVTDF----LSAATTTHISLDHHSMTLTPDEVKSLL 307

Query: 61  --------NQLFEEAYERCRTAPM--EGVSFTLEEFHSALE--KYDFNSELGTKVKGTVF 108
                     L  E      T P     ++ ++ +  +  +  K+    +L T ++ ++ 
Sbjct: 308 LKYLDCRPQDLPREV---LTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN 364

Query: 109 C---TDNRGALVDITA-KSSAYLPTQEACI--HKIKHVEEAGIVPGLKEEFVIIGENEAD 162
                + R     ++    SA++PT    +    +   +   +V  L +  ++    +  
Sbjct: 365 VLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV---EKQP 421

Query: 163 DSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGL-----RGFVPFS 217
               +S+  I  EL     +     +  +   +V         + + L       +  +S
Sbjct: 422 KESTISIPSIYLEL-----KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYF-YS 475

Query: 218 QISSKSTAEELLGKD-------LPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIG 270
            I       E   +        L  +F+E            +K   DS A    GS+ + 
Sbjct: 476 HIGHHLKNIEHPERMTLFRMVFLDFRFLE------------QKIRHDSTAWNASGSI-LN 522

Query: 271 TVQSLKPYGAFI-DIGGINGLLHVSQISHDRVADIATVL-QPGDTLKVMILSHDRERGRV 328
           T+Q LK Y  +I D                 V  I   L +  + L   I S   +  R+
Sbjct: 523 TLQQLKFYKPYICDNDPKY---------ERLVNAILDFLPKIEENL---ICSKYTDLLRI 570

Query: 329 SLSTKKLEPTPGDMIRNPKLVFEKAEEMAQ 358
           +L  +             + +FE+A +  Q
Sbjct: 571 ALMAED------------EAIFEEAHKQVQ 588

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E Length = 180

 Score = 45.7 bits (108), Expect = 5e-06
 Identities = 27/127 (21%), Positives = 53/127 (41%), Gaps = 23/127 (18%)

Query: 235 LKFVEVDEEQSRLVLSNRKAMADSQA------QLGIGSVVIGTVQSLKPYGAFIDIGGIN 288
           L  + V   +  +++    A               +  VV G V  +  YG F+++G ++
Sbjct: 46  LAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQEVVEGEVLQVDNYGVFVNLGPMD 105

Query: 289 GLLHVSQISHDRVADIAT-----------VLQPGDTLKVMILS----HDRERGRVSLSTK 333
           GL+H+SQI+ D +                V+Q GD ++  ++S          R++L+ +
Sbjct: 106 GLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTGRLPRIALTMR 165

Query: 334 KLEPTPG 340
             +P  G
Sbjct: 166 --QPYLG 170

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} Length = 101

 Score = 39.0 bits (91), Expect = 3e-04
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 231 KDLPLKFVEVDEEQSRLVL--SNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDI-GGI 287
            D    F+  D+    + +  S   + A  +     G  V G ++S+  +G FI + GGI
Sbjct: 26  ADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITDFGIFIGLDGGI 85

Query: 288 NGLLHVSQISHDRV 301
           +GL+H+S IS  + 
Sbjct: 86  DGLVHLSDISWAQA 99

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 172

 Score = 40.3 bits (94), Expect = 3e-04
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 10/76 (13%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIAT----------VLQPGDT 313
            G VV   V ++   G F +IG +N  +    +  D   D             V++ G  
Sbjct: 84  RGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSN 143

Query: 314 LKVMILSHDRERGRVS 329
           +++ I+    +   + 
Sbjct: 144 VRLKIVGTRTDATEIF 159

>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 Length = 172

 Score = 39.9 bits (93), Expect = 4e-04
 Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 12/78 (15%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIA------------TVLQPG 311
            G VV   V  +   G F +IG ++  +    I  +   D               V+Q  
Sbjct: 81  KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQD 140

Query: 312 DTLKVMILSHDRERGRVS 329
           D +++ I+    ++  + 
Sbjct: 141 DEIRLKIVGTRVDKNDIF 158

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	414
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
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.76
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.75
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.73
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.73
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.73
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.71
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.7
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.68
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.67
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.6
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.6
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.59
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.55
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.55
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.51
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.51
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.45
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.42
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.36
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.36
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.34
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.33
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.32
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.31
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	99.3
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.29
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	99.29
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.29
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	99.27
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.26
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	99.25
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.23
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.22
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.22
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.19
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	99.17
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.17
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.17
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	99.15
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	99.14
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	99.13
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.03
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	99.01
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	99.01
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.99
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.98
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.97
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.97
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.96
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.92
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.91
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.77
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.76
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.74
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.62
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.58
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.56
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	98.56
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.55
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.53
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.51
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.42
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.4
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	98.39
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.37
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	98.34
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	98.31
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.29
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	98.28
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	98.22
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.19
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	98.19
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	98.15
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.06
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.97
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.96
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	97.83
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	97.62
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.52
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.48
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.25
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	97.24
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	97.11
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	96.96
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	96.89
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	96.53
2r7d_A	469	Ribonuclease II family protein; structural genomic	94.67
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	93.24
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	90.5
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	88.4
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	87.16
1jjg_A	102	M156R; beta barrel, S1 motif, OB fold, MYXV156R, N	86.86
1wfq_A	89	UNR protein; beta-barrel, translational regulation	85.55
2r7d_A	469	Ribonuclease II family protein; structural genomic	83.86
3h8z_A	128	FragIle X mental retardation syndrome-related Pro;	82.13
2k5n_A	74	Putative cold-shock protein; GFT protein structure	81.33

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

Probab=100.00  E-value=2.6e-34  Score=278.10  Aligned_cols=209  Identities=16%  Similarity=0.102  Sum_probs=181.3

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhhHH
Q 015066           98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELA  177 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~~~  177 (414)
                      ..|++++|+|++++++|+||+++ +.+|+||.+|++.           ++|++++|.|+.  +.++++++|.+.+.    
T Consensus         5 ~~G~~v~g~V~~~~~~G~fv~~~-g~egllp~se~~~-----------~vGdevev~v~~--d~~~r~iat~~~p~----   66 (285)
T 3go5_A            5 NLASFIVGLIIDENDRFYFVQKD-GQTYALAKEEGQH-----------TVGDTVKGFAYT--DMKQKLRLTTLEVT----   66 (285)
T ss_dssp             TTTEEEEEEEEEECSSEEEEEET-TEEEEEEGGGCCC-----------CTTSEEEEEEEE--CTTSCEEEECSCCC----
T ss_pred             cCCCEEEEEEEEEECCEEEEEcC-CeEEEEEHHHCcc-----------ccCCEEEEEEEE--CCCCCEEEeccccc----
Confidence            57999999999999999999997 6999999999841           689999999974  45778888876532    


Q ss_pred             HHHhhhcccCCeEEEEEEEEEe-cCcEEEEECC--EEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehhhh
Q 015066          178 WERCRQLQSEDVVVKGKVVGAN-KGGVVAEVEG--LRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKA  254 (414)
Q Consensus       178 ~~~l~~~~~~g~iv~G~V~~v~-~~G~~V~i~g--i~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~  254 (414)
                             .+.|++++|+|++++ ++|+||++|.  .+||||+|+++|.......+||++.++ +++|+ ++||.+|+|+.
T Consensus        67 -------~~~G~~~~g~V~~v~~~~GaFVdiG~~~~d~lvp~sel~~~~~~~~~~Gd~v~v~-l~iD~-~~Ri~ls~k~~  137 (285)
T 3go5_A           67 -------ATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKELWPKKGDQLYIR-LEVDK-KDRIWGLLAYQ  137 (285)
T ss_dssp             -------SCSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGGSCSSGGGSCCTTCEEEEE-EEECT-TSCEEEEECCH
T ss_pred             -------ccCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHHCCcccccccCCCCEEEEE-EEECC-CCcEEEEehhh
Confidence                   367889999999999 7999999984  899999999998755445689999765 79998 78999999865


Q ss_pred             -hhhHH----hhccccEEEEEEEEEEeeceEEE-EEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCe
Q 015066          255 -MADSQ----AQLGIGSVVIGTVQSLKPYGAFI-DIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGR  327 (414)
Q Consensus       255 -l~~~~----~~l~~G~iv~g~V~~i~~~G~fV-~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~r  327 (414)
                       ..+.+    ..+++|++|+|+|+++++||+|| .++ |+.||||+||++.        .+++||+|+|+|+++|++++|
T Consensus       138 ~~~~~~~~~~~~~~~G~~V~g~V~~i~~~G~fV~~i~~g~~Glih~SEl~~--------~l~~Gd~v~~~V~~id~~d~k  209 (285)
T 3go5_A          138 EDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERYA--------EPRLGQVLDARVIGFREVDRT  209 (285)
T ss_dssp             HHHHHHCCCCCSCCTTCEEEEEEEEEETTEEEEEETTTTEEEEECGGGCSS--------CCCTTCEEEEEEEEEETTTTE
T ss_pred             hhcchhhhhhhhCCCCCEEEEEEEEEeCCcEEEEEeCCCeEEEEEHHHccc--------cCCCCCEEEEEEEEEECCCCe
Confidence             23333    57899999999999999999999 996 7999999999973        589999999999999999999


Q ss_pred             EEEEEeeCCCCCCc
Q 015066          328 VSLSTKKLEPTPGD  341 (414)
Q Consensus       328 i~LS~K~~~~~p~~  341 (414)
                      |+||+|++..++++
T Consensus       210 I~LSlk~~~~~~~~  223 (285)
T 3go5_A          210 LNLSLKPRSFEMLE  223 (285)
T ss_dssp             EEEECSCCCCCCCC
T ss_pred             EEEEeChhhhhccc
Confidence            99999999877664

>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=3.6e-21  Score=186.10  Aligned_cols=148  Identities=16%  Similarity=0.038  Sum_probs=129.9

Q ss_pred             cCCCCCEEEEEEEEEe-CCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh
Q 015066           96 NSELGTKVKGTVFCTD-NRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~-~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~  173 (414)
                      .+++|+++.|+|++++ ++|+||++|. +.+||+|.+|+++....     .+++|+++.+. +++|+ ++|+.+|+|...
T Consensus        66 ~~~~G~~~~g~V~~v~~~~GaFVdiG~~~~d~lvp~sel~~~~~~-----~~~~Gd~v~v~-l~iD~-~~Ri~ls~k~~~  138 (285)
T 3go5_A           66 TATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKEL-----WPKKGDQLYIR-LEVDK-KDRIWGLLAYQE  138 (285)
T ss_dssp             CSCSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGGSCSSGGG-----SCCTTCEEEEE-EEECT-TSCEEEEECCHH
T ss_pred             cccCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHHCCccccc-----ccCCCCEEEEE-EEECC-CCcEEEEehhhh
Confidence            4689999999999999 7999999997 68999999999864322     26899999655 68887 789999999876


Q ss_pred             hhHHHHHhhhcccCCeEEEEEEEEEecCcEEE-EEC-CEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeeh
Q 015066          174 YELAWERCRQLQSEDVVVKGKVVGANKGGVVA-EVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSN  251 (414)
Q Consensus       174 ~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V-~i~-gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~  251 (414)
                      ....|......+..|+.|+|+|.+++++|+|| .++ |+.||||.|+++....    +||+|+++|+++|++++||.||+
T Consensus       139 ~~~~~~~~~~~~~~G~~V~g~V~~i~~~G~fV~~i~~g~~Glih~SEl~~~l~----~Gd~v~~~V~~id~~d~kI~LSl  214 (285)
T 3go5_A          139 DFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERYAEPR----LGQVLDARVIGFREVDRTLNLSL  214 (285)
T ss_dssp             HHHHHCCCCCSCCTTCEEEEEEEEEETTEEEEEETTTTEEEEECGGGCSSCCC----TTCEEEEEEEEEETTTTEEEEEC
T ss_pred             hcchhhhhhhhCCCCCEEEEEEEEEeCCcEEEEEeCCCeEEEEEHHHccccCC----CCCEEEEEEEEEECCCCeEEEEe
Confidence            66789887777788999999999999999999 996 8999999999986433    89999999999999899999999


Q ss_pred             hhh
Q 015066          252 RKA  254 (414)
Q Consensus       252 K~~  254 (414)
                      |+.
T Consensus       215 k~~  217 (285)
T 3go5_A          215 KPR  217 (285)
T ss_dssp             SCC
T ss_pred             Chh
Confidence            985

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

Probab=99.76  E-value=1.9e-18  Score=145.44  Aligned_cols=96  Identities=30%  Similarity=0.518  Sum_probs=80.9

Q ss_pred             ehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcc-cccCcccccCCCCEEEEEEEEEeC
Q 015066          250 SNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHD-RVADIATVLQPGDTLKVMILSHDR  323 (414)
Q Consensus       250 S~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~-~~~~~~~~~~~G~~V~vkVl~id~  323 (414)
                      |+|+...+.+    .++++|++|.|+|+++++||+||+|+ |++||||+|++++. ++.++.+.|++||.|+|+|+++|.
T Consensus        12 ~~k~~~~~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~   91 (115)
T 2khi_A           12 SGLVPRGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDE   91 (115)
T ss_dssp             ---------CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEET
T ss_pred             chhhcccCCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEEC
Confidence            4555544443    46899999999999999999999998 89999999999984 788899999999999999999999


Q ss_pred             CCCeEEEEEeeCCCCCCcccCC
Q 015066          324 ERGRVSLSTKKLEPTPGDMIRN  345 (414)
Q Consensus       324 e~~ri~LS~K~~~~~p~~~~~~  345 (414)
                      ++++|.||+|++.++||+.+..
T Consensus        92 ~~~rI~lslk~~~~~p~~~~~~  113 (115)
T 2khi_A           92 ERRRISLGLKQCKANPWQQFAE  113 (115)
T ss_dssp             TTTEEEECCCCCCSSCCCCCCC
T ss_pred             CCCEEEEEEEecCcCHHHHHHh
Confidence            9999999999999999987654

>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=99.75  E-value=1.1e-18  Score=158.05  Aligned_cols=84  Identities=24%  Similarity=0.505  Sum_probs=67.3

Q ss_pred             ccccEEEEEEEEEEeeceEEEEE---CCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT  338 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l---~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~  338 (414)
                      +++|++|.|+|++|++||+||+|   +|++||||+|+|++.++.++.+.|++||.|+|+|+++|+++++|+||+|++.++
T Consensus        13 p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~~~~~   92 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPE   92 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTTCCHH
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeecCcC
Confidence            47999999999999999999999   489999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccCC
Q 015066          339 PGDMIRN  345 (414)
Q Consensus       339 p~~~~~~  345 (414)
                      ||+.+..
T Consensus        93 p~~~~~~   99 (182)
T 1kl9_A           93 EAIKCED   99 (182)
T ss_dssp             HHHHHHH
T ss_pred             hHHHHHH
Confidence            9875543

>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=99.73  E-value=2.7e-18  Score=145.20  Aligned_cols=86  Identities=28%  Similarity=0.440  Sum_probs=80.0

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEECC--EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEEEEeeC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIGG--INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRER--GRVSLSTKKL  335 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~g--v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~--~ri~LS~K~~  335 (414)
                      ..+++|++|.|+|++|++||+||+|.|  .+||||+|++++.++.++.+.|++||.|+|+|+++|+++  ++|.||+|++
T Consensus        18 ~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~~~~i~LSlk~~   97 (119)
T 2cqo_A           18 NLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVV   97 (119)
T ss_dssp             CSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECSSCEEEEEESTTB
T ss_pred             cccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEeccccCceEEEEEeec
Confidence            468899999999999999999999976  599999999999999999999999999999999999864  6999999999


Q ss_pred             CCCCCcccCC
Q 015066          336 EPTPGDMIRN  345 (414)
Q Consensus       336 ~~~p~~~~~~  345 (414)
                      .++||+++..
T Consensus        98 ~~~~~~~~~~  107 (119)
T 2cqo_A           98 NQGTGKDLDP  107 (119)
T ss_dssp             CSSSCCBSCT
T ss_pred             ccCCccccCc
Confidence            9999998854

>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=99.73  E-value=7.7e-18  Score=138.89  Aligned_cols=84  Identities=31%  Similarity=0.577  Sum_probs=77.8

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC----CEEEEEeeccc-CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG----GINGLLHVSQI-SHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK  334 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~----gv~Glvh~sel-s~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~  334 (414)
                      ..+++|++|.|+|++|.+||+||+|+    +++||||+|++ ++.++.++.+.|++||.|+|+|+++|+  +||.||+|+
T Consensus         8 ~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~--~~i~LSlk~   85 (103)
T 2eqs_A            8 EEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG--TKTSLSMKD   85 (103)
T ss_dssp             SSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET--TEEEEESTT
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC--CeeEEEEee
Confidence            46889999999999999999999998    69999999999 677888999999999999999999996  699999999


Q ss_pred             CCCCCCcccCC
Q 015066          335 LEPTPGDMIRN  345 (414)
Q Consensus       335 ~~~~p~~~~~~  345 (414)
                      +.++||+++..
T Consensus        86 ~~~~~~~~~~~   96 (103)
T 2eqs_A           86 VDQETGEDLNP   96 (103)
T ss_dssp             BCTTTCCBCCS
T ss_pred             cccCCchhcCc
Confidence            99999998743

>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=99.73  E-value=4.2e-18  Score=153.36  Aligned_cols=84  Identities=23%  Similarity=0.457  Sum_probs=71.0

Q ss_pred             cccEEEEEEEEEEeeceEEEEE---CCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCC
Q 015066          263 GIGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTP  339 (414)
Q Consensus       263 ~~G~iv~g~V~~i~~~G~fV~l---~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p  339 (414)
                      ++|++|.|+|++|++||+||+|   +|++||||+|+|++.++.++.+.|++||.|+|+|+++|+++++|+||+|++.++|
T Consensus        14 ~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~~~~~~   93 (175)
T 2a19_A           14 EIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSSED   93 (175)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTTCCHHH
T ss_pred             CCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEecCcCh
Confidence            4899999999999999999999   5899999999999999999999999999999999999999999999999999998


Q ss_pred             CcccCCc
Q 015066          340 GDMIRNP  346 (414)
Q Consensus       340 ~~~~~~~  346 (414)
                      |+.+.+.
T Consensus        94 ~~~~~~~  100 (175)
T 2a19_A           94 IIKCEEK  100 (175)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            8755443

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

Probab=99.71  E-value=8.7e-18  Score=134.56  Aligned_cols=76  Identities=25%  Similarity=0.377  Sum_probs=71.8

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC---CEEEEEeec-ccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVS-QISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~s-els~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      ..++|+++.|+|+ |++||+||+|.   |++||+|+| +++++++.++++.+ +||.|+|+|+++|++++||.||+|++.
T Consensus         8 ~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lslk~~~   85 (88)
T 1luz_A            8 LPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKRMC   85 (88)
T ss_dssp             CCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEEEC
T ss_pred             CCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEEeecC
Confidence            4689999999999 99999999995   699999999 99999999999999 999999999999999999999999987


Q ss_pred             CC
Q 015066          337 PT  338 (414)
Q Consensus       337 ~~  338 (414)
                      ++
T Consensus        86 ~~   87 (88)
T 1luz_A           86 RH   87 (88)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

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

Probab=99.70  E-value=2e-17  Score=142.03  Aligned_cols=82  Identities=38%  Similarity=0.706  Sum_probs=78.3

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT  338 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~  338 (414)
                      .++++|++|.|+|++|++||+||+|+ |++||||+|++++.++.++.+.|++||.|+|+|+++|.++++|.||+|++.++
T Consensus         3 ~~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk~~~~~   82 (130)
T 2k4k_A            3 AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIRATQAA   82 (130)
T ss_dssp             CCCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESHHHHHS
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEeecccC
Confidence            36889999999999999999999996 89999999999999999999999999999999999999999999999999999


Q ss_pred             CCc
Q 015066          339 PGD  341 (414)
Q Consensus       339 p~~  341 (414)
                      |+.
T Consensus        83 p~~   85 (130)
T 2k4k_A           83 PEK   85 (130)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            876

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

Probab=99.68  E-value=4.5e-17  Score=135.62  Aligned_cols=89  Identities=28%  Similarity=0.397  Sum_probs=75.5

Q ss_pred             eehhhhhhhHH----hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeC
Q 015066          249 LSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDR  323 (414)
Q Consensus       249 LS~K~~l~~~~----~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~  323 (414)
                      -|+|+...+++    .++++|++|.|+|+++.+||+||+|+ |++||||++++++.++.++.+.|++||.|+|+|+++|+
T Consensus        12 ~~iKq~~~~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~   91 (109)
T 2khj_A           12 SGLVPRGSHMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDR   91 (109)
T ss_dssp             ---------CHHHHTTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEET
T ss_pred             cchhhcccCHHHHHhhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEEC
Confidence            45666655443    57899999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             CCCeEEEEEeeCCC
Q 015066          324 ERGRVSLSTKKLEP  337 (414)
Q Consensus       324 e~~ri~LS~K~~~~  337 (414)
                      ++++|.||+|++++
T Consensus        92 ~~~ki~LS~k~~~~  105 (109)
T 2khj_A           92 KNRAISLSVRAKDE  105 (109)
T ss_dssp             TTTEEEEETTSSSS
T ss_pred             CCCEEEEEEeecCh
Confidence            88999999999865

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

Probab=99.67  E-value=2.7e-16  Score=123.57  Aligned_cols=73  Identities=26%  Similarity=0.441  Sum_probs=68.1

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCC
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEP  337 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~  337 (414)
                      ++++|++|.|+|+++.+||+||+++ +++||+|+|++++.++    +.|++||.|+|+|+++|++++||.||+|++.+
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 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRL----ENLNVGDEIIVQAIDVRPEKREIDFKYIPLEH   75 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSCCG----GGCCTTCEEEEEEEEEETTTTEEEEEECSCC-
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCcccc----eeeCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            4789999999999999999999998 8999999999998775    78999999999999999999999999998875

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

Probab=99.60  E-value=1.2e-15  Score=146.61  Aligned_cols=82  Identities=23%  Similarity=0.507  Sum_probs=77.7

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT  338 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~  338 (414)
                      +++|++|.|+|++|.+||+||+|+   |++||||+|+++++++.++.+.|++||.|.|+|+++|+++++|.||+|++.++
T Consensus         9 p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~~~~   88 (275)
T 3aev_A            9 PEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQQ   88 (275)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESTTCCHH
T ss_pred             CCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEEeecCcc
Confidence            468999999999999999999995   79999999999999999999999999999999999999999999999999988


Q ss_pred             CCccc
Q 015066          339 PGDMI  343 (414)
Q Consensus       339 p~~~~  343 (414)
                      ||...
T Consensus        89 ~~~~~   93 (275)
T 3aev_A           89 QRKAK   93 (275)
T ss_dssp             HHHHH
T ss_pred             hhHHH
Confidence            88644

>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=99.60  E-value=9.4e-18  Score=151.82  Aligned_cols=122  Identities=16%  Similarity=0.122  Sum_probs=100.3

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEe--CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066           97 SELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdi--g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      +++|+++.|+|+++.++|+||++  .++.+|+||.+|+++.+..++.+. +++||.++|+|+++|.+++++.||+|....
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 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKL-IRIGRNECVVVIRVDKEKGYIDLSKRRVSP   91 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC-------------CTTCEEEEEEEEEETTTTEEEEESTTCCH
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHh-cCCCCEEEEEEEEEECCCCEEEEEEeecCc
Confidence            48999999999999999999999  567999999999999988888887 999999999999999999999999998765


Q ss_pred             hHHHHHhhhcccCCeEEEEEEEEEec-CcEEEEEC-CEEEEEeccccCCC
Q 015066          175 ELAWERCRQLQSEDVVVKGKVVGANK-GGVVAEVE-GLRGFVPFSQISSK  222 (414)
Q Consensus       175 ~~~~~~l~~~~~~g~iv~G~V~~v~~-~G~~V~i~-gi~GfIp~sels~~  222 (414)
                       .+|..+.+.+..|..++|+|+++.+ +|  +.+. |++|++|.++++|.
T Consensus        92 -~p~~~~~~~~~~g~~v~g~v~~i~~~~g--v~l~~giegl~h~s~~~~~  138 (182)
T 1kl9_A           92 -EEAIKCEDKFTKSKTVYSILRHVAEVLE--YTKDEQLESLFQRTAWVFD  138 (182)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHHHHTT--CCSHHHHHHHHHHTHHHHH
T ss_pred             -ChHHHHHHhccCCCEEEEEEEEchhhcC--CcccCChhheEEeeecchh
Confidence             5799988888888899999999987 99  6775 99999999988654

>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=99.59  E-value=1e-15  Score=148.92  Aligned_cols=83  Identities=25%  Similarity=0.498  Sum_probs=78.2

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCC
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEP  337 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~  337 (414)
                      .+++|++|.|+|++|.+||+||+|+   |++||||+|+++|.++.++.+.|++||.|+|+|+++|+++++|.||+|++.+
T Consensus        10 ~~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~~~   89 (308)
T 1q8k_A           10 FPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRVSP   89 (308)
T ss_dssp             CCSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSSCCH
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEeccc
Confidence            3569999999999999999999995   7999999999999999999999999999999999999999999999999998


Q ss_pred             CCCccc
Q 015066          338 TPGDMI  343 (414)
Q Consensus       338 ~p~~~~  343 (414)
                      +||..+
T Consensus        90 ~p~~~~   95 (308)
T 1q8k_A           90 EEAIKC   95 (308)
T ss_dssp             HHHHHH
T ss_pred             ChHHHH
Confidence            888654

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

Probab=99.55  E-value=3.8e-16  Score=167.61  Aligned_cols=88  Identities=35%  Similarity=0.596  Sum_probs=0.0

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT  338 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~  338 (414)
                      .++++|++|.|+|++|.+||+||+|. |++||||+|+++++|+.++.+.|++||.|+|||+++|+ ++||+||+|++.++
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 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIKEATEQ  701 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCccccCcccccCCCCEEEEEEEEECC-CCcEEEEEEeccCC
Confidence            57899999999999999999999997 89999999999999999999999999999999999998 89999999999999


Q ss_pred             CCcccCCchh
Q 015066          339 PGDMIRNPKL  348 (414)
Q Consensus       339 p~~~~~~~~~  348 (414)
                      ||.++.+...
T Consensus       702 ~g~~~~p~~~  711 (723)
T 3cdi_A          702 SQPAAAPEAP  711 (723)
T ss_dssp             ----------
T ss_pred             CCcccCcccc
Confidence            9998744333

>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=99.55  E-value=1e-15  Score=146.62  Aligned_cols=87  Identities=26%  Similarity=0.448  Sum_probs=80.3

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEE---CCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l---~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      ..+++|++|.|+|++|.+||+||+|   +|++||||+|+++++++.++.+.|++||.|.|+|+++|+++++|.||+|.+.
T Consensus         7 ~~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~~~   86 (266)
T 3cw2_C            7 KLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKKVT   86 (266)
T ss_dssp             SSCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEESTTSC
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEEecc
Confidence            3578999999999999999999999   4799999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccCCc
Q 015066          337 PTPGDMIRNP  346 (414)
Q Consensus       337 ~~p~~~~~~~  346 (414)
                      ++||..+.+.
T Consensus        87 ~~~~~~~~~~   96 (266)
T 3cw2_C           87 DDERRKKNLQ   96 (266)
T ss_dssp             TTHHHHHHHH
T ss_pred             hhhHHHHHHh
Confidence            9888765443

>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=99.51  E-value=2.1e-16  Score=170.16  Aligned_cols=127  Identities=24%  Similarity=0.428  Sum_probs=51.7

Q ss_pred             EEEEE--EecCcEEEEECCEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehhhhhhhHHhhccccEEEEE
Q 015066          193 GKVVG--ANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIG  270 (414)
Q Consensus       193 G~V~~--v~~~G~~V~i~gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~~~~~~l~~G~iv~g  270 (414)
                      |++++  ..++|++|+++. +|.++.+..++.....                ...++     ..+.+. ..+++|++|.|
T Consensus       617 Gk~Ik~I~~~~G~~IdI~~-dG~v~Is~~~~~~~~~----------------a~~~i-----~~i~~p-~~~~vG~i~~G  673 (757)
T 1e3p_A          617 RQMINQIQEDTGAEITIED-DGTIYIGAADGPAAEA----------------ARATI-----NGIANP-TSPEVGERILG  673 (757)
T ss_dssp             ----CTTCCCCCSCC---------CCCBSSHHHHCC-------------------------------------------C
T ss_pred             ceeeehhhHhhCCEEEecC-CceEEEecCCHHHHHH----------------HHHHH-----HHhcch-hhcccccEEEE
Confidence            55555  367899999975 8999998877542100                00000     001111 46889999999


Q ss_pred             EEEEEeeceEEEEEC-CEEEEEeeccc----CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCCCCccc
Q 015066          271 TVQSLKPYGAFIDIG-GINGLLHVSQI----SHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMI  343 (414)
Q Consensus       271 ~V~~i~~~G~fV~l~-gv~Glvh~sel----s~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~p~~~~  343 (414)
                      +|++|.+||+||+|. |++||||+|+|    +|+|+.++.+.|++||.|+|+|+++|+ ++||+||+|++.++||+..
T Consensus       674 ~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s~~rv~~~~~~~~vGd~V~VkVi~vd~-~grI~LS~k~~~~~pw~~~  750 (757)
T 1e3p_A          674 SVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDS-RGKLSLIPVIEGEEAASDE  750 (757)
T ss_dssp             BEEECC-CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCS-SCC----------------
T ss_pred             EEEEccccEEEEEEcCCcEEEEEhHHhccccCCCcccCcccccCCCCEEEEEEEEECC-CCCEEEEEecCCCCchhhh
Confidence            999999999999996 89999999999    999999999999999999999999998 9999999999999999754

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

Probab=99.51  E-value=1.4e-15  Score=162.66  Aligned_cols=87  Identities=34%  Similarity=0.591  Sum_probs=0.0

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT  338 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~  338 (414)
                      .++++|++|.|+|++|.+||+||+|. |++||||+|+++++++.++.+.|++||.|+|||+++|+ ++||.||+|++.++
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 DEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDD-RGKTKLSMKVVDQE  711 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCcccccCccccCCCCCEEEEEEEEECC-CCcEEEEEeecccC
Confidence            68899999999999999999999997 89999999999999999999999999999999999998 79999999999999


Q ss_pred             CCcccCCch
Q 015066          339 PGDMIRNPK  347 (414)
Q Consensus       339 p~~~~~~~~  347 (414)
                      ||+++.+..
T Consensus       712 ~G~~~~~k~  720 (726)
T 4aid_A          712 TGEDLSKKE  720 (726)
T ss_dssp             ---------
T ss_pred             cchhhhhhh
Confidence            999886544

>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=99.45  E-value=1.8e-14  Score=129.55  Aligned_cols=104  Identities=16%  Similarity=0.170  Sum_probs=88.0

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhh
Q 015066           98 ELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE  175 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G~~Vdig--~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~  175 (414)
                      ++|+++.|+|+++.++|+||+|.  ++.+|+||.+|+++.+..++.+. +++||.+.|+|+++|++++++.||+|.... 
T Consensus        14 ~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~-~~vGd~V~vkVl~vd~~~~~I~LSlk~~~~-   91 (175)
T 2a19_A           14 EIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKL-IRVGKNDVAVVLRVDKEKGYIDLSKRRVSS-   91 (175)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--------CCCCC-CCTTSEEEEEEEEEETTTTEEEEESTTCCH-
T ss_pred             CCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHc-CCCCCEEEEEEEEEECCCCeEEEEEEecCc-
Confidence            48999999999999999999993  67999999999999888888887 999999999999999999999999998766 


Q ss_pred             HHHHHhhhcccCCeEEEEEEEEEe-cCcE
Q 015066          176 LAWERCRQLQSEDVVVKGKVVGAN-KGGV  203 (414)
Q Consensus       176 ~~~~~l~~~~~~g~iv~G~V~~v~-~~G~  203 (414)
                      .+|..+.+.++.|+.++|+|.++. ++|+
T Consensus        92 ~~~~~~~~~~~~g~~v~g~V~~i~~~~G~  120 (175)
T 2a19_A           92 EDIIKCEEKYQKSKTVHSILRYCAEKFQI  120 (175)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             ChHHHHHHhccCCCcceEEEEEchhhcCC
Confidence            689998888888889999999997 7787

>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=99.42  E-value=9.8e-14  Score=117.15  Aligned_cols=79  Identities=29%  Similarity=0.376  Sum_probs=67.2

Q ss_pred             HhhccccEEEEEEEEEEeeceEEEEEC--CEEEEEeeccc-CcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          259 QAQLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQI-SHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       259 ~~~l~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sel-s~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      ..++++|++|.|+|++|.+||+||+|+  +..|++|.++. +|.++.++.+.|++||.|+|+|+++|+++++|.||+|+.
T Consensus        16 ~~~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~Lslk~~   95 (119)
T 1wi5_A           16 AEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHS   95 (119)
T ss_dssp             TTTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCC
T ss_pred             HhcCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCCCCEEEEEEchh
Confidence            368999999999999999999999998  46666555553 344566889999999999999999999999999999976


Q ss_pred             CC
Q 015066          336 EP  337 (414)
Q Consensus       336 ~~  337 (414)
                      ..
T Consensus        96 ~l   97 (119)
T 1wi5_A           96 EV   97 (119)
T ss_dssp             CS
T ss_pred             hc
Confidence            43

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=99.36  E-value=1.5e-12  Score=118.42  Aligned_cols=79  Identities=25%  Similarity=0.462  Sum_probs=70.6

Q ss_pred             hccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCccccc-----------CcccccCCCCEEEEEEEEEeCCCC---
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVMILSHDRERG---  326 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~-----------~~~~~~~~G~~V~vkVl~id~e~~---  326 (414)
                      .+.+|++|.|+|+++.+||+||++++++||+|+|+++++++.           ++.+.|++||.|+|+|+++|.+++   
T Consensus        78 ~~~~Gev~~G~V~~v~~~G~fV~l~~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~p~  157 (187)
T 1go3_E           78 IPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKR  157 (187)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC----
T ss_pred             ccCCCCEEEEEEEEEeCcEEEEEEcCccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccCCCC
Confidence            377899999999999999999999989999999999988775           788999999999999999998755   


Q ss_pred             --eEEEEEeeCCCCC
Q 015066          327 --RVSLSTKKLEPTP  339 (414)
Q Consensus       327 --ri~LS~K~~~~~p  339 (414)
                        +|.||+|+...-|
T Consensus       158 ~~~I~lS~k~~~LG~  172 (187)
T 1go3_E          158 GSKIALTMRQPYLGK  172 (187)
T ss_dssp             -CEEEEECCSTTCEE
T ss_pred             ccEEEEEEcCCCCCc
Confidence              9999999865433

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

Probab=99.36  E-value=2e-12  Score=107.32  Aligned_cols=85  Identities=21%  Similarity=0.328  Sum_probs=76.5

Q ss_pred             HHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEE
Q 015066           88 SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVL  167 (414)
Q Consensus        88 ~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~L  167 (414)
                      ..|+.+...+++|++++|+|+++.++|+||+++.+.+||||.+++++.+..++.+. +.+|+.+.|+|+++|..++++.|
T Consensus        20 ~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~-~~vGd~V~v~V~~vd~~~~ki~L   98 (109)
T 2khj_A           20 HMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLV-LSVGDEVEAKFTGVDRKNRAISL   98 (109)
T ss_dssp             -CHHHHTTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSSSGGGS-CCTTCEEEEEEEEEETTTTEEEE
T ss_pred             CHHHHHhhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccccChhhc-cCCCCEEEEEEEEEECCCCEEEE
Confidence            45677777899999999999999999999999988999999999998877777776 99999999999999988889999


Q ss_pred             Eeeehh
Q 015066          168 SLRMIQ  173 (414)
Q Consensus       168 S~k~~~  173 (414)
                      |++...
T Consensus        99 S~k~~~  104 (109)
T 2khj_A           99 SVRAKD  104 (109)
T ss_dssp             ETTSSS
T ss_pred             EEeecC
Confidence            998754

>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=99.34  E-value=1.6e-13  Score=133.46  Aligned_cols=109  Identities=16%  Similarity=0.132  Sum_probs=98.6

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig--~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~  173 (414)
                      .+++|+++.|+|+++.++|+||+|+  ++.+||+|.+++++.+..++.+. +++||.+.|+|+++|++++++.||+|...
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 FPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKL-IRIGRNECVKVIRVDKEKGYIDLSKRRVS   88 (308)
T ss_dssp             CCSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCSCCTTT-CSSSCEEEEEEEEEETTTTEEEEECSSCC
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccccCHHHh-cCCCCEEEEEEEEEeCCCCEEEEEEEecc
Confidence            3569999999999999999999997  67999999999999888888887 99999999999999999999999999876


Q ss_pred             hhHHHHHhhhcccCCeEEEEEEEEEec-CcEEEE
Q 015066          174 YELAWERCRQLQSEDVVVKGKVVGANK-GGVVAE  206 (414)
Q Consensus       174 ~~~~~~~l~~~~~~g~iv~G~V~~v~~-~G~~V~  206 (414)
                      . .+|..+.+.+..|+++.|+|+++.+ +|+|+.
T Consensus        89 ~-~p~~~~~~~~~~G~~v~G~V~~v~~~~G~fi~  121 (308)
T 1q8k_A           89 P-EEAIKCEDKFTKSKTVYSILRHVAEVLEYTKD  121 (308)
T ss_dssp             H-HHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSS
T ss_pred             c-ChHHHHHHHccCCCeeEEEEEEcccccCCccC
Confidence            4 6899888888888899999999988 699763

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

Probab=99.33  E-value=1.1e-12  Score=147.01  Aligned_cols=77  Identities=9%  Similarity=0.078  Sum_probs=73.7

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccc-ccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR-VADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~-~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      .++++|++|.|+|++|++||+||+|+ |++||||+|+|++.+ +.++.+.|++||.|+|+|+++|.+++||.||||..+
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 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDHD  976 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEECCHHH
T ss_pred             hhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEecHHH
Confidence            58899999999999999999999998 899999999999998 899999999999999999999999999999999764

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

Probab=99.32  E-value=1.8e-12  Score=108.74  Aligned_cols=92  Identities=18%  Similarity=0.224  Sum_probs=77.7

Q ss_pred             HHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccc-ccCCccccCccCCcEEEEEEEEEeCCCCeEEE
Q 015066           89 ALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH-KIKHVEEAGIVPGLKEEFVIIGENEADDSLVL  167 (414)
Q Consensus        89 ~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~-~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~L  167 (414)
                      -|+.....+++|+++.|+|+++.++|+||+++++.+||+|.+++++. ...++.+. +.+||.++|+|+++|.+++++.|
T Consensus        20 p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~-~~vGd~V~vkV~~vd~~~~rI~l   98 (115)
T 2khi_A           20 HWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKV-VNVGDVVEVMVLDIDEERRRISL   98 (115)
T ss_dssp             -CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTT-CCTTCEEEEEEEEEETTTTEEEE
T ss_pred             CHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccE-ECCCCEEEEEEEEEECCCCEEEE
Confidence            34555567899999999999999999999999889999999999863 45566665 89999999999999998999999


Q ss_pred             EeeehhhhHHHHHhh
Q 015066          168 SLRMIQYELAWERCR  182 (414)
Q Consensus       168 S~k~~~~~~~~~~l~  182 (414)
                      |++.... .+|+.+.
T Consensus        99 slk~~~~-~p~~~~~  112 (115)
T 2khi_A           99 GLKQCKA-NPWQQFA  112 (115)
T ss_dssp             CCCCCCS-SCCCCCC
T ss_pred             EEEecCc-CHHHHHH
Confidence            9998765 4676553

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

Probab=99.31  E-value=2.7e-13  Score=145.11  Aligned_cols=155  Identities=10%  Similarity=0.126  Sum_probs=13.0

Q ss_pred             cCCCCCCccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCCCCC---HHHHHH-
Q 015066           13 CPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFT---LEEFHS-   88 (414)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~~~~---~~~f~~-   88 (414)
                      |-.-|...+|+|||       -|..++..|.++.-.|++++    ..+++|+++.-..++-..++.+...   .+..++ 
T Consensus       556 al~~~r~~~~~~ap-------~~~~~~i~~~ki~~vig~gg----~~i~~i~~~tg~~idi~ddG~v~I~~~~~~~~~~A  624 (726)
T 4aid_A          556 AMDAPRADVGDFAP-------KIETINIPTDKIREVIGSGG----KVIREIVATTGAKVDINDDGVVKVSASDGAKIKAA  624 (726)
T ss_dssp             TCSSCCSSCCSSCC-------C-----------------------------------------------CCSCHHHHHHH
T ss_pred             HHHhhhhhhcccCC-------eEEEEeCCHHHHHhhcCCCc----hhHHHHHHHHCCceeEECCceEEEEeCCHHHHHHH
Confidence            33445556999999       67888999999999999999    7888899987666654444444332   333333 


Q ss_pred             --HHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEE
Q 015066           89 --ALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV  166 (414)
Q Consensus        89 --~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~  166 (414)
                        .++.+...+++|++++|+|+++.++|+||+|.++.+|++|.+|+++.+..++++. +++||.|+|+|+++|+ ++++.
T Consensus       625 ~~~i~~i~~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~~rv~~~~d~-~kvGD~V~VkVi~iD~-~grI~  702 (726)
T 4aid_A          625 IDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDV-LKEGQMVKVKLLGFDD-RGKTK  702 (726)
T ss_dssp             HHC-----------------------------------------------------------------------------
T ss_pred             HHHHHHHhhhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCcccccCcccc-CCCCCEEEEEEEEECC-CCcEE
Confidence              3555557889999999999999999999999888999999999999988888887 9999999999999997 79999


Q ss_pred             EEeeehhhhHHHHHh
Q 015066          167 LSLRMIQYELAWERC  181 (414)
Q Consensus       167 LS~k~~~~~~~~~~l  181 (414)
                      ||+|....+ .|+.+
T Consensus       703 LS~K~~~~~-~G~~~  716 (726)
T 4aid_A          703 LSMKVVDQE-TGEDL  716 (726)
T ss_dssp             ---------------
T ss_pred             EEEeecccC-cchhh
Confidence            999987763 55555

>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=99.30  E-value=4.4e-12  Score=114.58  Aligned_cols=75  Identities=29%  Similarity=0.558  Sum_probs=66.8

Q ss_pred             hccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccc-----------cCcccccCCCCEEEEEEEEEeCC----C
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVMILSHDRE----R  325 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~-----------~~~~~~~~~G~~V~vkVl~id~e----~  325 (414)
                      .+.+|+++.|+|+++++||+||+++.++||+|+|++.++++           ++..+.|+.||.|+|||+++|.+    .
T Consensus        78 ~p~~Gev~~G~V~~v~~~G~fv~l~~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~~~~~  157 (180)
T 4ayb_E           78 VPVVQEVVEGEVLQVDNYGVFVNLGPMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTGRL  157 (180)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC------
T ss_pred             eccCCCEEEEEEeeeccceEEEEECCccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCCCCccc
Confidence            47799999999999999999999999999999999999876           57788999999999999999864    3


Q ss_pred             CeEEEEEeeC
Q 015066          326 GRVSLSTKKL  335 (414)
Q Consensus       326 ~ri~LS~K~~  335 (414)
                      .||.||||+-
T Consensus       158 ~rI~ls~k~~  167 (180)
T 4ayb_E          158 PRIALTMRQP  167 (180)
T ss_dssp             -CEEEECCST
T ss_pred             CcEEEEcCCC
Confidence            5899999974

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

Probab=99.29  E-value=1.8e-11  Score=95.93  Aligned_cols=74  Identities=15%  Similarity=0.194  Sum_probs=66.1

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      ++++|+++.|+|.++.++|+||+++++.+|++|.+++++.+.    +. +.+||.++|+|+++|++++++.||+++...
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 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRL----EN-LNVGDEIIVQAIDVRPEKREIDFKYIPLEH   75 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSCCG----GG-CCTTCEEEEEEEEEETTTTEEEEEECSCC-
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCcccc----ee-eCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            578999999999999999999999988999999999986543    33 899999999999999888999999987653

>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1

Probab=99.29  E-value=3.6e-12  Score=118.15  Aligned_cols=108  Identities=18%  Similarity=0.072  Sum_probs=66.3

Q ss_pred             ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCc----------ccccCCCCEEEEEEEEEeCCCC---eE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADI----------ATVLQPGDTLKVMILSHDRERG---RV  328 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~----------~~~~~~G~~V~vkVl~id~e~~---ri  328 (414)
                      ..+|+++.|+|+++++||+||+++..+||||+|+|++.+.-++          .+.+++||.|+|+|+++|.+.+   +|
T Consensus        81 p~vGev~~G~V~~vt~fG~FVelg~~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~~i~~I  160 (215)
T 2b8k_G           81 PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI  160 (215)
T ss_dssp             CCTTEEEEEEEEEEETTEEEEECTTSEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETTEEEEE
T ss_pred             cCCCCEEEEEEEEEecceEEEEecCcEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcCCCccEEE
Confidence            5799999999999999999999987999999999986533222          2679999999999999998774   77


Q ss_pred             EEEEeeCCCCCCcccCCchhhhhhHHHHHHHHHHHHHHHHHhH
Q 015066          329 SLSTKKLEPTPGDMIRNPKLVFEKAEEMAQTFRQRIAQAEAMA  371 (414)
Q Consensus       329 ~LS~K~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  371 (414)
                      . |||+.-.-|++..++.+...-.+.-.+ .-.++.+.+|++.
T Consensus       161 g-Smk~~~LG~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~  201 (215)
T 2b8k_G          161 G-SIKEDYLGAISHEKRRWKKNFIAVSAA-NRFKKISSSGALD  201 (215)
T ss_dssp             E-ECCSTTCEEC-------------------------------
T ss_pred             E-EcCCCCCCCcchhhHHHHhhhHhhhhh-hcccccccCCccc
Confidence            7 998876666765555554332232222 2234555555543

>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=99.29  E-value=4.4e-12  Score=117.20  Aligned_cols=76  Identities=20%  Similarity=0.284  Sum_probs=70.6

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC---------CEEEEEeecccCccccc--CcccccCCCCEEEEEEEEEeCCCCeEE
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG---------GINGLLHVSQISHDRVA--DIATVLQPGDTLKVMILSHDRERGRVS  329 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~---------gv~Glvh~sels~~~~~--~~~~~~~~G~~V~vkVl~id~e~~ri~  329 (414)
                      .+++|++|.|+|+++.++|+||+|.         +++|++|+|++++.+..  ++.+.|++||.|+|+|++++.+++++.
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            5889999999999999999999984         57999999999999888  899999999999999999998778999


Q ss_pred             EEEeeCC
Q 015066          330 LSTKKLE  336 (414)
Q Consensus       330 LS~K~~~  336 (414)
                      ||+|+.+
T Consensus       158 LS~k~~~  164 (209)
T 2nn6_I          158 LTTAENE  164 (209)
T ss_dssp             EECCSSS
T ss_pred             EEEecCC
Confidence            9999854

>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=99.27  E-value=1.2e-12  Score=141.44  Aligned_cols=77  Identities=38%  Similarity=0.604  Sum_probs=73.3

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      .++++|++|.|+|++|++||+||+++ +++||||+|+|++.++.++.+.|++||.|+|+|+++|.++++|.||||..+
T Consensus       650 ~~l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~LSlk~~~  727 (785)
T 3bzc_A          650 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMSD  727 (785)
T ss_dssp             TTCCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEECCSSCC
T ss_pred             hhcCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEEEecCC
Confidence            46889999999999999999999998 799999999999999999999999999999999999999999999999654

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

Probab=99.26  E-value=2.2e-11  Score=104.29  Aligned_cols=78  Identities=21%  Similarity=0.302  Sum_probs=72.4

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      ++++|+++.|+|+++.++|+||+|+++.+|+||.+++++.+..++.+. +.+||.|.|+|+++|.+++++.||++....
T Consensus         4 ~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~~~~~~~-~~vGd~V~vkV~~vd~~~~kI~LSlk~~~~   81 (130)
T 2k4k_A            4 KFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEH-LSVGDEVQVKVLAVDEEKGKISLSIRATQA   81 (130)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCCSCGGGT-CCTTCEEEEEEEEEETTTTEEEEESHHHHH
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccccCcccc-CCCCCEEEEEEEEEeCCCCEEEEEEeeccc
Confidence            678999999999999999999999888999999999998888887776 999999999999999889999999997654

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

Probab=99.25  E-value=5.8e-13  Score=147.30  Aligned_cols=78  Identities=9%  Similarity=0.069  Sum_probs=0.0

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccc-ccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR-VADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEP  337 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~-~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~  337 (414)
                      .++++|++|.|+|++|++||+||+|+ |++||||+|+|++.+ +.++.+.|++||.|+|+|+++|.+++||.||||..+.
T Consensus       901 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~dl  980 (1030)
T 3psf_A          901 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDHDV  980 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEechHHh
Confidence            57899999999999999999999998 899999999999998 8999999999999999999999999999999998764

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

Probab=99.23  E-value=1.8e-11  Score=97.63  Aligned_cols=75  Identities=11%  Similarity=0.190  Sum_probs=67.9

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCC--CeeEEEcCc-cccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITA--KSSAYLPTQ-EACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~--k~~g~lp~s-Els~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~  172 (414)
                      ..++|++++|+|+ +.++|+||++..  +.+|++|.+ ++++.+..++++. + +||+++++|+++|.+++++.||+|..
T Consensus         8 ~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~-~-~Gd~V~VkV~~vd~~~~kI~lslk~~   84 (88)
T 1luz_A            8 LPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDK-L-VGKTVKVKVIRVDYTKGYIDVNYKRM   84 (88)
T ss_dssp             CCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHH-H-TTCEEEEEEEEEETTTTEEEEEEEEE
T ss_pred             CCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHE-e-CCCEEEEEEEEEECCCCEEEEEEeec
Confidence            4589999999999 999999999963  699999999 9998887777776 6 99999999999999999999999976


Q ss_pred             h
Q 015066          173 Q  173 (414)
Q Consensus       173 ~  173 (414)
                      .
T Consensus        85 ~   85 (88)
T 1luz_A           85 C   85 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.22  E-value=5e-11  Score=133.83  Aligned_cols=120  Identities=12%  Similarity=-0.008  Sum_probs=102.5

Q ss_pred             hHHHHHHHHHHHHhhcccCCCCCCCCCHHHHHHHHHh-hcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccc
Q 015066           56 EREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEK-YDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI  134 (414)
Q Consensus        56 ~~~~l~~iiee~~~~~~~~~~~~~~~~~~~f~~~l~~-~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~  134 (414)
                      .+.+|++|+.|+.++.++.+.+...++..+.-.++.. ...++++|++|+|+|+++.++|+||+|+.+.+|+||.+++++
T Consensus       858 K~~TL~dI~~EL~~P~rD~R~~f~~~~~~e~~~mltget~~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd  937 (1219)
T 3psi_A          858 KLNNLNTIVLELLDGFEELRNDFHPLQGDEIFQSLTGESEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAG  937 (1219)
T ss_dssp             CHHHHHHHHHHHHSSSCCCSBCCCCBCHHHHHHHHTCCCTTTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSS
T ss_pred             ccchHHHHHHHHhccCCCCCcccCCCCHHHHHHhhccCcHhhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCC
Confidence            3679999999999999999988665555544444432 235899999999999999999999999989999999999999


Q ss_pred             cc-cCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhhH
Q 015066          135 HK-IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYEL  176 (414)
Q Consensus       135 ~~-~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~~  176 (414)
                      .+ ..++.+. +++||.|+|+|+++|.+++++.||+|......
T Consensus       938 ~~~v~~p~~v-~kvGd~V~vkVl~VD~~~~rI~LSlk~~dl~~  979 (1219)
T 3psi_A          938 AQLRRPANEI-YEIGKTYPAKVIYIDYANITAEVSLLDHDVKQ  979 (1219)
T ss_dssp             TTSCSCSTTT-SCTTCEEEEEEEEEEGGGTEEEEECCHHHHC-
T ss_pred             CcccCCHHHc-CCCCCEEEEEEEEEECCCCEEEEEecHHHhcc
Confidence            87 6788877 99999999999999999999999999876543

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

Probab=99.22  E-value=2.4e-12  Score=123.53  Aligned_cols=106  Identities=20%  Similarity=0.161  Sum_probs=95.2

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhh
Q 015066           97 SELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdig--~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~  174 (414)
                      .++|+++.|+|+++.++|+||+++  ++.+||||.+++++.+..++.+. +++||.+.|+|+++|.+++++.||++....
T Consensus         9 p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~-~kvGd~V~vkVi~vD~~~~~I~LSlk~~~~   87 (275)
T 3aev_A            9 PEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDY-LKEGQKVVAKVIRVDPRKGHIDLSLRRVTQ   87 (275)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGT-CCTTCEEEEEEEEEETTTTEEEEESTTCCH
T ss_pred             CCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhc-cCCCCEEEEEEEEEECCCCEEEEEEeecCc
Confidence            468999999999999999999997  57999999999999888888877 999999999999999999999999998765


Q ss_pred             hHHHHHhhhcccCCeEEEEEEEEEe-cCcEE
Q 015066          175 ELAWERCRQLQSEDVVVKGKVVGAN-KGGVV  204 (414)
Q Consensus       175 ~~~~~~l~~~~~~g~iv~G~V~~v~-~~G~~  204 (414)
                       ..|....+.+..|+.+.|.|..+. ++|+.
T Consensus        88 -~~~~~~~~~~~~g~~v~g~v~~v~~~~G~~  117 (275)
T 3aev_A           88 -QQRKAKLQEFKRAQKAENLLRLAAEKLGKD  117 (275)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             -chhHHHHHhccCCCeEEEEEEEchhhcCCC
Confidence             678877777778888999999997 88883

>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=99.19  E-value=2.1e-11  Score=102.75  Aligned_cols=90  Identities=17%  Similarity=0.196  Sum_probs=76.3

Q ss_pred             HhhcccCCCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC--CeEEE
Q 015066           91 EKYDFNSELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD--DSLVL  167 (414)
Q Consensus        91 ~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~--~~i~L  167 (414)
                      +.+...+++|+++.|+|+++.++|+||+|++ +.+||||.+++++.+..++.+. +++|+.|.|+|+++|..+  +++.|
T Consensus        14 ~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~-~~~Gd~V~VkV~~vd~~~~~~~i~L   92 (119)
T 2cqo_A           14 ETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEI-VDVGDKVWVKLIGREMKNDRIKVSL   92 (119)
T ss_dssp             CCSCCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHHH-CCTTCEEEEEEEEEEECSSCEEEEE
T ss_pred             hhhhcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhhc-CCCCCEEEEEEEEEeccccCceEEE
Confidence            3345678999999999999999999999965 4799999999998887777777 999999999999999754  69999


Q ss_pred             EeeehhhhHHHHHhh
Q 015066          168 SLRMIQYELAWERCR  182 (414)
Q Consensus       168 S~k~~~~~~~~~~l~  182 (414)
                      |+|.... ..|+.+.
T Consensus        93 Slk~~~~-~~~~~~~  106 (119)
T 2cqo_A           93 SMKVVNQ-GTGKDLD  106 (119)
T ss_dssp             ESTTBCS-SSCCBSC
T ss_pred             EEeeccc-CCccccC
Confidence            9998764 4666553

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

Probab=99.17  E-value=4.2e-11  Score=108.04  Aligned_cols=70  Identities=33%  Similarity=0.449  Sum_probs=65.4

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC-----------CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG-----------GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVS  329 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~-----------gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~  329 (414)
                      .++ |++|.|+|++|.++|+||+|.           +++|++|+|++++.++.++.+.|++||.|+|+|++     +++.
T Consensus        55 ~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~-----~~i~  128 (179)
T 3m7n_A           55 IVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG-----DNLR  128 (179)
T ss_dssp             CCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE-----TTTE
T ss_pred             cCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC-----CeEE
Confidence            467 999999999999999999995           58999999999999999999999999999999998     8899


Q ss_pred             EEEeeCC
Q 015066          330 LSTKKLE  336 (414)
Q Consensus       330 LS~K~~~  336 (414)
                      ||+|..+
T Consensus       129 LS~k~~~  135 (179)
T 3m7n_A          129 LSTKEEE  135 (179)
T ss_dssp             EECCSTT
T ss_pred             EEEecCC
Confidence            9999754

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

Probab=99.17  E-value=2.4e-12  Score=138.26  Aligned_cols=152  Identities=13%  Similarity=0.106  Sum_probs=0.0

Q ss_pred             CCCCccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCCCCCHHHH------HHH
Q 015066           16 ISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEF------HSA   89 (414)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~~~~~~~f------~~~   89 (414)
                      -+...+|+|||       -|..++..|.+..-.|++++    ..+++|+++.-..++-..+..+..+..+.      .+.
T Consensus       549 ~~~~~~~~~ap-------~~~~~~i~~~ki~~~ig~gG----k~I~~I~~~~G~~IdI~~dg~v~I~~~~~~~~~~a~~~  617 (723)
T 3cdi_A          549 APRGDISEFAP-------RIHTIKINPDKIKDVIGKGG----SVIRALTEETGTTIEIEDDGTVKIAATDGEKAKHAIRR  617 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hcchhccccCc-------eEEEEEECHHHhcccccccc----eeeeeeehhhCceEEecCCccEEEecCCHHHHHHHHHH
Confidence            34556899999       77888999999999999999    56677777743333322233333333322      234


Q ss_pred             HHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066           90 LEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus        90 l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      ++.+...+++|++++|+|+++.++|+||++..+.+||+|.+++++.+..++.+. +++||+|+++|+++|. ++++.||+
T Consensus       618 i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~~~~v~~~~~~-~~vGd~V~VkVi~vd~-~grI~LS~  695 (723)
T 3cdi_A          618 IEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDY-LQMGQEVPVKVLEVDR-QGRIRLSI  695 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHhhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCccccCcccc-cCCCCEEEEEEEEECC-CCcEEEEE
Confidence            555556789999999999999999999999888999999999999888888887 9999999999999997 89999999


Q ss_pred             eehhhhHHHHHh
Q 015066          170 RMIQYELAWERC  181 (414)
Q Consensus       170 k~~~~~~~~~~l  181 (414)
                      |.... ..|..+
T Consensus       696 k~~~~-~~g~~~  706 (723)
T 3cdi_A          696 KEATE-QSQPAA  706 (723)
T ss_dssp             ------------
T ss_pred             EeccC-CCCccc
Confidence            98754 345443

>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=99.17  E-value=9e-11  Score=96.40  Aligned_cols=82  Identities=13%  Similarity=0.193  Sum_probs=70.1

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCC---CeeEEEcCccc-cccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITA---KSSAYLPTQEA-CIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~---k~~g~lp~sEl-s~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      ..+++|+++.|+|+++.++|+||++++   +.+||||.+|+ ++.+..++.+. +++||.+.|+|+++|.  +++.||+|
T Consensus         8 ~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~-~~~Gd~V~VkV~~vd~--~~i~LSlk   84 (103)
T 2eqs_A            8 EEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADV-VSKGQRVKVKVLSFTG--TKTSLSMK   84 (103)
T ss_dssp             SSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHH-CCTTCEEEEEEEEEET--TEEEEEST
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccE-eCCCCEEEEEEEEEEC--CeeEEEEe
Confidence            467899999999999999999999986   79999999999 56666677666 8999999999999996  69999999


Q ss_pred             ehhhhHHHHH
Q 015066          171 MIQYELAWER  180 (414)
Q Consensus       171 ~~~~~~~~~~  180 (414)
                      .... ..|..
T Consensus        85 ~~~~-~~~~~   93 (103)
T 2eqs_A           85 DVDQ-ETGED   93 (103)
T ss_dssp             TBCT-TTCCB
T ss_pred             eccc-CCchh
Confidence            8655 34443

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...

Probab=99.15  E-value=7.7e-11  Score=105.57  Aligned_cols=72  Identities=21%  Similarity=0.210  Sum_probs=59.2

Q ss_pred             ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccc----cCc------ccccCCCCEEEEEEEEEeCCCC---eE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV----ADI------ATVLQPGDTLKVMILSHDRERG---RV  328 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~----~~~------~~~~~~G~~V~vkVl~id~e~~---ri  328 (414)
                      ..+|+++.|+|+++++||+||+++..+||+|+|+|++.+.    .++      ++.|++||.|+|||+++|.+.+   ++
T Consensus        81 ~~~Gev~~G~V~~v~~fG~FV~l~~~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~~~~i  160 (171)
T 1y14_B           81 PFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAI  160 (171)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTEEEEE
T ss_pred             CCCCCEEEEEEEEEecCEEEEEecCeEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEEcCCCCcEEE
Confidence            5699999999999999999999988999999999976522    211      2679999999999999998764   55


Q ss_pred             EEEEee
Q 015066          329 SLSTKK  334 (414)
Q Consensus       329 ~LS~K~  334 (414)
                      . |||+
T Consensus       161 g-sm~~  165 (171)
T 1y14_B          161 G-SIKE  165 (171)
T ss_dssp             E-ECCS
T ss_pred             E-EcCC
Confidence            5 6654

>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1

Probab=99.14  E-value=7.3e-11  Score=105.80  Aligned_cols=72  Identities=19%  Similarity=0.313  Sum_probs=60.7

Q ss_pred             ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccc----cC--------cccccCCCCEEEEEEEEEeCCCC---
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV----AD--------IATVLQPGDTLKVMILSHDRERG---  326 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~----~~--------~~~~~~~G~~V~vkVl~id~e~~---  326 (414)
                      ..+|+++.|+|+++++||+||+++..+||||+|+|++.+.    .+        ..+.|++||.|+|||+++|.+.+   
T Consensus        79 ~~~Gev~~G~V~~v~~fG~fV~l~~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~~~  158 (172)
T 2c35_B           79 PFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIF  158 (172)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEEE
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEECCEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCCCCcE
Confidence            3589999999999999999999988889999999975522    21        15579999999999999998766   


Q ss_pred             eEEEEEee
Q 015066          327 RVSLSTKK  334 (414)
Q Consensus       327 ri~LS~K~  334 (414)
                      ++. |||+
T Consensus       159 ~ig-sm~~  165 (172)
T 2c35_B          159 AIG-SLMD  165 (172)
T ss_dssp             EEE-ECCS
T ss_pred             EEE-EecC
Confidence            666 8875

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

Probab=99.13  E-value=1.8e-11  Score=135.53  Aligned_cols=123  Identities=11%  Similarity=-0.003  Sum_probs=28.1

Q ss_pred             hHHHHHHHHHHHHhhcccCCCCCCCCCHHHHHHHHHh-hcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccc
Q 015066           56 EREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEK-YDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI  134 (414)
Q Consensus        56 ~~~~l~~iiee~~~~~~~~~~~~~~~~~~~f~~~l~~-~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~  134 (414)
                      .+.+|++|+.|+.++.++.+.+...++..+.-.++.. ...++++|++|.|+|+++.++|+||+++.+.+|+||.+++++
T Consensus       861 k~~TL~dI~~EL~~P~~D~R~~f~~~~~~e~~~~LTget~~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd  940 (1030)
T 3psf_A          861 KLNNLNTIVLELLDGFEELRNDFHPLQGDEIFQSLTGESEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAG  940 (1030)
T ss_dssp             CHHHHHHHHHHHHSTTCCCSCCCCCCCHHHHHHHHHCCC-----------------------------------------
T ss_pred             ccchHHHHHHHHhccCCCCCcccCccchhhhhhhhccccHHHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCC
Confidence            3679999999999999999988665555554444432 235889999999999999999999999988999999999998


Q ss_pred             cc-cCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehhhhHHHH
Q 015066          135 HK-IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWE  179 (414)
Q Consensus       135 ~~-~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~~~~~~~  179 (414)
                      .+ ..++.+. +++|+.|+|+|+++|.+++++.||+|.......|.
T Consensus       941 ~~~v~~~~~v-~kvGd~V~vkVl~VD~~~~rI~LSlk~~dl~~~~~  985 (1030)
T 3psf_A          941 AQLRRPANEI-YEIGKTYPAKVIYIDYANITAEVSLLDHDVKQQYV  985 (1030)
T ss_dssp             ----------------------------------------------
T ss_pred             CcccCCHHHc-CCCCCEEEEEEEEEECCCCEEEEEechHHhccccc
Confidence            87 6788877 99999999999999999999999999877655553

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=99.03  E-value=3.6e-12  Score=137.39  Aligned_cols=152  Identities=15%  Similarity=0.118  Sum_probs=56.0

Q ss_pred             CccCcccchhhhhhhhhhcccCcceEEEEEEeCCcchhHHHHHHHHHHHHhhcccCCCCCCCCCHHHHHH------HHHh
Q 015066           19 TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHS------ALEK   92 (414)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~iiee~~~~~~~~~~~~~~~~~~~f~~------~l~~   92 (414)
                      ..+|+|||       -|..++..|.+..-.|++++    ..+++|+++.-..++-..+..+..+..+...      .++.
T Consensus       590 ~~~~~~ap-------~~~~~~I~~~ki~~vIG~gG----k~Ik~I~~~~G~~IdI~~dG~v~Is~~~~~~~~~a~~~i~~  658 (757)
T 1e3p_A          590 DEMSPNAP-------RIITVKIPVDKIGEVIGPKR----QMINQIQEDTGAEITIEDDGTIYIGAADGPAAEAARATING  658 (757)
T ss_dssp             CCCCTTSC-------BCCCC----------------------CTTCCCCCSCC--------CCCBSSHHHHCC-------
T ss_pred             ccccccCc-------eeEEEEEChHHeehcccccc----eeeehhhHhhCCEEEecCCceEEEecCCHHHHHHHHHHHHH
Confidence            66899999       77788999999999999999    4455555552211221123333333333221      2333


Q ss_pred             hc--ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccc----cccccCCccccCccCCcEEEEEEEEEeCCCCeEE
Q 015066           93 YD--FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEA----CIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV  166 (414)
Q Consensus        93 ~~--~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEl----s~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~  166 (414)
                      +.  ..+++|++++|+|+++.++|+||++.++.+|++|.+++    ++.+..++++. +++||+|+|+|+++|+ ++++.
T Consensus       659 i~~p~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s~~rv~~~~~~-~~vGd~V~VkVi~vd~-~grI~  736 (757)
T 1e3p_A          659 IANPTSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDV-LGVGQKVQVEIAEIDS-RGKLS  736 (757)
T ss_dssp             --------------CBEEECC-CSCEECCC---CCCCC--------------------CCSSCBCCCCCCCCCS-SCC--
T ss_pred             hcchhhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccCCCcccCcccc-cCCCCEEEEEEEEECC-CCCEE
Confidence            33  46789999999999999999999998889999999999    88888888887 9999999999999998 89999


Q ss_pred             EEeeehhhhHHHHHhhhc
Q 015066          167 LSLRMIQYELAWERCRQL  184 (414)
Q Consensus       167 LS~k~~~~~~~~~~l~~~  184 (414)
                      ||++.... .+|.....-
T Consensus       737 LS~k~~~~-~pw~~~~~~  753 (757)
T 1e3p_A          737 LIPVIEGE-EAASDEKKD  753 (757)
T ss_dssp             ------------------
T ss_pred             EEEecCCC-Cchhhhhhc
Confidence            99998765 588776543

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

Probab=99.01  E-value=9.8e-11  Score=104.99  Aligned_cols=73  Identities=19%  Similarity=0.309  Sum_probs=61.6

Q ss_pred             hccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCccccc----------CcccccCCCCEEEEEEEEEeCCCC---e
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA----------DIATVLQPGDTLKVMILSHDRERG---R  327 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~----------~~~~~~~~G~~V~vkVl~id~e~~---r  327 (414)
                      ...+|++++|+|+++++||+||+++.++||+|+|+|++.+.-          +..+.|++||.|+|||+++|.+.+   +
T Consensus        81 ~p~~Gev~~G~V~~v~~fG~FV~l~~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~~~~~~~~  160 (172)
T 3h0g_G           81 RPFRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDATEIFA  160 (172)
T ss_dssp             CCCTTCEEECCCCEEETTEEECCBTTBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEESSSCEEE
T ss_pred             ccCCCCEEEEEEEEEEcceEEEEeCCeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEECCCCCceE
Confidence            366899999999999999999999988999999999765332          345789999999999999998874   5


Q ss_pred             EEEEEee
Q 015066          328 VSLSTKK  334 (414)
Q Consensus       328 i~LS~K~  334 (414)
                      |. |||+
T Consensus       161 Ig-tm~~  166 (172)
T 3h0g_G          161 IA-TMKE  166 (172)
T ss_dssp             EE-ECCS
T ss_pred             EE-EcCC
Confidence            55 6663

>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=99.01  E-value=3.6e-10  Score=107.09  Aligned_cols=74  Identities=28%  Similarity=0.344  Sum_probs=68.4

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccc---cCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV---ADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~---~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      .+++|++|.|+|+++.++|+||+++ +.+|++|++++++.+.   .++.+.|++||.|.|+|++++. .+++.||+|..
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 YPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVLSVKGK  148 (251)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEEECCST
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECC-CCcEEEEEccc
Confidence            4789999999999999999999999 6999999999998777   8889999999999999999996 47999999865

>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=98.99  E-value=1.1e-09  Score=107.85  Aligned_cols=103  Identities=15%  Similarity=0.137  Sum_probs=81.7

Q ss_pred             ccccccCCeEEEEEEEeecccceEEeehhhhhhhH---------Hhhcc--ccEEEEEEEEEEeeceEEEEECCEEEEEe
Q 015066          224 TAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADS---------QAQLG--IGSVVIGTVQSLKPYGAFIDIGGINGLLH  292 (414)
Q Consensus       224 ~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~~~---------~~~l~--~G~iv~g~V~~i~~~G~fV~l~gv~Glvh  292 (414)
                      ++...+|+.+.+.|...|.. +....+.|+.+.+.         +++++  .|++|+|+|.++.++|+||++++.+|++|
T Consensus        84 d~~~~vGd~ie~~I~~~dfg-R~aa~~aKqvi~qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~v~VDlGk~EgiLp  162 (344)
T 1hh2_P           84 DPLAEVGSIVKKELNVKNFG-RIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIGKLETRLP  162 (344)
T ss_dssp             CTTCCTTCEEEEECCCCCSS-SCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEETTEEEEEE
T ss_pred             CccccCCCEEEEEEccccCc-cHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCcEEEEeCCeEEEEe
Confidence            34456899999999888753 44555556654321         23444  89999999999999999999999999999


Q ss_pred             ecccCcccccCcccccCCCCEEEEEEEEEeCCCC--eEEEEEe
Q 015066          293 VSQISHDRVADIATVLQPGDTLKVMILSHDRERG--RVSLSTK  333 (414)
Q Consensus       293 ~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~--ri~LS~K  333 (414)
                      .++++      |.+.|++||+|+|+|++++++++  +|.||.+
T Consensus       163 ~sE~i------p~E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt  199 (344)
T 1hh2_P          163 KKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVSRR  199 (344)
T ss_dssp             GGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEESS
T ss_pred             HHHcC------CCcCCCCCCEEEEEEEEEEcCCCCcEEEEEee
Confidence            99986      56789999999999999997665  5666655

>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=98.98  E-value=1.5e-10  Score=125.26  Aligned_cols=112  Identities=21%  Similarity=0.259  Sum_probs=94.0

Q ss_pred             HHHHHHHHHHHHhhcccCCCCCCCCCHHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccc
Q 015066           57 REELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK  136 (414)
Q Consensus        57 ~~~l~~iiee~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~  136 (414)
                      ...+.+|+.|+.++.++.+.+   |....|.+..+.. .++++|+++.|+|+++.++|+||+++.+.+|+||.+++++.+
T Consensus       616 l~tl~rIi~eL~kpg~d~R~~---~~~~~~~~~ve~~-~~l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~  691 (785)
T 3bzc_A          616 LPTVTDILKELDKPGRDPRPE---FKTAEFQEGVESL-KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKF  691 (785)
T ss_dssp             HHHHHHHHHHHHSTTCCCSCC---CCTTTTCCCCCSS-TTCCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSC
T ss_pred             cHHHHHHHHHHhccCCChhhh---cccchhhhcccch-hhcCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCccc
Confidence            348999999999999987764   3333333222333 368999999999999999999999998899999999999988


Q ss_pred             cCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh
Q 015066          137 IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (414)
Q Consensus       137 ~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~  173 (414)
                      ..++.+. +++||.|+|+|+++|.+++++.||++...
T Consensus       692 v~d~~~~-~~vGd~V~VkVi~VD~~~~rI~LSlk~~~  727 (785)
T 3bzc_A          692 VKDPYEV-VKAGDIVKVKVMEVDIPRNRVGLSMRMSD  727 (785)
T ss_dssp             CSCHHHH-CCTTCCCCCBEEEEETTTTEEEECCSSCC
T ss_pred             cCChhhe-eCCCCEEEEEEEEEECCCCEEEEEEecCC
Confidence            8888877 99999999999999999999999998543

>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=98.97  E-value=1.7e-10  Score=110.33  Aligned_cols=102  Identities=14%  Similarity=0.092  Sum_probs=87.6

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig--~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~  173 (414)
                      .+++|+++.|+|.++.++|+||+++  ++.+||||.+|+++.+..++.+. +++||.+.|+|+++|++++++.||++...
T Consensus         8 ~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~~~~~~-~~vGd~V~VkVi~vd~~~g~I~LSlk~~~   86 (266)
T 3cw2_C            8 LPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDV-LKENRKVIVKVIRVDRRKGTVDVSLKKVT   86 (266)
T ss_dssp             SCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCCCHHHH-SCTTCEEEEEECCCCSSSCCCBEESTTSC
T ss_pred             cCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccccCHHHh-CcCCCEEEEEEEEEeCCCCEEEEEEEecc
Confidence            6789999999999999999999997  67999999999998888888777 99999999999999988999999999876


Q ss_pred             hhHHHHHhhhcccCCeEEEEEEEEEe
Q 015066          174 YELAWERCRQLQSEDVVVKGKVVGAN  199 (414)
Q Consensus       174 ~~~~~~~l~~~~~~g~iv~G~V~~v~  199 (414)
                      . ..|..+.+.+..|+.+.+.|..+.
T Consensus        87 ~-~~~~~~~~~~~~~~~~~~iv~~la  111 (266)
T 3cw2_C           87 D-DERRKKNLQWKKIQRLDKILELVS  111 (266)
T ss_dssp             T-THHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             h-hhHHHHHHhccccCccceeeeehh
Confidence            4 688887776666655555555554

>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=98.97  E-value=4.2e-10  Score=105.79  Aligned_cols=75  Identities=27%  Similarity=0.373  Sum_probs=67.0

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcc----cccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHD----RVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~----~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      .+++|++|.|+|+++.++|+||+++ +.+|++|++++++.    ...++.+.|++||.|.|+|++++. .+++.||+|..
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 VPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPLLTVQGE  141 (235)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEEEECCSS
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECC-CCcEEEEEecc
Confidence            5789999999999999999999999 69999999999863    346788899999999999999996 46899999864


Q ss_pred             C
Q 015066          336 E  336 (414)
Q Consensus       336 ~  336 (414)
                      .
T Consensus       142 ~  142 (235)
T 2z0s_A          142 G  142 (235)
T ss_dssp             S
T ss_pred             c
Confidence            3

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

Probab=98.96  E-value=8.6e-10  Score=90.18  Aligned_cols=81  Identities=31%  Similarity=0.407  Sum_probs=64.8

Q ss_pred             CCeEEEEEEEEEe---cCcEEEEE--CCEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehhhhhhhHHhh
Q 015066          187 EDVVVKGKVVGAN---KGGVVAEV--EGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQ  261 (414)
Q Consensus       187 ~g~iv~G~V~~v~---~~G~~V~i--~gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~~~~~~  261 (414)
                      .++..+|+|+..+   .+| |+..  ++.++|+|+|.+.+..-                                 ....
T Consensus        13 ~~~~~~G~Vk~fn~~kGfG-FI~~~~gg~dvfvH~s~l~~~~~---------------------------------~~~~   58 (101)
T 2bh8_A           13 QSGKMTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAGSSGAA---------------------------------VRGN   58 (101)
T ss_dssp             ---CEEEEEEEEEGGGTEE-EEEESSSSCEEEEECCCSCSSSC---------------------------------CCCC
T ss_pred             ccccceeEEEEEECCCCCE-EEEeCCCCcEEEEEEEEEecCCc---------------------------------cccC
Confidence            3457899999983   457 5554  37999999999986521                                 0145


Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccc
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV  301 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~  301 (414)
                      +++|+.|.+.|+++.+||+||+|. +++||||+|+|+|.++
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            789999999999999999999996 8999999999999875

>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=98.92  E-value=2.2e-09  Score=90.27  Aligned_cols=78  Identities=22%  Similarity=0.244  Sum_probs=65.0

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC-CCeeEEEcCcccc-ccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEAC-IHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig-~k~~g~lp~sEls-~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~  173 (414)
                      ++++|++++|+|.++.++|+||+++ .+..|++|.+++. +....++.+. +++||.++|+|+++|..++++.||+++..
T Consensus        18 ~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~~~~~~~~~~~-~~~Gd~V~vkV~~vd~~~~~i~Lslk~~~   96 (119)
T 1wi5_A           18 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAK-LKVGQYLNCIVEKVKGNGGVVSLSVGHSE   96 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCC-CCTTCEEEEEEEECCTTSCEEEEECCCCC
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccccccccCccCE-eCCCCEEEEEEEEEeCCCCEEEEEEchhh
Confidence            6899999999999999999999998 5677888877753 2222345555 89999999999999988899999998765


Q ss_pred             h
Q 015066          174 Y  174 (414)
Q Consensus       174 ~  174 (414)
                      .
T Consensus        97 l   97 (119)
T 1wi5_A           97 V   97 (119)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=98.91  E-value=2.3e-09  Score=100.35  Aligned_cols=75  Identities=27%  Similarity=0.339  Sum_probs=68.1

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcc-cccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHD-RVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~-~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      .+++||+|.|+|+++.++|+||+++ ...|++|+++++.. ...+..+.|++||.|.|+|++++. .+++.||+|+..
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 TPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMKDRI  130 (229)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECCSSS
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECC-CCcEEEEEcccc
Confidence            4789999999999999999999999 69999999999964 667889999999999999999986 579999998753

>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=98.77  E-value=1.7e-08  Score=93.01  Aligned_cols=78  Identities=15%  Similarity=0.150  Sum_probs=68.5

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeC--------CCeeEEEcCccccccccC--CccccCccCCcEEEEEEEEEeCCCCe
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDIT--------AKSSAYLPTQEACIHKIK--HVEEAGIVPGLKEEFVIIGENEADDS  164 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig--------~k~~g~lp~sEls~~~~~--~~~e~~~~vG~~v~v~Vl~id~~~~~  164 (414)
                      +.+++|++|.|+|+++.++|+||+|+        .+.+|+||.+|++..+..  ++.+. |++||.|.++|+++++.+++
T Consensus        77 y~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~-l~~GD~V~akVisi~~~~~~  155 (209)
T 2nn6_I           77 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKS-FRPGDIVLAKVISLGDAQSN  155 (209)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGT-CCSSSEEEEEEEEEETTTTE
T ss_pred             CCCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhh-cCCCCEEEEEEEEEeCCCCe
Confidence            46899999999999999999999984        357899999999977766  67776 99999999999999977779


Q ss_pred             EEEEeeehh
Q 015066          165 LVLSLRMIQ  173 (414)
Q Consensus       165 i~LS~k~~~  173 (414)
                      +.||+|...
T Consensus       156 i~LS~k~~~  164 (209)
T 2nn6_I          156 YLLTTAENE  164 (209)
T ss_dssp             EEEECCSSS
T ss_pred             EEEEEecCC
Confidence            999998653

>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=98.76  E-value=3e-08  Score=89.84  Aligned_cols=77  Identities=12%  Similarity=0.139  Sum_probs=66.1

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC-----------CccccCccCCcEEEEEEEEEeCCCC
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADD  163 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~-----------~~~e~~~~vG~~v~v~Vl~id~~~~  163 (414)
                      +...+|+++.|+|+++.++|+||+++. .+|++|.++++..+..           ++.+. +.+|+.++|+|++++...+
T Consensus        77 ~~~~~Gev~~G~V~~v~~~G~fV~l~~-~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~-~~~Gd~V~vkV~~vd~~~~  154 (187)
T 1go3_E           77 YIPEMYELIEGEVVDVVEFGSFVRLGP-LDGLIHVSQIMDDYVSYDPKREAIIGKETGKV-LEIGDYVRARIVAISLKAE  154 (187)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEECSS-SEEEEEGGGSCSSCEEECCC--CEEETTTCCE-ECTTCEEEEEEEEEECCC-
T ss_pred             EccCCCCEEEEEEEEEeCcEEEEEEcC-ccEEEEhHHhCCCcceECCccceEEecCCCeE-EcCCCEEEEEEEEEEcccC
Confidence            467899999999999999999999986 9999999999876543           45555 8999999999999997654


Q ss_pred             -----eEEEEeeehh
Q 015066          164 -----SLVLSLRMIQ  173 (414)
Q Consensus       164 -----~i~LS~k~~~  173 (414)
                           ++.||++...
T Consensus       155 ~p~~~~I~lS~k~~~  169 (187)
T 1go3_E          155 RKRGSKIALTMRQPY  169 (187)
T ss_dssp             ----CEEEEECCSTT
T ss_pred             CCCccEEEEEEcCCC
Confidence                 9999999854

>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=98.74  E-value=1.4e-08  Score=99.83  Aligned_cols=78  Identities=21%  Similarity=0.174  Sum_probs=67.6

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC--CeEEEEeeehhh
Q 015066           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD--DSLVLSLRMIQY  174 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~--~~i~LS~k~~~~  174 (414)
                      .+.|++|+|+|.+++++|+||++| +.+|+||.+|+.      +.+. +++|++++++|++++.++  .++.||++....
T Consensus       132 ~~~GeIV~G~V~ri~~~~v~VDlG-k~EgiLp~sE~i------p~E~-~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p~~  203 (344)
T 1hh2_P          132 ELKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKEWI------PGEE-IKAGDLVKVYIIDVVKTTKGPKILVSRRVPEF  203 (344)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGSC------TTCC-CCTTCEEEEEEEEEEEETTEEEEEEESSSHHH
T ss_pred             hcCCCEEEEEEEEEecCcEEEEeC-CeEEEEeHHHcC------CCcC-CCCCCEEEEEEEEEEcCCCCcEEEEEeeccHH
Confidence            458999999999999999999998 799999999996      3344 899999999999998654  479999998888


Q ss_pred             hHHHHHhh
Q 015066          175 ELAWERCR  182 (414)
Q Consensus       175 ~~~~~~l~  182 (414)
                      ...|..++
T Consensus       204 lk~LfelE  211 (344)
T 1hh2_P          204 VIGLMKLE  211 (344)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhh
Confidence            78887764

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

Probab=98.62  E-value=6.2e-08  Score=87.25  Aligned_cols=71  Identities=24%  Similarity=0.181  Sum_probs=64.2

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCC----------CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCe
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITA----------KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS  164 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~----------k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~  164 (414)
                      +..+ |++|.|+|+++.++|+||+|+.          ..+|+||.++++..+..++.+. |++||.|.++|++     ++
T Consensus        54 y~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~-~~~GD~V~akVi~-----~~  126 (179)
T 3m7n_A           54 EIVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEA-VGYLDILKARVIG-----DN  126 (179)
T ss_dssp             CCCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGT-CCTTCEEEEEEEE-----TT
T ss_pred             ccCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhc-CCCCCEEEEEEEC-----Ce
Confidence            3568 9999999999999999999987          7899999999998888888887 9999999999997     78


Q ss_pred             EEEEeeeh
Q 015066          165 LVLSLRMI  172 (414)
Q Consensus       165 i~LS~k~~  172 (414)
                      +.||+|..
T Consensus       127 i~LS~k~~  134 (179)
T 3m7n_A          127 LRLSTKEE  134 (179)
T ss_dssp             TEEECCST
T ss_pred             EEEEEecC
Confidence            99998864

>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=98.58  E-value=1e-07  Score=90.20  Aligned_cols=75  Identities=24%  Similarity=0.193  Sum_probs=65.7

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc---CCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI---KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~---~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~  171 (414)
                      +..++|++|.|+|+++.++|+||+++...+|+||.+++...+.   .++.+. +++||.|.++|+++++ ++++.||++.
T Consensus        70 y~p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei~~~~~~~~~~~~~~-l~vGD~V~arVi~v~~-~~~i~LS~r~  147 (251)
T 2je6_I           70 YYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRY-LDVGDYVIARIENFDR-SIDPVLSVKG  147 (251)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSS-CCTTCEEEEEEEEEET-TEEEEEECCS
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCccccccchhhc-CCCCCEEEEEEEEECC-CCcEEEEEcc
Confidence            4679999999999999999999999988999999999986555   455555 8999999999999985 4789999864

>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=98.56  E-value=2.1e-07  Score=86.94  Aligned_cols=75  Identities=20%  Similarity=0.220  Sum_probs=65.4

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccc-ccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH-KIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~-~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~  171 (414)
                      +..++||+|.|+|+.+.++|+||+|+...+|+||.+++... ...+..+. +++||.|.++|+++++ ++.+.||+|.
T Consensus        53 y~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~~~~~~~~~~-l~~GD~V~arVi~v~~-~~~i~LS~r~  128 (229)
T 2ba0_A           53 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEV-LDIGDAIIAKVLNIDP-KMKVTLTMKD  128 (229)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGT-CCTTCEEEEEEEEECT-TCCEEEECCS
T ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHccccccccchhcc-cCCCCEEEEEEEEECC-CCcEEEEEcc
Confidence            36799999999999999999999999889999999999853 44556665 8999999999999985 5789999864

>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=98.56  E-value=1.2e-07  Score=101.32  Aligned_cols=72  Identities=14%  Similarity=0.151  Sum_probs=62.4

Q ss_pred             hccccE--EEEEEEEEEeeceEEEEEC--CEEEEEeecccCc--cc--cc--------CcccccCCCCEEEEEEEEEeCC
Q 015066          261 QLGIGS--VVIGTVQSLKPYGAFIDIG--GINGLLHVSQISH--DR--VA--------DIATVLQPGDTLKVMILSHDRE  324 (414)
Q Consensus       261 ~l~~G~--iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~--~~--~~--------~~~~~~~~G~~V~vkVl~id~e  324 (414)
                      .-++|+  +++|+|++|++||+||+|.  |++||||+|+|++  ++  +.        +....|++||.|+|+|+++|.+
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            456899  9999999999999999994  8999999999973  22  11        4456799999999999999999


Q ss_pred             CCeEEEEE
Q 015066          325 RGRVSLST  332 (414)
Q Consensus       325 ~~ri~LS~  332 (414)
                      +++|.|++
T Consensus       635 ~~~I~~~l  642 (644)
T 2id0_A          635 TRSIIARP  642 (644)
T ss_dssp             TTEEEEEE
T ss_pred             CCEEEEEE
Confidence            99999987

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

Probab=98.55  E-value=1.3e-07  Score=86.90  Aligned_cols=63  Identities=16%  Similarity=0.191  Sum_probs=55.3

Q ss_pred             ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccc-------------------cCcccccCCCCEEEEEEEEEe
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV-------------------ADIATVLQPGDTLKVMILSHD  322 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~-------------------~~~~~~~~~G~~V~vkVl~id  322 (414)
                      ..+|+++.|+|++++++|+||+++.++|++|++++.+++.                   ++....|+.||.|++||.+++
T Consensus        79 p~~GEv~~G~Vs~vt~~GifV~lg~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~  158 (203)
T 3ayh_B           79 PFRGEVMLGKIKSCSEEGIRVTISFFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQIESED  158 (203)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECSSCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEEEEEE
T ss_pred             cCCCCEEEEEEEEEeccEEEEEEeCceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEEEEEE
Confidence            4689999999999999999999977899999999977643                   445667999999999999998


Q ss_pred             CC
Q 015066          323 RE  324 (414)
Q Consensus       323 ~e  324 (414)
                      ..
T Consensus       159 ~~  160 (203)
T 3ayh_B          159 FV  160 (203)
T ss_dssp             EC
T ss_pred             cc
Confidence            63

>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=98.53  E-value=3.1e-07  Score=82.63  Aligned_cols=77  Identities=17%  Similarity=0.237  Sum_probs=63.6

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc-----------CCccccCccCCcEEEEEEEEEeCC--
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI-----------KHVEEAGIVPGLKEEFVIIGENEA--  161 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~-----------~~~~e~~~~vG~~v~v~Vl~id~~--  161 (414)
                      +...+|++++|+|++++++|+||+++. .+|++|.+++.+++.           ++..+. +.+|+.|+++|++++.+  
T Consensus        77 ~~p~~Gev~~G~V~~v~~~G~fv~l~~-~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~-~~~Gd~VrvkV~~v~~~~~  154 (180)
T 4ayb_E           77 YVPVVQEVVEGEVLQVDNYGVFVNLGP-MDGLVHISQITDDTLKYDNVRGIIFGEKSKKV-IQKGDKVRARVISVASTVT  154 (180)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEECSS-SEEEEEGGGSCSSCEEECSSSCCEEETTTCCC-CCTTCEEEEEEEEECC---
T ss_pred             eeccCCCEEEEEEeeeccceEEEEECC-ccceEEeeecCCCccccchhcceEEEeccCeE-ECCCCEEEEEEEEEeCCCC
Confidence            467899999999999999999999986 899999999987655           233444 88999999999999854  


Q ss_pred             --CCeEEEEeeehh
Q 015066          162 --DDSLVLSLRMIQ  173 (414)
Q Consensus       162 --~~~i~LS~k~~~  173 (414)
                        ..++.||+|..-
T Consensus       155 ~~~~rI~ls~k~~g  168 (180)
T 4ayb_E          155 GRLPRIALTMRQPY  168 (180)
T ss_dssp             ----CEEEECCSTT
T ss_pred             cccCcEEEEcCCCC
Confidence              358999999753

>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=98.51  E-value=1.8e-07  Score=87.85  Aligned_cols=74  Identities=16%  Similarity=0.184  Sum_probs=64.0

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccc----ccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH----KIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~----~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      +.+++|++|.|+|+++.++|+||+|+.+.+|+||.++++..    +..++.+. +++||.|.++|+++++ ++++.||++
T Consensus        62 y~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~~~~~~~~~~~~~-l~~GD~V~a~Vi~v~~-~~~i~LS~k  139 (235)
T 2z0s_A           62 YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSL-LKVGDYIKAKVVAFDK-TRSPLLTVQ  139 (235)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTS-SCTTCEEEEEEEEECT-TSCEEEECC
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCccccchhhHhhc-CCCCCEEEEEEEEECC-CCcEEEEEe
Confidence            47899999999999999999999999999999999999862    23445555 8999999999999985 468999986

>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=98.42  E-value=3e-07  Score=94.97  Aligned_cols=74  Identities=24%  Similarity=0.430  Sum_probs=63.6

Q ss_pred             hhccccEEEEEEEEEEeec--eEEEEEC-CEEEEEeecccCcccc---------cCcccccCCCCEEEEEEEEEeCCCCe
Q 015066          260 AQLGIGSVVIGTVQSLKPY--GAFIDIG-GINGLLHVSQISHDRV---------ADIATVLQPGDTLKVMILSHDRERGR  327 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~--G~fV~l~-gv~Glvh~sels~~~~---------~~~~~~~~~G~~V~vkVl~id~e~~r  327 (414)
                      ....+|++|.|+|++|.++  ||||+++ |..||+|++++++.++         .++.+.+++||.|.|+|++....++.
T Consensus        41 ~~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g~KG  120 (517)
T 2bx2_L           41 HEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKG  120 (517)
T ss_dssp             SCCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCTTCC
T ss_pred             CcCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeeccccCC
Confidence            4567899999999999999  9999999 8999999999988763         34678899999999999998876666


Q ss_pred             EEEEEe
Q 015066          328 VSLSTK  333 (414)
Q Consensus       328 i~LS~K  333 (414)
                      -.||..
T Consensus       121 a~lTt~  126 (517)
T 2bx2_L          121 AALTTF  126 (517)
T ss_dssp             CEEESS
T ss_pred             ceEEee
Confidence            666654

>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=98.40  E-value=1e-06  Score=78.55  Aligned_cols=67  Identities=18%  Similarity=0.153  Sum_probs=55.8

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCc----------cccCccCCcEEEEEEEEEeCCCC
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV----------EEAGIVPGLKEEFVIIGENEADD  163 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~----------~e~~~~vG~~v~v~Vl~id~~~~  163 (414)
                      ....+|++++|+|++++++|+||+++. .+||+|.+++++.+..++          ++. +++|+.++|+|+++|.+.+
T Consensus        79 ~~~~~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~-~~~Gd~V~vkV~~vd~~~~  155 (171)
T 1y14_B           79 FKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDV-ITIKSRIRVKIEGCISQVS  155 (171)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCE-ECTTCEEEEEEEEEEEETT
T ss_pred             ccCCCCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceE-ECCCCEEEEEEEEEEcCCC
Confidence            467899999999999999999999998 999999999975432111          144 8899999999999987654

>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=98.39  E-value=1e-06  Score=82.60  Aligned_cols=79  Identities=16%  Similarity=0.144  Sum_probs=66.9

Q ss_pred             cCCCCCEEEEEEEE----EeCCeEEEEeCC---CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC--CeEE
Q 015066           96 NSELGTKVKGTVFC----TDNRGALVDITA---KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD--DSLV  166 (414)
Q Consensus        96 ~l~~G~iV~G~V~~----v~~~G~~Vdig~---k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~--~~i~  166 (414)
                      .-+.|++|+|+|.+    ++++.++|++|.   +.+|+||.+|+.      +.+. |++|++++++|++++...  .++.
T Consensus         4 ~~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqi------p~E~-~~~GDrIkayV~~V~~~~~gpqIi   76 (251)
T 2asb_A            4 STREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGES-YEHGNRLRCYVVGVTRGAREPLIT   76 (251)
T ss_dssp             CCCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC------TTCC-CCTTCEEEEEEEEEECCSSSCEEE
T ss_pred             hhcCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcC------CCcc-CCCCCEEEEEEEEEEcCCCCCEEE
Confidence            45799999999999    899999999987   699999999985      3344 899999999999998764  6899


Q ss_pred             EEeeehhhhHHHHHh
Q 015066          167 LSLRMIQYELAWERC  181 (414)
Q Consensus       167 LS~k~~~~~~~~~~l  181 (414)
                      ||+........|-.+
T Consensus        77 LSRt~p~lvk~Lfe~   91 (251)
T 2asb_A           77 LSRTHPNLVRKLFSL   91 (251)
T ss_dssp             EESSCHHHHHHHHHH
T ss_pred             EEeccHHHHHHHHHh
Confidence            999988776665544

>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=98.37  E-value=9.3e-07  Score=81.70  Aligned_cols=76  Identities=16%  Similarity=0.113  Sum_probs=60.6

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCcc----------ccCccCCcEEEEEEEEEeCCCC-
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE----------EAGIVPGLKEEFVIIGENEADD-  163 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~----------e~~~~vG~~v~v~Vl~id~~~~-  163 (414)
                      ...++|++++|+|++++++|+||+++. .+|++|.++|++.+..++.          +. +.+|+.|+|+|+++|.+.+ 
T Consensus        79 ~~p~vGev~~G~V~~vt~fG~FVelg~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~-~~~Gd~VrVkV~~vd~~~~~  156 (215)
T 2b8k_G           79 FKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDV-ITIKSRIRVKIEGCISQVSS  156 (215)
T ss_dssp             ECCCTTEEEEEEEEEEETTEEEEECTT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCE-EETTCEEEEEEEEEEEETTE
T ss_pred             eccCCCCEEEEEEEEEecceEEEEecC-cEEEEEHHHCCccceeccccccceeeccccE-ECCCCEEEEEEEEEEcCCCc
Confidence            456899999999999999999999998 9999999999764332221          34 8899999999999997665 


Q ss_pred             -eEEEEeeeh
Q 015066          164 -SLVLSLRMI  172 (414)
Q Consensus       164 -~i~LS~k~~  172 (414)
                       ..+-|++..
T Consensus       157 i~~IgSmk~~  166 (215)
T 2b8k_G          157 IHAIGSIKED  166 (215)
T ss_dssp             EEEEEECCST
T ss_pred             cEEEEEcCCC
Confidence             223377654

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

Probab=98.34  E-value=6e-07  Score=83.20  Aligned_cols=64  Identities=8%  Similarity=0.098  Sum_probs=53.8

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccc--------------cCcccccCCCCEEEEEEEEEeCCC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV--------------ADIATVLQPGDTLKVMILSHDRER  325 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~--------------~~~~~~~~~G~~V~vkVl~id~e~  325 (414)
                      ..+|+++.|+|+++++||+||++. .++|++|++++..+.+              .+-...|+.||.|++||.++|.+.
T Consensus        79 p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~~~  157 (218)
T 2ckz_B           79 PFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVD  157 (218)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEECC
T ss_pred             CCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEccc
Confidence            568999999999999999999995 5899999999976543              334567999999999999999644

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=98.31  E-value=1.8e-06  Score=85.12  Aligned_cols=72  Identities=18%  Similarity=0.208  Sum_probs=61.0

Q ss_pred             cCCCCCEEEEEEEE----EeCCeEEEEeCC---CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCC--CeEE
Q 015066           96 NSELGTKVKGTVFC----TDNRGALVDITA---KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD--DSLV  166 (414)
Q Consensus        96 ~l~~G~iV~G~V~~----v~~~G~~Vdig~---k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~--~~i~  166 (414)
                      .-+.|++|+|+|.+    ++++++||++|.   +.+|+||.+|+.      +.+. |++|++++|+|++++...  .++.
T Consensus       127 ~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi------P~E~-~~~GDrVkvyV~~V~~~~kgpqI~  199 (366)
T 1k0r_A          127 STREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGES-YEHGNRLRCYVVGVTRGAREPLIT  199 (366)
T ss_dssp             CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC------TTCC-CCTTCEEEEEEEEEECCSSSCEEE
T ss_pred             HhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC------CCcc-CCCCCEEEEEEEEEecCCCccEEE
Confidence            35699999999999    999999999987   699999999986      2344 899999999999998764  4688


Q ss_pred             EEeeehhh
Q 015066          167 LSLRMIQY  174 (414)
Q Consensus       167 LS~k~~~~  174 (414)
                      ||+.....
T Consensus       200 LSRT~p~l  207 (366)
T 1k0r_A          200 LSRTHPNL  207 (366)
T ss_dssp             EESSCHHH
T ss_pred             EEeCChHH
Confidence            88876654

>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=98.29  E-value=1.7e-06  Score=77.11  Aligned_cols=76  Identities=16%  Similarity=0.141  Sum_probs=57.6

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCcc-----------ccCccCCcEEEEEEEEEeCCCC
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE-----------EAGIVPGLKEEFVIIGENEADD  163 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~-----------e~~~~vG~~v~v~Vl~id~~~~  163 (414)
                      +...+|++++|+|++++++|+||+++. .+|++|.+++++.+..++.           ...+.+|+.|+|+|+++|.+.+
T Consensus        77 ~~~~~Gev~~G~V~~v~~fG~fV~l~~-~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  155 (172)
T 2c35_B           77 FRPFKGEVVDAVVTQVNKVGLFTEIGP-MSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKN  155 (172)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETT
T ss_pred             eeCCCCCEEEEEEEEEeCCEEEEEECC-EEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCCC
Confidence            456899999999999999999999975 6799999999754321111           1128899999999999987655


Q ss_pred             e--EEEEeee
Q 015066          164 S--LVLSLRM  171 (414)
Q Consensus       164 ~--i~LS~k~  171 (414)
                      .  .+.|++.
T Consensus       156 ~~~~igsm~~  165 (172)
T 2c35_B          156 DIFAIGSLMD  165 (172)
T ss_dssp             EEEEEEECCS
T ss_pred             CcEEEEEecC
Confidence            1  3336553

>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=98.28  E-value=6.8e-07  Score=97.13  Aligned_cols=68  Identities=18%  Similarity=0.223  Sum_probs=52.0

Q ss_pred             EEEEEEEEEEeeceEEEEEC--CEEEEEeecccC--cccc-----------cC----cccccCCCCEEEEEEEEEeCC--
Q 015066          266 SVVIGTVQSLKPYGAFIDIG--GINGLLHVSQIS--HDRV-----------AD----IATVLQPGDTLKVMILSHDRE--  324 (414)
Q Consensus       266 ~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels--~~~~-----------~~----~~~~~~~G~~V~vkVl~id~e--  324 (414)
                      +++.|+|+++.+||+||.|.  |++|+||+++++  .+++           .+    ....|++||+|+|+|+.+|.+  
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            79999999999999999997  899999999996  3321           22    257899999999999999988  


Q ss_pred             -CCeEEEEEe
Q 015066          325 -RGRVSLSTK  333 (414)
Q Consensus       325 -~~ri~LS~K  333 (414)
                       ++||.||+|
T Consensus       751 ~~~kI~lslk  760 (760)
T 2vnu_D          751 SKRKAELLLK  760 (760)
T ss_dssp             -CCEEEC---
T ss_pred             cCCcEEEEeC
Confidence             699999987

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

Probab=98.22  E-value=8.5e-07  Score=98.47  Aligned_cols=69  Identities=17%  Similarity=0.216  Sum_probs=59.5

Q ss_pred             cEEEEEEEEEEeeceEEEEEC--CEEEEEeecccC--cccc-----------cC----cccccCCCCEEEEEEEEEeCC-
Q 015066          265 GSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQIS--HDRV-----------AD----IATVLQPGDTLKVMILSHDRE-  324 (414)
Q Consensus       265 G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels--~~~~-----------~~----~~~~~~~G~~V~vkVl~id~e-  324 (414)
                      |+++.|+|++|.+||+||.|.  |++|+||+++|+  .+++           .+    ....|++||+|+|+|..+|.+ 
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            899999999999999999996  799999999997  3321           22    357899999999999999874 


Q ss_pred             --CCeEEEEEe
Q 015066          325 --RGRVSLSTK  333 (414)
Q Consensus       325 --~~ri~LS~K  333 (414)
                        ++||.||||
T Consensus       967 ~~~~kI~Lslk  977 (977)
T 2wp8_J          967 TSKRKAELLLK  977 (977)
T ss_dssp             SCCCCCCEEEC
T ss_pred             cCCCceEEEeC
Confidence              489999997

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

Probab=98.19  E-value=7.6e-07  Score=79.54  Aligned_cols=67  Identities=21%  Similarity=0.269  Sum_probs=54.1

Q ss_pred             cCCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCC--Cccc----------c--ccCCeEEEEEEEeecccc---eEE
Q 015066          186 SEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAE----------E--LLGKDLPLKFVEVDEEQS---RLV  248 (414)
Q Consensus       186 ~~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~--~~~~----------~--~vGq~V~vkVl~vD~e~~---ri~  248 (414)
                      ..|++++|+|++++++|+||+++.++||+|.|++++.  ++..          .  .+|++|++||+++|.+.+   ++.
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            3578999999999999999999988999999999754  2221          1  279999999999998774   344


Q ss_pred             eehhh
Q 015066          249 LSNRK  253 (414)
Q Consensus       249 LS~K~  253 (414)
                       |+|+
T Consensus       163 -tm~~  166 (172)
T 3h0g_G          163 -TMKE  166 (172)
T ss_dssp             -ECCS
T ss_pred             -EcCC
Confidence             6654

>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=98.19  E-value=1e-06  Score=85.54  Aligned_cols=73  Identities=21%  Similarity=0.324  Sum_probs=61.2

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcc----ccc------CcccccCCCCEEEEEEEEEeCCCCeEE
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHD----RVA------DIATVLQPGDTLKVMILSHDRERGRVS  329 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~----~~~------~~~~~~~~G~~V~vkVl~id~e~~ri~  329 (414)
                      .+++|++|.|+|+.+.++|+||+|+ ...|++|+|+++..    |..      +..+.|++||.|.|+|++++. .+++.
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 IGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-DGAVS  170 (308)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-TTEEE
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCC-CCCEE
Confidence            5789999999999999999999999 58999999998752    222      344789999999999999994 67899


Q ss_pred             EEEee
Q 015066          330 LSTKK  334 (414)
Q Consensus       330 LS~K~  334 (414)
                      ||+|+
T Consensus       171 LStr~  175 (308)
T 2nn6_H          171 LHTRS  175 (308)
T ss_dssp             EECCS
T ss_pred             EEecC
Confidence            99985

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=98.15  E-value=2.6e-06  Score=84.06  Aligned_cols=71  Identities=14%  Similarity=0.260  Sum_probs=58.2

Q ss_pred             hhcc--ccEEEEEEEEE----EeeceEEEEECC----EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 015066          260 AQLG--IGSVVIGTVQS----LKPYGAFIDIGG----INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVS  329 (414)
Q Consensus       260 ~~l~--~G~iv~g~V~~----i~~~G~fV~l~g----v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~  329 (414)
                      ++++  +|++|+|+|.+    +.++++||++++    ++|++|.+|+.      |.+.|++||+|+|.|++++.+.+...
T Consensus       124 ~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi------P~E~~~~GDrVkvyV~~V~~~~kgpq  197 (366)
T 1k0r_A          124 GEFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPL  197 (366)
T ss_dssp             ---CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCE
T ss_pred             HHHHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC------CCccCCCCCEEEEEEEEEecCCCccE
Confidence            4555  99999999999    999999999996    99999999986      45899999999999999998765555


Q ss_pred             EEEeeCC
Q 015066          330 LSTKKLE  336 (414)
Q Consensus       330 LS~K~~~  336 (414)
                      +.+....
T Consensus       198 I~LSRT~  204 (366)
T 1k0r_A          198 ITLSRTH  204 (366)
T ss_dssp             EEEESSC
T ss_pred             EEEEeCC
Confidence            5554443

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

Probab=98.06  E-value=6.4e-06  Score=67.03  Aligned_cols=83  Identities=18%  Similarity=0.246  Sum_probs=61.0

Q ss_pred             CCCCCEEEEEEEEEeC---CeEEEEeC-CCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066           97 SELGTKVKGTVFCTDN---RGALVDIT-AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~---~G~~Vdig-~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~  172 (414)
                      .+.++.++|+|...+.   +| |+... ++.+.|+|.+.+....        +                           
T Consensus        11 ~~~~~~~~G~Vk~fn~~kGfG-FI~~~~gg~dvfvH~s~l~~~~--------~---------------------------   54 (101)
T 2bh8_A           11 RLQSGKMTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAGSSGA--------A---------------------------   54 (101)
T ss_dssp             -----CEEEEEEEEEGGGTEE-EEEESSSSCEEEEECCCSCSSS--------C---------------------------
T ss_pred             ccccccceeEEEEEECCCCCE-EEEeCCCCcEEEEEEEEEecCC--------c---------------------------
Confidence            4567889999999854   56 66654 4589999999885321        1                           


Q ss_pred             hhhHHHHHhhhcccCCeEEEEEEEEEecCcEEEEEC-CEEEEEeccccCCCC
Q 015066          173 QYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS  223 (414)
Q Consensus       173 ~~~~~~~~l~~~~~~g~iv~G~V~~v~~~G~~V~i~-gi~GfIp~sels~~~  223 (414)
                              +......|+.++++|..++++|+||.+. +++||||.|+++|..
T Consensus        55 --------~~~~l~~Ge~V~g~V~~i~~fG~fv~l~~~~eGlvhis~i~~~~   98 (101)
T 2bh8_A           55 --------VRGNPQQGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISWAQ   98 (101)
T ss_dssp             --------CCCCCCTTCEEEEEEEECCSEEEEECTTSCEEEEEEEEEEEECC
T ss_pred             --------cccCCCCCCEEEEEEEEeCCcEEEEEcCCCceEEEEHHHCccCc
Confidence                    0112356889999999999999999995 999999999999753

>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=97.97  E-value=1.1e-05  Score=72.14  Aligned_cols=68  Identities=12%  Similarity=0.122  Sum_probs=60.2

Q ss_pred             ccccEEEEEEEEEEeeceEEEEECC--EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIGG--INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLS  331 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~g--v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS  331 (414)
                      +++||+|.|.|+.+..++++|+++.  ..|++|++.+.. ...+....|++||.|.|+|.+++. ...+.||
T Consensus         5 P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~g-~~k~~r~~l~~GDlV~ArV~~~~~-~~~~~Lt   74 (175)
T 2ja9_A            5 PSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPN-ASKKNRPTLQVGDLVYARVCTAEK-ELEAEIE   74 (175)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTT-CCSSSCCCCCTTCEEEEEEEECCT-TSCCEEE
T ss_pred             CCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCCc-hhhhhhccCCCCCEEEEEEEEecC-CCceEEE
Confidence            6789999999999999999999997  999999998863 345677889999999999999986 4688999

>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=97.96  E-value=1.9e-05  Score=73.99  Aligned_cols=66  Identities=18%  Similarity=0.287  Sum_probs=58.5

Q ss_pred             cccEEEEEEEEE----EeeceEEEEECC----EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCC--CeEEEEE
Q 015066          263 GIGSVVIGTVQS----LKPYGAFIDIGG----INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRER--GRVSLST  332 (414)
Q Consensus       263 ~~G~iv~g~V~~----i~~~G~fV~l~g----v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~--~ri~LS~  332 (414)
                      ++|++|+|+|.+    +.+..+||+++.    .+|+++.+|+.      |.+.|++||+|+|.|++++.+.  .+|.||.
T Consensus         6 r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqi------p~E~~~~GDrIkayV~~V~~~~~gpqIiLSR   79 (251)
T 2asb_A            6 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGESYEHGNRLRCYVVGVTRGAREPLITLSR   79 (251)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC------TTCCCCTTCEEEEEEEEEECCSSSCEEEEES
T ss_pred             cCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcC------CCccCCCCCEEEEEEEEEEcCCCCCEEEEEe
Confidence            579999999999    888899999985    99999999975      5688999999999999999764  6899987


Q ss_pred             ee
Q 015066          333 KK  334 (414)
Q Consensus       333 K~  334 (414)
                      ..
T Consensus        80 t~   81 (251)
T 2asb_A           80 TH   81 (251)
T ss_dssp             SC
T ss_pred             cc
Confidence            64

>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=97.83  E-value=3.9e-05  Score=79.29  Aligned_cols=74  Identities=18%  Similarity=0.251  Sum_probs=60.3

Q ss_pred             cCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEcCcccccccc---------CCccccCccCCcEEEEEEEEEeCCCCe
Q 015066           96 NSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACIHKI---------KHVEEAGIVPGLKEEFVIIGENEADDS  164 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~--G~~Vdig~k~~g~lp~sEls~~~~---------~~~~e~~~~vG~~v~v~Vl~id~~~~~  164 (414)
                      ...+|.++.|+|.++.++  |+||++|.+..||+|.+|++..+.         .++++. +++||++.|.|++....++.
T Consensus        42 ~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~-lk~Gq~VlVQV~Ke~~g~KG  120 (517)
T 2bx2_L           42 EQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDV-LREGQEVIVQIDKEERGNKG  120 (517)
T ss_dssp             CCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC-------CCCGGGT-CCTTCEEEEEEEECCCTTCC
T ss_pred             cCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcChhhhccccccccccchhhh-ccCCCEEEEEEEeeccccCC
Confidence            457899999999999998  999999999999999999975542         234455 88999999999997665555


Q ss_pred             EEEEee
Q 015066          165 LVLSLR  170 (414)
Q Consensus       165 i~LS~k  170 (414)
                      ..||..
T Consensus       121 a~lTt~  126 (517)
T 2bx2_L          121 AALTTF  126 (517)
T ss_dssp             CEEESS
T ss_pred             ceEEee
Confidence            555554

>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=97.62  E-value=0.00021  Score=76.23  Aligned_cols=73  Identities=12%  Similarity=0.119  Sum_probs=60.2

Q ss_pred             cCCCCC--EEEEEEEEEeCCeEEEEe-CCCeeEEEcCccccc--ccc-C---------CccccCccCCcEEEEEEEEEeC
Q 015066           96 NSELGT--KVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACI--HKI-K---------HVEEAGIVPGLKEEFVIIGENE  160 (414)
Q Consensus        96 ~l~~G~--iV~G~V~~v~~~G~~Vdi-g~k~~g~lp~sEls~--~~~-~---------~~~e~~~~vG~~v~v~Vl~id~  160 (414)
                      .-++|+  .++|+|+++.++|+||.+ ..+.+|++|.+++++  .+. -         +.... +++|+.|+|+|+++|.
T Consensus       555 ~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~-~~lGD~V~VkV~~vd~  633 (644)
T 2id0_A          555 KDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETV-YKVTDVIDVTIAEVRM  633 (644)
T ss_dssp             GGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEE-EETTCEEEEEEEEEET
T ss_pred             hhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCceeEEcccccEEEecCCCE-eCCCCEEEEEEEEEeC
Confidence            447899  999999999999999999 467999999999963  210 0         12233 8899999999999999


Q ss_pred             CCCeEEEEe
Q 015066          161 ADDSLVLSL  169 (414)
Q Consensus       161 ~~~~i~LS~  169 (414)
                      ..+++.+++
T Consensus       634 ~~~~I~~~l  642 (644)
T 2id0_A          634 ETRSIIARP  642 (644)
T ss_dssp             TTTEEEEEE
T ss_pred             CCCEEEEEE
Confidence            999999986

>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=97.52  E-value=0.0003  Score=62.70  Aligned_cols=72  Identities=13%  Similarity=0.003  Sum_probs=59.1

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      |..++||+|.|+|+.+..++++|+|+. ...|+||.+.+.. ..+..... +.+||.|.++|..++. ++.+.||+
T Consensus         3 Y~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~g-~~k~~r~~-l~~GDlV~ArV~~~~~-~~~~~Ltc   75 (175)
T 2ja9_A            3 YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPN-ASKKNRPT-LQVGDLVYARVCTAEK-ELEAEIEC   75 (175)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTT-CCSSSCCC-CCTTCEEEEEEEECCT-TSCCEEES
T ss_pred             ccCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCCc-hhhhhhcc-CCCCCEEEEEEEEecC-CCceEEEe
Confidence            367899999999999999999999998 7999999998752 22333333 8899999999999874 46788884

>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=97.48  E-value=0.00014  Score=70.52  Aligned_cols=75  Identities=13%  Similarity=0.119  Sum_probs=60.0

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccc-cc---C------CccccCccCCcEEEEEEEEEeCCCCe
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH-KI---K------HVEEAGIVPGLKEEFVIIGENEADDS  164 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~-~~---~------~~~e~~~~vG~~v~v~Vl~id~~~~~  164 (414)
                      +..++|++|.|+|+.+..++++|+|+....|+++.+++++. ..   .      +..+. |.+||.|.++|++++ .++.
T Consensus        91 Y~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~-l~vGDlV~ArVisv~-~~~~  168 (308)
T 2nn6_H           91 YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGF-LQEGDLISAEVQAVF-SDGA  168 (308)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHH-SCSSCEECCEEEEEE-TTTE
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhccccceeecccchhhhhhhcc-CCCCCEEEEEEEEcC-CCCC
Confidence            46799999999999999999999999878999999988652 21   1      11133 899999999999998 4678


Q ss_pred             EEEEeee
Q 015066          165 LVLSLRM  171 (414)
Q Consensus       165 i~LS~k~  171 (414)
                      +.||.+.
T Consensus       169 i~LStr~  175 (308)
T 2nn6_H          169 VSLHTRS  175 (308)
T ss_dssp             EEEECCS
T ss_pred             EEEEecC
Confidence            9998874

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

Probab=97.25  E-value=0.00068  Score=62.56  Aligned_cols=69  Identities=17%  Similarity=0.044  Sum_probs=54.1

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc--------------CCccccCccCCcEEEEEEEEEeCC
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI--------------KHVEEAGIVPGLKEEFVIIGENEA  161 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~--------------~~~~e~~~~vG~~v~v~Vl~id~~  161 (414)
                      ...+|+++.|+|.+++++|+||.+.+..+|+++.+++..++.              +.. ...+.+|+.|+|+|.+++..
T Consensus        78 ~p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t-~~~~~~Gd~VrvrV~~v~~~  156 (218)
T 2ckz_B           78 KPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEET-KLYFDVNEKIRFRIEREVFV  156 (218)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--C-EEEECTTCEEEEEEEEEEEC
T ss_pred             cCCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccC-CcEEcCCCEEEEEEEEEEcc
Confidence            567899999999999999999999556899999999865432              111 22278999999999999876


Q ss_pred             CCeE
Q 015066          162 DDSL  165 (414)
Q Consensus       162 ~~~i  165 (414)
                      ++..
T Consensus       157 ~~~p  160 (218)
T 2ckz_B          157 DVKP  160 (218)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            5533

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

Probab=97.24  E-value=0.00072  Score=61.71  Aligned_cols=66  Identities=15%  Similarity=0.073  Sum_probs=52.5

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc-------------------CCccccCccCCcEEEEEEE
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI-------------------KHVEEAGIVPGLKEEFVII  156 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~-------------------~~~~e~~~~vG~~v~v~Vl  156 (414)
                      ...+|+++.|+|.++++.|+||+++ ..+|+++.+++...+.                   ++.. ..+.+|+.|+|+|+
T Consensus        78 ~p~~GEv~~G~Vs~vt~~GifV~lg-~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~-~~~~~Gd~VrvrV~  155 (203)
T 3ayh_B           78 RPFRGEVMLGKIKSCSEEGIRVTIS-FFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTE-LYFDIDEEIRFQIE  155 (203)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECS-SCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEE-EECCTTCEEEEEEE
T ss_pred             ccCCCCEEEEEEEEEeccEEEEEEe-CceEEEEcHHhCCCCceECccCceEEeecccccccccCC-cEEcCCCEEEEEEE
Confidence            4679999999999999999999996 5899999999865432                   1212 23889999999999


Q ss_pred             EEeCCCC
Q 015066          157 GENEADD  163 (414)
Q Consensus       157 ~id~~~~  163 (414)
                      +++..+.
T Consensus       156 ~v~~~~~  162 (203)
T 3ayh_B          156 SEDFVDI  162 (203)
T ss_dssp             EEEECC-
T ss_pred             EEEcccc
Confidence            9886443

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=97.11  E-value=0.00088  Score=72.77  Aligned_cols=69  Identities=13%  Similarity=0.042  Sum_probs=50.1

Q ss_pred             CEEEEEEEEEeCCeEEEEeCC-CeeEEEcCcccc--cccc-----------CC----ccccCccCCcEEEEEEEEEeCC-
Q 015066          101 TKVKGTVFCTDNRGALVDITA-KSSAYLPTQEAC--IHKI-----------KH----VEEAGIVPGLKEEFVIIGENEA-  161 (414)
Q Consensus       101 ~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls--~~~~-----------~~----~~e~~~~vG~~v~v~Vl~id~~-  161 (414)
                      +.+.|+|+++.++|+||.+.. +.+|++|.++++  ..+.           .+    .... |++|++|+|+|+.+|.+ 
T Consensus       671 ~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d~~~fd~~~~~l~g~~~~~~~~~~-~~lGD~V~VkV~~vd~~~  749 (760)
T 2vnu_D          671 STETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRD-VYVFDKVEVQVRSVMDPI  749 (760)
T ss_dssp             SEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEE-EETTCEEEEEEC------
T ss_pred             eEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCceeEEcccccEEEEecCCCccCcE-EecCCEEEEEEEEEECcc
Confidence            799999999999999999976 799999999995  3220           11    1233 88999999999999877 


Q ss_pred             --CCeEEEEee
Q 015066          162 --DDSLVLSLR  170 (414)
Q Consensus       162 --~~~i~LS~k  170 (414)
                        ++++.||+|
T Consensus       750 ~~~~kI~lslk  760 (760)
T 2vnu_D          750 TSKRKAELLLK  760 (760)
T ss_dssp             --CCEEEC---
T ss_pred             ccCCcEEEEeC
Confidence              589999875

>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=96.96  E-value=0.0011  Score=63.72  Aligned_cols=70  Identities=16%  Similarity=0.081  Sum_probs=60.4

Q ss_pred             hccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST  332 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~  332 (414)
                      -+++||+|.|+|+.+....+.|+|. -..|++|.+++. ....+....|++||.|.|+|++++. .....||+
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 VPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVC  194 (289)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCT-TSCCEEEC
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcC-cchhhhhhhcCCCCEEEEEEEEcCC-CCceEEEe
Confidence            4689999999999999999999998 588999999876 2345677889999999999999985 45788888

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

Probab=96.89  E-value=0.0013  Score=73.06  Aligned_cols=70  Identities=13%  Similarity=0.054  Sum_probs=56.8

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCcccc--ccc---------c--CC----ccccCccCCcEEEEEEEEEeCC
Q 015066          100 GTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEAC--IHK---------I--KH----VEEAGIVPGLKEEFVIIGENEA  161 (414)
Q Consensus       100 G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls--~~~---------~--~~----~~e~~~~vG~~v~v~Vl~id~~  161 (414)
                      |+.+.|+|+.+.++|+||.+.. +.+|++|.+++.  ..+         +  .+    .... +++|++|+|+|..++..
T Consensus       887 ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~-~~lGD~V~VkV~~vd~~  965 (977)
T 2wp8_J          887 ESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRD-VYVFDKVEVQVRSVMDP  965 (977)
T ss_dssp             TCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEE-EETTCEEEEEECCCCCS
T ss_pred             ceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcE-EccCCEEEEEEEEEcCc
Confidence            9999999999999999999976 799999999996  322         0  11    1233 88999999999998863


Q ss_pred             ---CCeEEEEee
Q 015066          162 ---DDSLVLSLR  170 (414)
Q Consensus       162 ---~~~i~LS~k  170 (414)
                         ++++.||+|
T Consensus       966 ~~~~~kI~Lslk  977 (977)
T 2wp8_J          966 ITSKRKAELLLK  977 (977)
T ss_dssp             SSCCCCCCEEEC
T ss_pred             ccCCCceEEEeC
Confidence               378999885

>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=96.53  E-value=0.0051  Score=58.99  Aligned_cols=73  Identities=16%  Similarity=-0.004  Sum_probs=59.5

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      +-.++||+|-|+|+++....+.|+|+....|+||.+++.- ..+...+. |.+||.|.++|++.+ ..+.+.||+-
T Consensus       123 YiP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~G-atk~~r~~-f~~GDlV~ArV~s~~-~~~~~eLsc~  195 (289)
T 2nn6_G          123 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEG-ATKRNRPN-VQVGDLIYGQFVVAN-KDMEPEMVCI  195 (289)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSC-CSSCSSSS-SCTTCEEEEEEEECC-TTSCCEEECS
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcCc-chhhhhhh-cCCCCEEEEEEEEcC-CCCceEEEec
Confidence            4679999999999999999999999988889999987652 22333444 899999999999987 3456788873

>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure initiative, northeast structural genomics consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5 b.40.4.16 PDB: 2r7f_A

Probab=94.67  E-value=0.045  Score=56.06  Aligned_cols=59  Identities=22%  Similarity=0.253  Sum_probs=47.2

Q ss_pred             cccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEE
Q 015066          263 GIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLST  332 (414)
Q Consensus       263 ~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~  332 (414)
                      .+|+.+.|.|..         +.+..|+||++++..+  -.....|+.||.|+|+|.++|..+++|.+..
T Consensus       402 ~~g~~f~g~vv~---------l~~~~glV~v~~l~~d--~~~~~~~~lGd~V~V~v~~vd~~~~~i~f~~  460 (469)
T 2r7d_A          402 QPERVWDAVVVD---------RRGAQATLLIPDLAFD--VQVNTPAAPGTALQVQFADIDLPQMRVRARS  460 (469)
T ss_dssp             CTTCCEEEEEEE---------EETTEEEEEEGGGTEE--EEEECCCCTTCEEEEEEEEEETTTTEEEEEE
T ss_pred             CCCCEEEEEEEE---------EeCcEEEEEECCCCeE--EecCCcCCCCCEEEEEEEEEccCCCEEEEEE
Confidence            578999988754         3355899999998765  2234579999999999999999999998865

>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=93.24  E-value=0.31  Score=44.50  Aligned_cols=69  Identities=12%  Similarity=0.085  Sum_probs=49.3

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccc-----------cCccCCcEEEEEEEEEeCCCCe
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEE-----------AGIVPGLKEEFVIIGENEADDS  164 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e-----------~~~~vG~~v~v~Vl~id~~~~~  164 (414)
                      ...+|+++.|+|..+++.|+.+-+-+-..++||...+.....-++.+           ..-.+|++|+|+|.+++..++.
T Consensus       126 rPf~GevL~G~V~~~s~~~Ig~~~~G~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~~~~~~~~~  205 (214)
T 2rf4_A          126 QPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGRV  205 (214)
T ss_dssp             CCCTTCEEEEEECCCCSSCEEEEETTTEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEEEEECCSSS
T ss_pred             ecCCCCEEEEEEEEECCCcEEEEEeCCEEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEEEEEecCCE
Confidence            46899999999999999888775544577899999885432211111           1124699999999999864443

>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=90.50  E-value=0.77  Score=41.79  Aligned_cols=69  Identities=16%  Similarity=0.053  Sum_probs=48.9

Q ss_pred             hccccEEEEEEEEEEeeceEEEEECC-EEEEEeecccCcccccCcc------------cccCCCCEEEEEEEEEeCCCCe
Q 015066          261 QLGIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIA------------TVLQPGDTLKVMILSHDRERGR  327 (414)
Q Consensus       261 ~l~~G~iv~g~V~~i~~~G~fV~l~g-v~Glvh~sels~~~~~~~~------------~~~~~G~~V~vkVl~id~e~~r  327 (414)
                      .+.+|+++.|+|+.+.+.|+.+-+-| .+.+|+...|..++.-++.            +.-++|+.|+.+|.+++.+++-
T Consensus       126 rPf~GevL~G~V~~~s~~~Ig~~~~G~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~~~~~~~~~  205 (214)
T 2rf4_A          126 QPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGRV  205 (214)
T ss_dssp             CCCTTCEEEEEECCCCSSCEEEEETTTEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEEEEECCSSS
T ss_pred             ecCCCCEEEEEEEEECCCcEEEEEeCCEEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEEEEEecCCE
Confidence            47789999999999999777765544 7889999887533211111            1224699999999999875544


Q ss_pred             EE
Q 015066          328 VS  329 (414)
Q Consensus       328 i~  329 (414)
                      ++
T Consensus       206 ls  207 (214)
T 2rf4_A          206 VS  207 (214)
T ss_dssp             CE
T ss_pred             EE
Confidence            33

>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=88.40  E-value=0.94  Score=36.27  Aligned_cols=56  Identities=13%  Similarity=0.058  Sum_probs=47.5

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccc-----cC-cccccCCCCEEEEE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV-----AD-IATVLQPGDTLKVM  317 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~-----~~-~~~~~~~G~~V~vk  317 (414)
                      ...|+.+.+.|+++.+.++-|.+. |-.+.|..+.+.|-+-     .. +++.+++||.|.|+
T Consensus        31 ~~~~~~~~AvV~~v~~~~~~v~~~~g~~~~l~~~~~~WA~~~~~~~~~~~~~~l~~GdvI~V~   93 (106)
T 3d0f_A           31 GNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAHRFLSNDPKIGEKRIRPGALIRVK   93 (106)
T ss_dssp             CTTTTCEEEEEEEEETTEEEEEETTSCEEEECGGGGSTTGGGTTTCTTTGGGSCCTTEEEEEE
T ss_pred             CccCCeEEEEEEEeCCCeEEEEEcCCCeEEEcHHHChhhhhcccccccchhccCCCCCEEEEE
Confidence            445889999999999999999996 6888899999998752     34 67789999999997

>3d0f_A Penicillin-binding 1 transmembrane protein MRCA; BIG_1156.2, STR genomics, PSI-2, protein structure initiative; 1.64A {Nitrosomonas europaea atcc 19718}

Probab=87.16  E-value=3.5  Score=32.81  Aligned_cols=57  Identities=9%  Similarity=-0.018  Sum_probs=46.3

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc-----CC-ccccCccCCcEEEEE
Q 015066           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI-----KH-VEEAGIVPGLKEEFV  154 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~-----~~-~~e~~~~vG~~v~v~  154 (414)
                      ...|+.+.+.|+++.+.++.|.+.++..+.|+...|.+...     +. +.+. +++|+.|.++
T Consensus        31 ~~~~~~~~AvV~~v~~~~~~v~~~~g~~~~l~~~~~~WA~~~~~~~~~~~~~~-l~~GdvI~V~   93 (106)
T 3d0f_A           31 GNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAHRFLSNDPKIGEKR-IRPGALIRVK   93 (106)
T ss_dssp             CTTTTCEEEEEEEEETTEEEEEETTSCEEEECGGGGSTTGGGTTTCTTTGGGS-CCTTEEEEEE
T ss_pred             CccCCeEEEEEEEeCCCeEEEEEcCCCeEEEcHHHChhhhhcccccccchhcc-CCCCCEEEEE
Confidence            45689999999999999999999777888899999987532     22 4444 8899999887

>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=86.86  E-value=1.2  Score=34.82  Aligned_cols=62  Identities=23%  Similarity=0.215  Sum_probs=46.3

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC---CEEEEEeec-ccCcccccCcccccCCCCEEEEEEEEEeC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVS-QISHDRVADIATVLQPGDTLKVMILSHDR  323 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~s-els~~~~~~~~~~~~~G~~V~vkVl~id~  323 (414)
                      -++.+|++.+|.|. ++++-++|.|.   |.++++--+ ++..++..++++.+ +|-+|+++|+.+|.
T Consensus        28 ~~~~~g~VtkGiVy-~kd~~fyV~L~dY~glEaii~dYvnv~~dr~~klkkkL-VGKtIkVqVIRvD~   93 (102)
T 1jjg_A           28 MDLSPGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRADG   93 (102)
T ss_dssp             CCCCSSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEECS
T ss_pred             cccCCCceEeeEEE-EeCCEEEEEecCCCCceeeeehhhhhhHHHHHHHHHHh-cCceEEEEEEEecc
Confidence            46889999999887 55777788885   688887543 34445555555553 79999999999984

>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=85.55  E-value=8.1  Score=29.94  Aligned_cols=69  Identities=19%  Similarity=0.253  Sum_probs=47.9

Q ss_pred             ccccEEEEEEEEEEeeceE-EEEEC--CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCC-eEEEEEeeCCC
Q 015066          262 LGIGSVVIGTVQSLKPYGA-FIDIG--GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERG-RVSLSTKKLEP  337 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~-fV~l~--gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~-ri~LS~K~~~~  337 (414)
                      +.......|+|+... .|. ||.-.  +-+-++|++.|...     ...+..||.|...+..-+ .++ .-...++.+.+
T Consensus        13 ~s~~~~~~G~Vkwf~-KGfGFI~~ddgg~DVFvH~s~i~~~-----~~~L~~G~~V~F~v~~~~-k~Gk~~A~~V~~~~~   85 (89)
T 1wfq_A           13 TSAALRETGVIEKLL-TSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDR-RTGKPIAVKLVKISG   85 (89)
T ss_dssp             SSCCCEEEEEEEEEC-SSEEEEEETTTTEEEEEETTTCSSC-----TTTCCTTCCEEEEEEECS-SSCCEEEEEEEESSC
T ss_pred             CCcccccceEEEEEe-CCeeEEecCCCCccEEEEhHHhhCc-----cCCCCCCCEEEEEEEECC-CCCCcEEEEEEECCc
Confidence            344567899999985 555 77775  48999999998653     256889999999886533 224 34555555543

>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=83.86  E-value=3  Score=42.43  Aligned_cols=94  Identities=7%  Similarity=-0.032  Sum_probs=56.4

Q ss_pred             HHHHHHHHHHHhhcccCCCCCCCCCHHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc
Q 015066           58 EELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI  137 (414)
Q Consensus        58 ~~l~~iiee~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~  137 (414)
                      +.|.++++.+-.+-+.+..     -+.+....|......-..|+...|.|+.+..          ..|+++.+++.... 
T Consensus       367 ~~l~~~~~~~~~~er~a~~-----aer~~~~~~~~~~l~~~~g~~f~g~vv~l~~----------~~glV~v~~l~~d~-  430 (469)
T 2r7d_A          367 KVMAAHIAESQMNADATRQ-----AERLSRRHHTLRFIAAQPERVWDAVVVDRRG----------AQATLLIPDLAFDV-  430 (469)
T ss_dssp             HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHTCTTCCEEEEEEEEET----------TEEEEEEGGGTEEE-
T ss_pred             HHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHhCCCCEEEEEEEEEeC----------cEEEEEECCCCeEE-
Confidence            5566666655544443211     0112233332221233689999998876542          35666666665431 


Q ss_pred             CCccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066          138 KHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus       138 ~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      . .. ..+.+|+.|+++|.++|..++++.+..
T Consensus       431 ~-~~-~~~~lGd~V~V~v~~vd~~~~~i~f~~  460 (469)
T 2r7d_A          431 Q-VN-TPAAPGTALQVQFADIDLPQMRVRARS  460 (469)
T ss_dssp             E-EE-CCCCTTCEEEEEEEEEETTTTEEEEEE
T ss_pred             e-cC-CcCCCCCEEEEEEEEEccCCCEEEEEE
Confidence            1 11 238899999999999999999887754

>3h8z_A FragIle X mental retardation syndrome-related Pro; tudor domains, FXR2, structura genomics, structural genomics consortium, SGC; 1.92A {Homo sapiens} PDB: 3o8v_A 3kuf_A 2bkd_N*

Probab=82.13  E-value=2.7  Score=35.10  Aligned_cols=56  Identities=16%  Similarity=0.159  Sum_probs=40.3

Q ss_pred             ccEEEEEEEEEEeeceEEEEECC-E--EEEEeecccCcccccCcccccCCCCEEEEEEE
Q 015066          264 IGSVVIGTVQSLKPYGAFIDIGG-I--NGLLHVSQISHDRVADIATVLQPGDTLKVMIL  319 (414)
Q Consensus       264 ~G~iv~g~V~~i~~~G~fV~l~g-v--~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl  319 (414)
                      .|.-|.|+|+.+.+.+++|.+.+ .  +-.+|.+++..-.-......|.+||+|.|.--
T Consensus        14 ~G~~y~a~V~~v~~d~~~V~f~n~w~~~~~vp~~~vRlpP~~~~~~~f~~gd~VEV~~~   72 (128)
T 3h8z_A           14 NGAFYKGFVKDVHEDSVTIFFENNWQSERQIPFGDVRLPPPADYNKEITEGDEVEVYSR   72 (128)
T ss_dssp             TSCEEEEEEEEECSSEEEEEETTCTTCCEEEEGGGEECCCCC----CCCTTCEEEEEEC
T ss_pred             CCCEEEEEEEEEeCCcEEEEEccccCcceEechhhEEcCCCcccccCCCCCCEEEEEec
Confidence            38999999999999999999974 2  45778777754322223356899999998543

>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, cold shock structural genomics; NMR {Pectobacterium atrosepticum}

Probab=81.33  E-value=15  Score=27.42  Aligned_cols=60  Identities=17%  Similarity=0.298  Sum_probs=41.0

Q ss_pred             EEEEEEEEee-ceE-EEEEC-C-EEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          268 VIGTVQSLKP-YGA-FIDIG-G-INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       268 v~g~V~~i~~-~G~-fV~l~-g-v~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      .+|+|+...+ .|. ||.-. | -. ++|+|.|....      .++.||.|...+..-  .++.-...++.+.
T Consensus         3 ~~G~Vkwfn~~KGfGFI~~~dg~~d-FvH~s~i~~~g------~l~~G~~V~F~~~~g--~kG~~A~~V~~~~   66 (74)
T 2k5n_A            3 MNGTITTWFKDKGFGFIKDENGDNR-YFHVIKVANPD------LIKKDAAVTFEPTTN--NKGLSAYAVKVVP   66 (74)
T ss_dssp             EEEEEEEEETTTTEEEEEESSSCEE-EEEGGGBSSGG------GCCTTCEEEEEEEEC--SSSEEEEEEEECC
T ss_pred             cceEEEEEECCCCeEEEecCCCCce-EEEHhHcccCC------CCCCCCEEEEEEEeC--CCCceeEEEEeCC
Confidence            5799998863 343 55554 4 56 99999996542      689999999888643  3555555555443

---

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	414
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	4e-16
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	5e-15
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	0.003
d1kl9a2	86	b.40.4.5 (A:3-88) Eukaryotic initiation factor 2al	3e-14
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	2e-13
d1e3pa2	62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	2e-13
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	3e-13
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	6e-13
d2ahob2	84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	6e-13
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	4e-11
d1y14b1	91	b.40.4.5 (B:81-171) C-terminal domain of RNA polym	5e-11
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	1e-10
d2c35b1	94	b.40.4.5 (B:78-171) C-terminal domain of RNA polym	1e-08
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	2e-07
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	6e-07
d2nn6i1	125	b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {H	6e-06
d2ix0a3	87	b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Esche	1e-05

>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 = 70.6 bits (173), Expect = 4e-16
 Identities = 30/76 (39%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMI 318
           A++ +G V  G V  +  +GAF+ IG G  GL+H+SQI+  RV  +   LQ G  + V +
Sbjct: 1   AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKV 60

Query: 319 LSHDRERGRVSLSTKK 334
           L  D  +GR+ LS K+
Sbjct: 61  LEVD-RQGRIRLSIKE 75

>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 = 68.0 bits (166), Expect = 5e-15
 Identities = 32/81 (39%), Positives = 48/81 (59%), Gaps = 2/81 (2%)

Query: 261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMIL 319
            L  G V+ G V ++  +GAF+DIG   +GL+H+S +S   V D   V++ GD +KV ++
Sbjct: 15  DLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVM 74

Query: 320 SHDRERGRVSLSTKKLEPTPG 340
             D  R RV LS +  + TPG
Sbjct: 75  EVDIPRNRVGLSMRMSD-TPG 94

>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 = 34.9 bits (80), Expect = 0.003
 Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 2/91 (2%)

Query: 81  FTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV 140
           F   EF   +E    + + G  ++G V    N GA VDI       +         +K  
Sbjct: 1   FKTAEFQEGVESLK-DLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDP 59

Query: 141 EEAGIVPGLKEEFVIIGENEADDSLVLSLRM 171
            E  +  G   +  ++  +   + + LS+RM
Sbjct: 60  YE-VVKAGDIVKVKVMEVDIPRNRVGLSMRM 89

>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 = 65.8 bits (160), Expect = 3e-14
 Identities = 19/74 (25%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
           +  VV+  V+S+   GA++ +     I G++ +S++S  R+  I  +++ G    V+++ 
Sbjct: 13  VEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIR 72

Query: 321 HDRERGRVSLSTKK 334
            D+E+G + LS ++
Sbjct: 73  VDKEKGYIDLSKRR 86

>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 = 63.4 bits (154), Expect = 2e-13
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV----ADIATVLQPGDTLKVMI 318
            G VVIG +QS+     F+DI      +L V             D+ ++L+ GD +K  +
Sbjct: 7   AGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKV 66

Query: 319 LSHDRERGRVSLSTK 333
           ++ D +     L+ +
Sbjct: 67  VAFD-KTRSPLLTVQ 80

>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 = 62.4 bits (152), Expect = 2e-13
 Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 270 GTVQSLKPYGAFIDI-GGINGLLHVSQISHD----RVADIATVLQPGDTLKVMILSHDRE 324
           G+V     +GAF+ +  G +GLLH+SQI       RV ++  VL  G  ++V I   D  
Sbjct: 1   GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSR 60

Query: 325 R 325
            
Sbjct: 61  G 61

>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 = 63.5 bits (154), Expect = 3e-13
 Identities = 23/100 (23%), Positives = 48/100 (48%), Gaps = 16/100 (16%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA-----------DIATVLQPGD 312
           +  ++ G V  +  +G+F+ +G ++GL+HVSQI  D V+           +   VL+ GD
Sbjct: 3   MYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGD 62

Query: 313 TLKVMILSHDRERGR-----VSLSTKKLEPTPGDMIRNPK 347
            ++  I++   +  R     ++L+ ++      + I   K
Sbjct: 63  YVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIEEEK 102

>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 = 62.3 bits (151), Expect = 6e-13
 Identities = 15/84 (17%), Positives = 36/84 (42%), Gaps = 12/84 (14%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQIS----------HDRVADIATVLQPGD 312
           +G +V+G +  ++     ++    ++ +L +S ++           +    +   LQ GD
Sbjct: 8   VGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGD 67

Query: 313 TLKVMILSHDRERGRVSLSTKKLE 336
            +   + +     G VSL T+ L+
Sbjct: 68  LISAEVQAVFS-DGAVSLHTRSLK 90

>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 = 62.0 bits (150), Expect = 6e-13
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVMILS 320
            G ++I TV+ +  YG+++ +   GG+   L  S++S   V +I  VL+    + V ++ 
Sbjct: 11  EGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIR 70

Query: 321 HDRERGRVSLSTKK 334
            DR +G V +S KK
Sbjct: 71  VDRRKGTVDVSLKK 84

>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 = 56.5 bits (136), Expect = 4e-11
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 5/74 (6%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATV---LQPGDTLKVMIL 319
           I  +VIG V+ ++ YG  +DI       L  S +    +     +   L  GD +   I 
Sbjct: 7   INDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIE 66

Query: 320 SHDRERGRVSLSTK 333
           + DR      LS K
Sbjct: 67  NFDRSI-DPVLSVK 79

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 91

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 56.8 bits (137), Expect = 5e-11
 Identities = 13/77 (16%), Positives = 24/77 (31%), Gaps = 10/77 (12%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA----------DIATVLQPGDT 313
            G VV GTV S   +G  + +G +   +    +  D                 V+     
Sbjct: 3   KGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSR 62

Query: 314 LKVMILSHDRERGRVSL 330
           ++V I     +   +  
Sbjct: 63  IRVKIEGCISQVSSIHA 79

>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 = 55.4 bits (133), Expect = 1e-10
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHD-RVADIATVLQPGDTLKVMILSH 321
           +G VVIG ++ +   G  +DI       L VS+            VL  GD +   +L+ 
Sbjct: 5   VGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNI 64

Query: 322 DRERGRVSLSTKKLEPTP 339
           D  + +V+L+ K     P
Sbjct: 65  D-PKMKVTLTMKDRICRP 81

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.3 bits (120), Expect = 1e-08
 Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 12/79 (15%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA------------DIATVLQPG 311
            G VV   V  +   G F +IG ++  +    I  +               D   V+Q  
Sbjct: 4   KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQD 63

Query: 312 DTLKVMILSHDRERGRVSL 330
           D +++ I+    ++  +  
Sbjct: 64  DEIRLKIVGTRVDKNDIFA 82

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.8 bits (111), Expect = 2e-07
 Identities = 12/71 (16%), Positives = 22/71 (30%), Gaps = 3/71 (4%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
            G  VIG V +       +D+GG     L                +Q GD +    +  +
Sbjct: 6   KGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEG-ATKRNRPNVQVGDLIYGQFVVAN 64

Query: 323 RERGRVSLSTK 333
           ++     +   
Sbjct: 65  KD-MEPEMVCI 74

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]} Length = 90

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Saccharomyces cerevisiae [TaxId: 4932]

 Score = 45.2 bits (107), Expect = 6e-07
 Identities = 8/71 (11%), Positives = 21/71 (29%), Gaps = 2/71 (2%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD 322
           +   VIG +         + +    + +        +        LQ GD +   + + +
Sbjct: 7   VNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAE 66

Query: 323 RERGRVSLSTK 333
           +E     +   
Sbjct: 67  KE-LEAEIECF 76

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Length = 125

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (101), Expect = 6e-06
 Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 11/81 (13%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGIN---------GLLHVSQI--SHDRVADIATVLQPGD 312
           +G++V   V S+    A + I  +          G +    +  +     +I    +PGD
Sbjct: 7   VGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGD 66

Query: 313 TLKVMILSHDRERGRVSLSTK 333
            +   ++S    +    L+T 
Sbjct: 67  IVLAKVISLGDAQSNYLLTTA 87

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Length = 87

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 10/82 (12%), Positives = 20/82 (24%), Gaps = 14/82 (17%)

Query: 263 GIGSVVIGTVQSLKPYGAFIDI--GGINGLLHVSQISHDR------------VADIATVL 308
           G  +     +  +   G  + +   G    +    +   R                 TV 
Sbjct: 2   GTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVY 61

Query: 309 QPGDTLKVMILSHDRERGRVSL 330
           +  D + V I     E   +  
Sbjct: 62  KVTDVIDVTIAEVRMETRSIIA 83

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	414
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.76
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.75
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.74
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.72
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.68
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.63
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.57
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.56
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.56
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.53
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.53
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.5
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.45
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.43
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.36
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.35
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.33
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.23
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.23
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	99.22
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	99.18
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.12
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	99.05
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	98.91
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.83
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	98.74
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.64
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.61
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.6
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.58
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.49
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.48
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.47
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	98.37
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.29
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	98.26
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.97
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.75
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.47
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.43
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	95.11
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	93.07
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	92.74
d3d31a1	119	Sulfate/molybdate ABC transporter, ATP-binding pro	89.74
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	88.38
d1c9oa_	66	Major cold shock protein {Bacillus caldolyticus [T	85.1
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	84.78
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	84.65
d1ah9a_	71	Translational initiation factor 1, IF1 {Escherichi	83.93
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	82.03
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	81.72
d2vnud2	88	Exosome complex exonuclease RRP44 {Saccharomyces c	81.23
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	80.24

>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=99.76  E-value=1.2e-19  Score=139.55  Aligned_cols=75  Identities=41%  Similarity=0.734  Sum_probs=70.9

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      +++++|++|.|+|+++.+||+||+|+ |++||||+++++|.++.+|.+.|++||+|+|+|+++|+ ++||.||||+.
T Consensus         1 ad~kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~-~~ri~LS~k~a   76 (76)
T d1sroa_           1 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR-QGRIRLSIKEA   76 (76)
T ss_dssp             CCCCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCT-TCCCEEEECCC
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECC-CCCEEEEEEcC
Confidence            36899999999999999999999998 89999999999999999999999999999999999996 57999999973

>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=99.75  E-value=1.3e-18  Score=139.32  Aligned_cols=81  Identities=40%  Similarity=0.623  Sum_probs=77.3

Q ss_pred             HhhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCC
Q 015066          259 QAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEP  337 (414)
Q Consensus       259 ~~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~  337 (414)
                      .+++++|++|.|+|+++.++|+||+|+ |++|+||.+++++.++.++++.|++||.|+|+|+++|+++++|.||+|+. +
T Consensus        13 ~~~~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          13 LKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRMS-D   91 (94)
T ss_dssp             GGGCCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEESCTT-C
T ss_pred             HhcCCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEEecc-C
Confidence            478999999999999999999999998 89999999999999999999999999999999999999999999999975 6


Q ss_pred             CCC
Q 015066          338 TPG  340 (414)
Q Consensus       338 ~p~  340 (414)
                      +||
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=99.74  E-value=2.4e-18  Score=135.35  Aligned_cols=73  Identities=26%  Similarity=0.532  Sum_probs=58.3

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK  334 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~  334 (414)
                      +++|++|.|+|+++.+||+||+|.   |++||||+++++|.++.++.+.|++||.|+|+|+++|++++||.||+|+
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            368999999999999999999995   7999999999999999999999999999999999999999999999985

>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=99.72  E-value=2.5e-18  Score=134.62  Aligned_cols=73  Identities=30%  Similarity=0.546  Sum_probs=65.3

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEee
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKK  334 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~  334 (414)
                      +++|++|+|+|+++++||+||+|.   |++||||.++++|.++.++.+.|++||.|+|+|+++|+++++|.||+|+
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            468999999999999999999995   7999999999999999999999999999999999999999999999985

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.68  E-value=2.1e-17  Score=134.89  Aligned_cols=80  Identities=26%  Similarity=0.459  Sum_probs=72.0

Q ss_pred             ccccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccc-----------cCcccccCCCCEEEEEEEEEeCCCCe---
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVMILSHDRERGR---  327 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~-----------~~~~~~~~~G~~V~vkVl~id~e~~r---  327 (414)
                      +++|++|.|+|++|.+||+||+|++++||||+++|+++++           .++.+.|++||.|+|+|+++|.++++   
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~~~~~~~   80 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKRG   80 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC-----
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEeeCeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchhhccccC
Confidence            4689999999999999999999999999999999999876           47889999999999999999998876   


Q ss_pred             --EEEEEeeCCCCCCc
Q 015066          328 --VSLSTKKLEPTPGD  341 (414)
Q Consensus       328 --i~LS~K~~~~~p~~  341 (414)
                        |.||+|+...+||+
T Consensus        81 ~~i~ls~K~~~~~~~e   96 (106)
T d1go3e1          81 SKIALTMRQPYLGKLE   96 (106)
T ss_dssp             CEEEEECCSTTCEEHH
T ss_pred             ceeecccccCCCCcch
Confidence              78999998887765

>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=99.63  E-value=2.7e-16  Score=122.55  Aligned_cols=76  Identities=26%  Similarity=0.336  Sum_probs=69.8

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccc-ccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCCCC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR-VADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT  338 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~-~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~~~  338 (414)
                      +++|++|.|+|+++.++|+||+++ ++.|++|++++++.+ ..++.+.|++||.|+|+|+++|+ +++|.||||+....
T Consensus         3 Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~-~~~i~LS~k~~~~~   80 (83)
T d2ba0a1           3 PSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMKDRICR   80 (83)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECT-TCCEEEECCSSSCE
T ss_pred             CCCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEEEEECC-CCCEEEEecCCCCC
Confidence            578999999999999999999998 799999999999875 77899999999999999999996 57899999987654

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Tex S1-domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.57  E-value=3.1e-15  Score=119.25  Aligned_cols=89  Identities=21%  Similarity=0.274  Sum_probs=81.2

Q ss_pred             CHHHHHHHHHhhcccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCC
Q 015066           82 TLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA  161 (414)
Q Consensus        82 ~~~~f~~~l~~~~~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~  161 (414)
                      ...+|++.++.+. ++++|++++|+|.++.++|+||+++++.+||||.+++++.+..++.+. |++||.+.|+|+++|.+
T Consensus         2 k~a~~~~~ie~~~-~~k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~-~~vGq~v~~~V~~id~~   79 (94)
T d3bzka4           2 KTAEFQEGVESLK-DLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEV-VKAGDIVKVKVMEVDIP   79 (94)
T ss_dssp             CHHHHHHTCCCGG-GCCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSCHHHH-CCTTCEEEEEEEEEETT
T ss_pred             chhHHHhhhhHHh-cCCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccChhhh-hccCcEEEEEEEEEECC
Confidence            3456777776654 899999999999999999999999999999999999999998999888 99999999999999999


Q ss_pred             CCeEEEEeeeh
Q 015066          162 DDSLVLSLRMI  172 (414)
Q Consensus       162 ~~~i~LS~k~~  172 (414)
                      ++++.||+|..
T Consensus        80 ~~~i~LS~K~~   90 (94)
T d3bzka4          80 RNRVGLSMRMS   90 (94)
T ss_dssp             TTEEEEESCTT
T ss_pred             CCEEEEEEecc
Confidence            99999999964

>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=99.56  E-value=1.6e-15  Score=126.19  Aligned_cols=80  Identities=29%  Similarity=0.392  Sum_probs=73.8

Q ss_pred             HhhccccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCcc-cccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          259 QAQLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHD-RVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       259 ~~~l~~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~-~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      .+++++|++|.|+|++|.+||+||+|+  +++||||++++++. +..+|.+.|++||.|+|+|+++|+++++|.||+|+.
T Consensus        16 ~~~l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~k~~   95 (119)
T d1wi5a_          16 AEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHS   95 (119)
T ss_dssp             TTTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCC
T ss_pred             HhhcCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEEecHH
Confidence            367999999999999999999999995  79999999999987 478899999999999999999999999999999987


Q ss_pred             CCC
Q 015066          336 EPT  338 (414)
Q Consensus       336 ~~~  338 (414)
                      ...
T Consensus        96 ~~~   98 (119)
T d1wi5a_          96 EVS   98 (119)
T ss_dssp             CSC
T ss_pred             Hhh
Confidence            643

>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=99.56  E-value=2.1e-15  Score=118.54  Aligned_cols=73  Identities=29%  Similarity=0.355  Sum_probs=66.8

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccccc---CcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVA---DIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~---~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      +++|++|.|+|+++.+||+||+++ +++||+|++++++.++.   ++.+.|++||.|.|+|+++|+ .+++.||+|+.
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 PKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDR-SIDPVLSVKGK   81 (87)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEET-TEEEEEECCST
T ss_pred             CCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECC-CCCEEEEEecC
Confidence            678999999999999999999998 79999999999998654   577789999999999999996 57999999975

>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=99.53  E-value=5.5e-15  Score=113.10  Aligned_cols=75  Identities=16%  Similarity=0.241  Sum_probs=70.4

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~  172 (414)
                      ++++|++++|+|.++.++|+||+++++.+||+|.+|+++.+..++++. |++|++++|+|+++|+ ++++.||+|++
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 EIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDY-LQMGQEVPVKVLEVDR-QGRIRLSIKEA   76 (76)
T ss_dssp             CCCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCSCHHHH-CCTTCEEEEEEEECCT-TCCCEEEECCC
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccCCHHHc-cCCCCEEEEEEEEECC-CCCEEEEEEcC
Confidence            689999999999999999999999988999999999999999999988 9999999999999985 57899999863

>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=99.53  E-value=4e-15  Score=117.14  Aligned_cols=73  Identities=26%  Similarity=0.377  Sum_probs=66.7

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCccccc----CcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVA----DIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~----~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      +++|++|.|+|+++++||+||+|+ +.+||+|.+++++.+..    ++++.|++||.|+|+|+++|+ .+++.||+|+.
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 PQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDK-TRSPLLTVQGE   82 (88)
T ss_dssp             CCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECT-TSCEEEECCSS
T ss_pred             CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECC-CCCEEEEEecC
Confidence            578999999999999999999998 79999999999988654    677889999999999999996 47899999964

>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=99.50  E-value=4.2e-14  Score=110.66  Aligned_cols=73  Identities=22%  Similarity=0.228  Sum_probs=58.0

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066           98 ELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G~~Vdig--~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~  171 (414)
                      ++|++|+|+|+++.++|+||++.  ++.+||||.+|+++.+..++.+. +.+|+.++|+|+++|++++++.||+|+
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 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKL-IRIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC-------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEE-eecccEEEEEEEEEECCCCEEEEEeeC
Confidence            68999999999999999999996  46999999999999999998887 999999999999999999999999984

>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=99.45  E-value=7.8e-14  Score=108.57  Aligned_cols=75  Identities=19%  Similarity=0.217  Sum_probs=65.1

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig--~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~  171 (414)
                      ..++|++++|+|.+++++|+||+++  ++.+||||.+|+++.+..++.+. |++|+.++|+|+++|++++++.||+|+
T Consensus         8 ~p~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~-~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2           8 LPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDV-LKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             SCCTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----CHHHH-TCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccccceE-eecccEEEEEEEEEECCCCEEEEEEcC
Confidence            3468999999999999999999997  36899999999999988888888 999999999999999999999999984

>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=99.43  E-value=1.3e-15  Score=111.97  Aligned_cols=56  Identities=38%  Similarity=0.639  Sum_probs=36.0

Q ss_pred             EEEEEEeeceEEEEEC-CEEEEEeecccCc----ccccCcccccCCCCEEEEEEEEEeCCC
Q 015066          270 GTVQSLKPYGAFIDIG-GINGLLHVSQISH----DRVADIATVLQPGDTLKVMILSHDRER  325 (414)
Q Consensus       270 g~V~~i~~~G~fV~l~-gv~Glvh~sels~----~~~~~~~~~~~~G~~V~vkVl~id~e~  325 (414)
                      |+|++|.+|||||+|. |++||||+|+|++    .++.+|++.|++||+|+|+|+++|+++
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCSSC
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCCC
Confidence            7899999999999998 8999999999985    478899999999999999999999754

>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=99.36  E-value=1.5e-13  Score=114.05  Aligned_cols=87  Identities=22%  Similarity=0.195  Sum_probs=75.9

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC-CCeeEEEcCccccccc-cCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEACIHK-IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig-~k~~g~lp~sEls~~~-~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~  173 (414)
                      ++++|++|+|+|.++.++|+||+|+ .+.+||||.+|+++.+ ..++.+. |++||.++|+|+++|+.++++.||+|+..
T Consensus        18 ~l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~-~~vGq~v~~~V~~vd~~~~~i~LS~k~~~   96 (119)
T d1wi5a_          18 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAK-LKVGQYLNCIVEKVKGNGGVVSLSVGHSE   96 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCC-CCTTCEEEEEEEECCTTSCEEEEECCCCC
T ss_pred             hcCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhccccccCCHHHh-cccceEEEEEEEEEeCCCCEEEEEecHHH
Confidence            7899999999999999999999996 6789999999999764 5566665 89999999999999999999999999987


Q ss_pred             hhHHHHHhhh
Q 015066          174 YELAWERCRQ  183 (414)
Q Consensus       174 ~~~~~~~l~~  183 (414)
                      ....|....+
T Consensus        97 ~~~~~~~~~~  106 (119)
T d1wi5a_          97 VSTAIATEQQ  106 (119)
T ss_dssp             SCCCCCCSSC
T ss_pred             hhhhhhhhhh
Confidence            7666654433

>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=99.35  E-value=1.9e-12  Score=100.28  Aligned_cols=76  Identities=21%  Similarity=0.193  Sum_probs=67.1

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccc-cCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeehh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK-IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~-~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~~  173 (414)
                      ..++|++|.|+|.++.++|+||+|++...||||.+|+++.. ..++.+. |.+|+.+.|+|+++|+ ++++.||+|...
T Consensus         2 ~Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~-~~vGd~V~~kV~~vd~-~~~i~LS~k~~~   78 (83)
T d2ba0a1           2 TPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEV-LDIGDAIIAKVLNIDP-KMKVTLTMKDRI   78 (83)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGT-CCTTCEEEEEEEEECT-TCCEEEECCSSS
T ss_pred             cCCCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccccccccChhhh-cccccEEEEEEEEECC-CCCEEEEecCCC
Confidence            46899999999999999999999999999999999998754 4566666 8999999999999984 678999998743

>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=99.33  E-value=2.6e-13  Score=108.05  Aligned_cols=73  Identities=21%  Similarity=0.326  Sum_probs=63.6

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcc----------cccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHD----------RVADIATVLQPGDTLKVMILSHDRERGRVSL  330 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~----------~~~~~~~~~~~G~~V~vkVl~id~e~~ri~L  330 (414)
                      +++|++|.|+|+++.++|+||+|+ +.+|++|+|++++.          .+.++++.|++||.|.|+|+++|. .+++.|
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 GEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFS-DGAVSL   84 (95)
T ss_dssp             CCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEET-TTEEEE
T ss_pred             CCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECC-CCCEEE
Confidence            578999999999999999999998 79999999999753          334567789999999999999997 589999


Q ss_pred             EEeeC
Q 015066          331 STKKL  335 (414)
Q Consensus       331 S~K~~  335 (414)
                      |+|..
T Consensus        85 s~r~~   89 (95)
T d2nn6h1          85 HTRSL   89 (95)
T ss_dssp             ECCSS
T ss_pred             Eeccc
Confidence            99864

>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=99.23  E-value=1.2e-11  Score=96.52  Aligned_cols=76  Identities=24%  Similarity=0.179  Sum_probs=66.6

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC---CccccCccCCcEEEEEEEEEeCCCCeEEEEeee
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK---HVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~---~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~  171 (414)
                      |..++|++|.|+|+++.++|+||++++..+|+||.+++++.+..   ++.+. +.+||.+.|+|+++|+ ++++.||+|.
T Consensus         3 Y~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~-~~~Gd~v~~kV~~vd~-~~~i~LS~k~   80 (87)
T d2je6i1           3 YYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRY-LDVGDYVIARIENFDR-SIDPVLSVKG   80 (87)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSS-CCTTCEEEEEEEEEET-TEEEEEECCS
T ss_pred             ccCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceeccccccchh-hcccceEEEEEEEECC-CCCEEEEEec
Confidence            45789999999999999999999999999999999999986554   34445 8999999999999995 5899999986


Q ss_pred             h
Q 015066          172 I  172 (414)
Q Consensus       172 ~  172 (414)
                      .
T Consensus        81 ~   81 (87)
T d2je6i1          81 K   81 (87)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.23  E-value=9.7e-12  Score=97.30  Aligned_cols=76  Identities=16%  Similarity=0.144  Sum_probs=66.3

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccC----CccccCccCCcEEEEEEEEEeCCCCeEEEEee
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK----HVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~----~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k  170 (414)
                      |..++|++|.|+|+++.++|+||+|++..+||||.+|+++.+.+    ++.+. +.+||.+.|+|+++|+ ++++.||+|
T Consensus         3 Y~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~-~~vGd~V~~kV~~vd~-~~~i~Ls~k   80 (88)
T d2z0sa1           3 YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSL-LKVGDYIKAKVVAFDK-TRSPLLTVQ   80 (88)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTS-SCTTCEEEEEEEEECT-TSCEEEECC
T ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcccccccccchhhh-cccCcEEEEEEEEECC-CCCEEEEEe
Confidence            35789999999999999999999999999999999999887654    33444 8899999999999984 578999998


Q ss_pred             eh
Q 015066          171 MI  172 (414)
Q Consensus       171 ~~  172 (414)
                      ..
T Consensus        81 ~~   82 (88)
T d2z0sa1          81 GE   82 (88)
T ss_dssp             SS
T ss_pred             cC
Confidence            64

>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=99.22  E-value=1.7e-11  Score=95.65  Aligned_cols=67  Identities=13%  Similarity=0.113  Sum_probs=58.7

Q ss_pred             ccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCccccc------------CcccccCCCCEEEEEEEEEeCCCCeEE
Q 015066          264 IGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRVA------------DIATVLQPGDTLKVMILSHDRERGRVS  329 (414)
Q Consensus       264 ~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~~------------~~~~~~~~G~~V~vkVl~id~e~~ri~  329 (414)
                      .|+.++|+|++|++||+||+|.  +++||||+|+|.+++..            +....|+.||+|+|+|+++|+++++|.
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            4678999999999999999995  79999999999987532            234579999999999999999999986


Q ss_pred             E
Q 015066          330 L  330 (414)
Q Consensus       330 L  330 (414)
                      +
T Consensus        83 ~   83 (87)
T d2ix0a3          83 A   83 (87)
T ss_dssp             E
T ss_pred             E
Confidence            4

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.18  E-value=5.4e-11  Score=93.54  Aligned_cols=72  Identities=18%  Similarity=0.212  Sum_probs=62.3

Q ss_pred             ccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccc----------cCcccccCCCCEEEEEEEEEeCCCCeEEEEEe
Q 015066          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV----------ADIATVLQPGDTLKVMILSHDRERGRVSLSTK  333 (414)
Q Consensus       264 ~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~----------~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K  333 (414)
                      .|+++.|+|+++++||+||+++.++||+|+++|.+++.          .+....|+.||.|+|||+++|.+.++|.. +.
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~i~~-ig   81 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHA-IG   81 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTEEEE-EE
T ss_pred             CCCEEEEEEEEEEeeEEEEEEcCeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccCccEE-EE
Confidence            69999999999999999999999999999999987643          34566799999999999999999999865 33


Q ss_pred             eCC
Q 015066          334 KLE  336 (414)
Q Consensus       334 ~~~  336 (414)
                      .+.
T Consensus        82 ~~~   84 (91)
T d1y14b1          82 SIK   84 (91)
T ss_dssp             ECC
T ss_pred             Ecc
Confidence            433

>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=99.12  E-value=1e-10  Score=94.52  Aligned_cols=82  Identities=13%  Similarity=0.111  Sum_probs=65.7

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCcccccccc-----------CCccccCccCCcEEEEEEEEEeCCCCe--
Q 015066           98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI-----------KHVEEAGIVPGLKEEFVIIGENEADDS--  164 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~-----------~~~~e~~~~vG~~v~v~Vl~id~~~~~--  164 (414)
                      ++|+++.|+|+++.++|+||+++ +.+||+|.++|++.+.           .++.+. |.+|+.++++|+++|.+.++  
T Consensus         2 ~~gei~~g~V~~v~~~G~FVel~-~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~-~~~Gd~v~vkV~~vd~~~~~~~   79 (106)
T d1go3e1           2 EMYELIEGEVVDVVEFGSFVRLG-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKV-LEIGDYVRARIVAISLKAERKR   79 (106)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSCSSCEEECCC--CEEETTTCCE-ECTTCEEEEEEEEEECCC----
T ss_pred             CCCCEEEEEEEEEeeeEEEEEee-CeEEEEEeecccCceeeeccceeEEeecccccc-eeecceEEEEEEEEchhhcccc
Confidence            68999999999999999999997 4999999999997664           244455 89999999999999987765  


Q ss_pred             ---EEEEeeehhhhHHHHHhh
Q 015066          165 ---LVLSLRMIQYELAWERCR  182 (414)
Q Consensus       165 ---i~LS~k~~~~~~~~~~l~  182 (414)
                         +.||+|+... .+|+.+.
T Consensus        80 ~~~i~ls~K~~~~-~~~e~~~   99 (106)
T d1go3e1          80 GSKIALTMRQPYL-GKLEWIE   99 (106)
T ss_dssp             -CEEEEECCSTTC-EEHHHHH
T ss_pred             CceeecccccCCC-Ccchhhh
Confidence               6788887654 3454443

>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=99.05  E-value=2.7e-10  Score=89.99  Aligned_cols=67  Identities=21%  Similarity=0.366  Sum_probs=59.8

Q ss_pred             ccEEEEEEEEEEeeceEEEEECCEEEEEeecccCccc-c-----------cCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDR-V-----------ADIATVLQPGDTLKVMILSHDRERGRVSL  330 (414)
Q Consensus       264 ~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~-~-----------~~~~~~~~~G~~V~vkVl~id~e~~ri~L  330 (414)
                      .|++++|+|++++++|+||+++.++|++|+++|.++. +           .+....|+.||.|++||++++.+.++|..
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~I~~   82 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFA   82 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEecCceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCcceE
Confidence            5999999999999999999999899999999998874 2           33455799999999999999999999874

>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=98.91  E-value=5e-10  Score=88.61  Aligned_cols=76  Identities=13%  Similarity=0.105  Sum_probs=63.1

Q ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccc----------cCCccccCccCCcEEEEEEEEEeCCCCe
Q 015066           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK----------IKHVEEAGIVPGLKEEFVIIGENEADDS  164 (414)
Q Consensus        95 ~~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~----------~~~~~e~~~~vG~~v~v~Vl~id~~~~~  164 (414)
                      |..++|++|.|+|+++..+|+||+|+...+|+||.+++++..          ..++.+. +++||.+.|+|++++. +++
T Consensus         4 Y~P~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~-~~~Gd~V~~kV~~v~~-dg~   81 (95)
T d2nn6h1           4 YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGF-LQEGDLISAEVQAVFS-DGA   81 (95)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHH-SCSSCEECCEEEEEET-TTE
T ss_pred             ccCCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchhhhhhhhh-cccccEEEEEEEEECC-CCC
Confidence            357899999999999999999999998899999999996532          1223344 8999999999999985 689


Q ss_pred             EEEEeeeh
Q 015066          165 LVLSLRMI  172 (414)
Q Consensus       165 i~LS~k~~  172 (414)
                      +.||+|..
T Consensus        82 i~Ls~r~~   89 (95)
T d2nn6h1          82 VSLHTRSL   89 (95)
T ss_dssp             EEEECCSS
T ss_pred             EEEEeccc
Confidence            99999864

>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=98.83  E-value=2.9e-09  Score=82.81  Aligned_cols=73  Identities=15%  Similarity=0.054  Sum_probs=65.9

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      +++||+|-|+|+++..+|.||+++ ...|++|++++. .+..+....|++||.|.|+|.++|+ .+++.||..+..
T Consensus         4 P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~-g~~k~~r~~l~~GD~V~arV~~v~~-~~~~~Lscvd~~   77 (88)
T d2nn6g1           4 PVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFE-GATKRNRPNVQVGDLIYGQFVVANK-DMEPEMVCIDSC   77 (88)
T ss_dssp             CCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEEEECCT-TSCCEEECSBTT
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcC-ccccccCcccCCCCEEEEEEEEeCC-CCCEEEEEEccc
Confidence            678999999999999999999999 799999999995 4677888999999999999999996 689999987653

>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=98.74  E-value=1.6e-10  Score=84.24  Aligned_cols=57  Identities=21%  Similarity=0.271  Sum_probs=35.6

Q ss_pred             EEEEEEeCCeEEEEeCCCeeEEEcCcccccc----ccCCccccCccCCcEEEEEEEEEeCCC
Q 015066          105 GTVFCTDNRGALVDITAKSSAYLPTQEACIH----KIKHVEEAGIVPGLKEEFVIIGENEAD  162 (414)
Q Consensus       105 G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~----~~~~~~e~~~~vG~~v~v~Vl~id~~~  162 (414)
                      |+|.++.++|+||+++.+.+||||.+|+++.    +..++++. +++||+++|+|+++|+++
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~~~~~~v~~~~~~-~~~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDV-LGVGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC--------------------CCSSCBCCCCCCCCCSSC
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHcccccccccccCHHHh-cCCCCEEEEEEEEEcCCC
Confidence            7899999999999999999999999999853    56678887 999999999999999653

>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=98.64  E-value=6.5e-08  Score=75.40  Aligned_cols=63  Identities=22%  Similarity=0.261  Sum_probs=53.2

Q ss_pred             CCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCCc--c----------c-c-ccCCeEEEEEEEeecccceEEe
Q 015066          187 EDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKST--A----------E-E-LLGKDLPLKFVEVDEEQSRLVL  249 (414)
Q Consensus       187 ~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~~--~----------~-~-~vGq~V~vkVl~vD~e~~ri~L  249 (414)
                      .|+++.|+|++++++|+||+++.++||+|.+++.+.+.  .          . . .+|+.|++||+.+|.+++++..
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~i~~   79 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHA   79 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETTEEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEEcCeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccCccEE
Confidence            36899999999999999999999999999999986521  1          1 1 1699999999999999888743

>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=98.61  E-value=1.1e-07  Score=70.81  Aligned_cols=66  Identities=23%  Similarity=0.162  Sum_probs=55.8

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCC--eEEEEe
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD--SLVLSL  169 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~--~i~LS~  169 (414)
                      .-+.|++|+|+|.++++++++|++| +.+|+||.+|..      +.+. |.+|+.++|.|.+++...+  ++.||+
T Consensus         5 ~~~~geiv~G~V~r~~~~~~~Vdlg-~~eaiLp~~eqi------p~E~-~~~Gdrik~~i~~V~~~~kgpqI~lSR   72 (72)
T d1hh2p1           5 SELKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKEWI------PGEE-IKAGDLVKVYIIDVVKTTKGPKILVSR   72 (72)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGSC------TTCC-CCTTCEEEEEEEEEEEETTEEEEEEES
T ss_pred             hhccCcEEEEEEEEEcCCCEEEEEC-CcEEECCHHHcC------CCCC-CCCCCEEEEEEEEEEEcCCCCeEEEeC
Confidence            4579999999999999999999998 599999999874      3444 8999999999999875544  577774

>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=98.60  E-value=6.7e-08  Score=74.73  Aligned_cols=62  Identities=18%  Similarity=0.341  Sum_probs=52.8

Q ss_pred             CeEEEEEEEEEecCcEEEEEC--CEEEEEeccccCCCC---c-----------ccc--ccCCeEEEEEEEeecccceEEe
Q 015066          188 DVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKS---T-----------AEE--LLGKDLPLKFVEVDEEQSRLVL  249 (414)
Q Consensus       188 g~iv~G~V~~v~~~G~~V~i~--gi~GfIp~sels~~~---~-----------~~~--~vGq~V~vkVl~vD~e~~ri~L  249 (414)
                      ++.++|+|++++++|+||++.  +++||||.|+|.+..   +           .+.  .+||+|+|+|+++|+++++|..
T Consensus         4 ~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~~r~I~~   83 (87)
T d2ix0a3           4 DTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETRSIIA   83 (87)
T ss_dssp             CCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTTEEEE
T ss_pred             CCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecccCeEEE
Confidence            568999999999999999994  899999999998752   1           111  2799999999999999999865

>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=98.58  E-value=3.8e-08  Score=76.66  Aligned_cols=73  Identities=10%  Similarity=0.034  Sum_probs=66.0

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKL  335 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~  335 (414)
                      +++||+|-|+|+++..+|.||+|+ ...|++|.++.......+....|++||.|.|+|.++|+ .+.+.||+++.
T Consensus         5 P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~-~~~~~Lsc~~~   78 (90)
T d2ja9a1           5 PSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEK-ELEAEIECFDS   78 (90)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCT-TSCCEEESSCT
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCccccccCCccCCCCEEEEEEEEECC-CCCEEEEEecc
Confidence            578999999999999999999999 58999999988888888889999999999999999996 67899998654

>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=98.49  E-value=4.2e-07  Score=67.48  Aligned_cols=63  Identities=22%  Similarity=0.209  Sum_probs=55.2

Q ss_pred             cccEEEEEEEEEEeeceEEEEECCEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCC--eEEEE
Q 015066          263 GIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERG--RVSLS  331 (414)
Q Consensus       263 ~~G~iv~g~V~~i~~~G~fV~l~gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~--ri~LS  331 (414)
                      ++|++++|+|.++.+.+++|++++.+|++|.++..      |.+.|++||.|+|.|.+++.+.+  +|.||
T Consensus         7 ~~geiv~G~V~r~~~~~~~Vdlg~~eaiLp~~eqi------p~E~~~~Gdrik~~i~~V~~~~kgpqI~lS   71 (72)
T d1hh2p1           7 LKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWI------PGEEIKAGDLVKVYIIDVVKTTKGPKILVS   71 (72)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTEEEEEEGGGSC------TTCCCCTTCEEEEEEEEEEEETTEEEEEEE
T ss_pred             ccCcEEEEEEEEEcCCCEEEEECCcEEECCHHHcC------CCCCCCCCCEEEEEEEEEEEcCCCCeEEEe
Confidence            57999999999999999999999999999999863      57789999999999999986654  45555

>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=98.48  E-value=1.7e-07  Score=72.56  Aligned_cols=74  Identities=16%  Similarity=-0.034  Sum_probs=63.9

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~  172 (414)
                      ..++||+|-|+|+++..++++|||+....|+||.+++. ...++..+. +.+|+.+.|+|.+++ .++.+.||+...
T Consensus         3 ~P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~-g~~k~~r~~-l~~GD~V~arV~~v~-~~~~~~Lscvd~   76 (88)
T d2nn6g1           3 VPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFE-GATKRNRPN-VQVGDLIYGQFVVAN-KDMEPEMVCIDS   76 (88)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSS-CCSSCSSSS-SCTTCEEEEEEEECC-TTSCCEEECSBT
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcC-ccccccCcc-cCCCCEEEEEEEEeC-CCCCEEEEEEcc
Confidence            56899999999999999999999999999999999985 344555555 899999999999997 567899988654

>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=98.47  E-value=4e-07  Score=71.27  Aligned_cols=62  Identities=21%  Similarity=0.311  Sum_probs=52.6

Q ss_pred             CCeEEEEEEEEEecCcEEEEECCEEEEEeccccCCCC----ccc----------c--ccCCeEEEEEEEeecccceEE
Q 015066          187 EDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS----TAE----------E--LLGKDLPLKFVEVDEEQSRLV  248 (414)
Q Consensus       187 ~g~iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~----~~~----------~--~vGq~V~vkVl~vD~e~~ri~  248 (414)
                      .|++++|+|++++++|+||+++.++||+|.+++.+..    +.+          .  .+|+.|++||+.+|.+.+++.
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~I~   81 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIF   81 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEecCceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCcce
Confidence            3689999999999999999999999999999999652    111          1  169999999999999888864

>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=98.37  E-value=6.1e-07  Score=73.91  Aligned_cols=74  Identities=19%  Similarity=0.282  Sum_probs=63.6

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC---------CEEEEEeecccCcc--cccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG---------GINGLLHVSQISHD--RVADIATVLQPGDTLKVMILSHDRERGRVSL  330 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~---------gv~Glvh~sels~~--~~~~~~~~~~~G~~V~vkVl~id~e~~ri~L  330 (414)
                      +++|++|.|+|+++.+..++|++.         .+.|++|.+++...  ...++.+.|++||.|+|+|+++...+..+.|
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            578999999999999999999983         37899999998543  4457889999999999999999876667999


Q ss_pred             EEeeC
Q 015066          331 STKKL  335 (414)
Q Consensus       331 S~K~~  335 (414)
                      |++.-
T Consensus        85 st~~~   89 (125)
T d2nn6i1          85 TTAEN   89 (125)
T ss_dssp             ECCSS
T ss_pred             EecCC
Confidence            98863

>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=98.29  E-value=9.6e-07  Score=68.46  Aligned_cols=75  Identities=12%  Similarity=-0.067  Sum_probs=63.9

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~  172 (414)
                      ..++||+|-|+|+++..++++|||++...|++|.++......++.... +.+|+.|-|+|.+++ .++.+.||++..
T Consensus         4 ~P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g~~k~~r~~-l~~GDlV~arV~~v~-~~~~~~Lsc~~~   78 (90)
T d2ja9a1           4 IPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPT-LQVGDLVYARVCTAE-KELEAEIECFDS   78 (90)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSSSCCC-CCTTCEEEEEEEECC-TTSCCEEESSCT
T ss_pred             cCCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCccccccCCc-cCCCCEEEEEEEEEC-CCCCEEEEEecc
Confidence            568999999999999999999999988999999777666655655555 899999999999998 567899998654

>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.26  E-value=1.1e-06  Score=65.93  Aligned_cols=65  Identities=20%  Similarity=0.260  Sum_probs=53.2

Q ss_pred             CCCCEEEEEEEEEeCCe----EEEEeC---CCeeEEEcCccccccccCCccccCccCCcEEEEEEEEEeCCCC--eEEEE
Q 015066           98 ELGTKVKGTVFCTDNRG----ALVDIT---AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD--SLVLS  168 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G----~~Vdig---~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~--~i~LS  168 (414)
                      +.|++|+|+|.+++...    ++|++|   ++.+|+||.+|.-      +.+. |.+|+.++|.|.+++...+  ++.||
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------PGES-YEHGNRLRCYVVGVTRGAREPLITLS   75 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC------TTCC-CCTTCEEEEEEEEEECCSSSCEEEEE
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcC------CCcc-cCCCCEEEEEEEEEEecCCCCEEEEe
Confidence            68999999999998643    899998   4699999999874      3444 8999999999999986543  67777


Q ss_pred             e
Q 015066          169 L  169 (414)
Q Consensus       169 ~  169 (414)
                      +
T Consensus        76 R   76 (76)
T d2asba1          76 R   76 (76)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=97.97  E-value=1.3e-05  Score=59.83  Aligned_cols=63  Identities=19%  Similarity=0.307  Sum_probs=51.7

Q ss_pred             cccEEEEEEEEEEeec----eEEEEEC----CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCC--eEEEE
Q 015066          263 GIGSVVIGTVQSLKPY----GAFIDIG----GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERG--RVSLS  331 (414)
Q Consensus       263 ~~G~iv~g~V~~i~~~----G~fV~l~----gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~--ri~LS  331 (414)
                      ++|++++|+|.++...    -++|+|+    +++|+++.+|.      -|.+.|+.||.|+|.|.+++...+  +|.||
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eq------ip~E~y~~Gdrik~~i~~V~~~~kGp~IilS   75 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQ------VPGESYEHGNRLRCYVVGVTRGAREPLITLS   75 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGS------CTTCCCCTTCEEEEEEEEEECCSSSCEEEEE
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHc------CCCcccCCCCEEEEEEEEEEecCCCCEEEEe
Confidence            5799999999998753    2799996    59999999885      456789999999999999987644  45555

>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=97.75  E-value=5.5e-05  Score=61.82  Aligned_cols=76  Identities=16%  Similarity=0.129  Sum_probs=60.6

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeC--------CCeeEEEcCccccc--cccCCccccCccCCcEEEEEEEEEeCCCCeE
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDIT--------AKSSAYLPTQEACI--HKIKHVEEAGIVPGLKEEFVIIGENEADDSL  165 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig--------~k~~g~lp~sEls~--~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i  165 (414)
                      -.++|++|.|+|+++....++|+|.        ....|+++.++...  ....+..+. |.+||.|.++|+++.+....+
T Consensus         4 vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~-fr~GDiV~A~Vis~~~~~~~~   82 (125)
T d2nn6i1           4 LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKS-FRPGDIVLAKVISLGDAQSNY   82 (125)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGT-CCSSSEEEEEEEEEETTTTEE
T ss_pred             CCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHh-cCCCCEEEEEEEEccCCCccE
Confidence            4579999999999999999999992        24568898887742  223345565 899999999999998766679


Q ss_pred             EEEeeeh
Q 015066          166 VLSLRMI  172 (414)
Q Consensus       166 ~LS~k~~  172 (414)
                      .||.+..
T Consensus        83 ~Lst~~~   89 (125)
T d2nn6i1          83 LLTTAEN   89 (125)
T ss_dssp             EEECCSS
T ss_pred             EEEecCC
Confidence            9998753

>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=97.47  E-value=0.0001  Score=56.25  Aligned_cols=66  Identities=26%  Similarity=0.499  Sum_probs=52.0

Q ss_pred             EEEEEEEEEEee--ceEEEEEC-CEEEEEeecccCcccc---------cCcccccCCCCEEEEEEEEEeCCCCeEEEE
Q 015066          266 SVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISHDRV---------ADIATVLQPGDTLKVMILSHDRERGRVSLS  331 (414)
Q Consensus       266 ~iv~g~V~~i~~--~G~fV~l~-gv~Glvh~sels~~~~---------~~~~~~~~~G~~V~vkVl~id~e~~ri~LS  331 (414)
                      +||.|+|++|.+  .++||+++ +-.|++|.+++.....         .+..+.++.||.|-|.|.+=-...+--.||
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~KGprlT   79 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALT   79 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTTBCCEEE
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecccCCCCceEE
Confidence            589999999998  59999999 8999999999876532         245778999999999999754334434444

>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=97.43  E-value=0.00019  Score=54.64  Aligned_cols=69  Identities=19%  Similarity=0.268  Sum_probs=54.1

Q ss_pred             CEEEEEEEEEeC--CeEEEEeCCCeeEEEcCccccccccC---------CccccCccCCcEEEEEEEEEeCCCCeEEEEe
Q 015066          101 TKVKGTVFCTDN--RGALVDITAKSSAYLPTQEACIHKIK---------HVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (414)
Q Consensus       101 ~iV~G~V~~v~~--~G~~Vdig~k~~g~lp~sEls~~~~~---------~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~  169 (414)
                      .|+.|+|.++.+  +++|||+|....||||.+++...+..         +.++. +++|+.+-+.|.......+-..||.
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~-l~~G~~ilVQV~Ke~~~~KGprlT~   80 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDV-LREGQEVIVQIDKEERGNKGAALTT   80 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGT-CCTTCEEEEEEEECCBTTBCCEEES
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccceeeeccccccccccchhhh-ccCCCeEEEEEeecccCCCCceEEE
Confidence            478999999999  79999999999999999998654322         22333 7899999999998665556677765


Q ss_pred             e
Q 015066          170 R  170 (414)
Q Consensus       170 k  170 (414)
                      .
T Consensus        81 ~   81 (87)
T d1smxa_          81 F   81 (87)
T ss_dssp             C
T ss_pred             E
Confidence            4

>d1luza_ b.40.4.5 (A:) Viral structural mimic of eIF2alpha {Vaccinia virus [TaxId: 10245]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Viral structural mimic of eIF2alpha
species: Vaccinia virus [TaxId: 10245]

Probab=95.11  E-value=0.034  Score=40.59  Aligned_cols=73  Identities=26%  Similarity=0.405  Sum_probs=56.6

Q ss_pred             ccccEEEEEEEEEEeeceEEEEEC---CEEEEEeec-ccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          262 LGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVS-QISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       262 l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~s-els~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      +.+|++.+|.|. ++++-++|.|.   |.++++--+ ++..++..+.++.+ +|-+|+++|+.+|.-++-|.+..|...
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 45777789985   688887543 34445555665554 799999999999999999999998753

>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=93.07  E-value=0.087  Score=39.27  Aligned_cols=67  Identities=24%  Similarity=0.206  Sum_probs=49.5

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC---CEEEEEee-cccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEE
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG---GINGLLHV-SQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSL  330 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~---gv~Glvh~-sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~L  330 (414)
                      -++.+|++.+|.|. +.++-++|.|.   |.++++-- -++..++..+..+.+ +|-+|+|+|+.+|  +..|.+
T Consensus        28 ~~~~~G~V~kGiVy-~rd~~fyV~L~dY~g~eail~dY~n~~~dr~~klkkkL-VGKTIkVqVIRvD--klYIDV   98 (102)
T d1jjga_          28 MDLSPGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKERL-VGRVIKTRVVRAD--GLYVDL   98 (102)
T ss_dssp             CCCCSSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHHH-TTCEEEEEEEEEC--SSEEEE
T ss_pred             cccCCCcEeeeEEE-EeCCEEEEEecCCCCceeeeeehhhhhHHHHHHHHHHh-cCceEEEEEEEec--cEEEEE
Confidence            46889999999886 55777789885   67888533 345556666666554 7999999999999  445543

>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=92.74  E-value=0.21  Score=35.25  Aligned_cols=49  Identities=20%  Similarity=0.203  Sum_probs=40.4

Q ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEcCccccccccCCccccCccCCcEEEEEEEEE
Q 015066           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE  158 (414)
Q Consensus        96 ~l~~G~iV~G~V~~v~~~G~~Vdig~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~i  158 (414)
                      ..++|++=+|.+++..+.|+|||||...-+++--              .+.+|+.+.|+|+++
T Consensus         7 ~p~vGEiReG~~~rr~~~g~~vDiGlD~la~~k~--------------~~~~~~r~tfrIvs~   55 (71)
T d1k3ra1           7 KPVTGEYRQGLTVKRVKKGTLVDIGADKLALCRE--------------KLTVNRIMSFRVVRL   55 (71)
T ss_dssp             SCCTTCEEEEEEEEECSSSEEEESSSSCEEECSS--------------CCCSSCEEEEEEEEC
T ss_pred             CCcccceeeEEEEEecCCcEEEEecCCceeeeec--------------ccccCcEEEEEEEEc
Confidence            4689999999999999999999999755444322              167899999999996

>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=89.74  E-value=3  Score=31.16  Aligned_cols=104  Identities=21%  Similarity=0.268  Sum_probs=63.9

Q ss_pred             EEEEEEEEEecCcEEEEECCEEEEEeccccCCCCccccccCCeEEEEEEEeecccceEEeehhhhhhhHHhhccccEEEE
Q 015066          190 VVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVI  269 (414)
Q Consensus       190 iv~G~V~~v~~~G~~V~i~gi~GfIp~sels~~~~~~~~vGq~V~vkVl~vD~e~~ri~LS~K~~l~~~~~~l~~G~iv~  269 (414)
                      ++.|+|.+...+.+.+.+++....+|.. +        ..|+.+.+   .+-++  .+.++....      .......+.
T Consensus         4 ~l~g~v~~~~~~~~~v~~~~~~l~~~~~-~--------~~g~~v~~---~iRPE--~i~l~~~~~------~~~~~N~l~   63 (119)
T d3d31a1           4 VLKGRVISAEQGLLRIRVGEVVIDAAGD-M--------EVGDQVYA---FLRPE--NIALSKSST------QSSIRNSLQ   63 (119)
T ss_dssp             EEEEEEEEEETTEEEEEETTEEEEEESS-C--------CTTCEEEE---EECGG--GEEEESSCC------CBSCSEEEE
T ss_pred             EEEEEEEEecCCEEEEEECCEEEECCCC-C--------CCCCEEEE---EEchH--Hcccccccc------ccccceEEE
Confidence            7899999999988999999887766531 1        15887754   45544  344543211      112235799


Q ss_pred             EEEEEEeeceEEEEEC---CEEEEEeecccCcccccCcccccCCCCEEEEEE
Q 015066          270 GTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVMI  318 (414)
Q Consensus       270 g~V~~i~~~G~fV~l~---gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkV  318 (414)
                      |+|..+...|..+.+.   |-.-.+.++.-+..     ...+++||.|.+.+
T Consensus        64 g~V~~~~~~G~~~~v~l~~g~~~~~~v~~~~~~-----~~~l~~G~~V~v~~  110 (119)
T d3d31a1          64 GRVTEAWVLGALVRVKVDCGVPLNVLITRRSAE-----EMELSPGVQIYARF  110 (119)
T ss_dssp             EEEEEEEECSSEEEEEEESSSEEEEEEETTHHH-----HSCCCTTCEEEEEE
T ss_pred             EEEEEEEECCCeEEEEEEeCCEEEEEEecCchh-----hcCcCCCCEEEEEE
Confidence            9999999988776653   32211122111111     22478999998754

>d1k3ra1 b.40.4.10 (A:93-163) Hypothetical protein MTH1 (MT0001), insert domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Hypothetical protein MTH1 (MT0001), insert domain
domain: Hypothetical protein MTH1 (MT0001), insert domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=88.38  E-value=0.46  Score=33.42  Aligned_cols=49  Identities=16%  Similarity=0.165  Sum_probs=40.4

Q ss_pred             hhccccEEEEEEEEEEeeceEEEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEE
Q 015066          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSH  321 (414)
Q Consensus       260 ~~l~~G~iv~g~V~~i~~~G~fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~i  321 (414)
                      ..+++|++=.|.+.+-...|+||+++ +--++|             ...|.+|+.+.++|.++
T Consensus         6 g~p~vGEiReG~~~rr~~~g~~vDiGlD~la~~-------------k~~~~~~~r~tfrIvs~   55 (71)
T d1k3ra1           6 GKPVTGEYRQGLTVKRVKKGTLVDIGADKLALC-------------REKLTVNRIMSFRVVRL   55 (71)
T ss_dssp             SSCCTTCEEEEEEEEECSSSEEEESSSSCEEEC-------------SSCCCSSCEEEEEEEEC
T ss_pred             CCCcccceeeEEEEEecCCcEEEEecCCceeee-------------ecccccCcEEEEEEEEc
Confidence            35789999999999999999999986 544443             22578999999999998

>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=85.10  E-value=3.3  Score=28.45  Aligned_cols=50  Identities=22%  Similarity=0.435  Sum_probs=35.8

Q ss_pred             EEEEEEEee-ceE-EEEEC-CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEe
Q 015066          269 IGTVQSLKP-YGA-FIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHD  322 (414)
Q Consensus       269 ~g~V~~i~~-~G~-fV~l~-gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id  322 (414)
                      +|+|+-..+ .|. ||... |-+-++|+|.+.....    ..+..||.|.+.+..-+
T Consensus         3 ~G~Vk~fn~~kGfGFI~~d~g~DiF~H~s~l~~~~~----~~L~~G~~V~f~~~~~~   55 (66)
T d1c9oa_           3 RGKVKWFNNEKGYGFIEVEGGSDVFVHFTAIQGEGF----KTLEEGQEVSFEIVQGN   55 (66)
T ss_dssp             EEEEEEEETTTTEEEEEETTEEEEEEEGGGBCSSSC----CCCCTTCEEEEEEEEET
T ss_pred             CeEEEEEECCCCEEEEEecCCceEEEEehhcccccC----CcCCCCCEEEEEEEECC
Confidence            688988753 333 46666 6899999999965422    35789999999876543

>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=84.78  E-value=2.7  Score=30.05  Aligned_cols=56  Identities=20%  Similarity=0.326  Sum_probs=39.7

Q ss_pred             EEEEEEEEEEee-ceE-EEEEC--CEEEEEeecccCcccccCcccccCCCCEEEEEEEEE
Q 015066          266 SVVIGTVQSLKP-YGA-FIDIG--GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSH  321 (414)
Q Consensus       266 ~iv~g~V~~i~~-~G~-fV~l~--gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~i  321 (414)
                      ..+.|+|+-..+ .|. ||.-.  +-+-++|.|.|...-....-..+..||.|...+..-
T Consensus         7 ~r~~G~VKwfn~~KGfGFI~~ddg~~DvFvH~s~i~~~g~~~~~~~L~~G~~V~f~~~~~   66 (79)
T d1h95a_           7 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEG   66 (79)
T ss_dssp             EEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCSCCSSCEEEEEEEEC
T ss_pred             CcccEEEEEEcCCCCeEEEEECCCCccEEEEhhHcccCCCcceeeecCCCCEEEEEEEeC
Confidence            568899998763 444 56654  588999999996643222334578999999987753

>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=84.65  E-value=2.4  Score=29.46  Aligned_cols=51  Identities=16%  Similarity=0.144  Sum_probs=35.2

Q ss_pred             EEEEEEEEEeC--CeEEEEe-CCCeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066          102 KVKGTVFCTDN--RGALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG  157 (414)
Q Consensus       102 iV~G~V~~v~~--~G~~Vdi-g~k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~  157 (414)
                      .++|+|...+.  +.=|+.- ++..+.|+|.+.+.....+.     +.+|+.|++.+..
T Consensus         3 r~~G~Vk~f~~~kGfGFI~~d~g~~diFvH~s~l~~~~~~~-----L~~G~~V~f~~~~   56 (69)
T d1mjca_           3 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKS-----LDEGQKVSFTIES   56 (69)
T ss_dssp             CEEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCCTTTCC-----CCTTCEEEEEEEC
T ss_pred             CEEEEEEEEeCCCCEEEEEEcCCCccEEEEhHHhcccCCCc-----CCCCCEEEEEEEe
Confidence            47999999865  2234444 44478999999986432222     5789999998754

>d1ah9a_ b.40.4.5 (A:) Translational initiation factor 1, IF1 {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Translational initiation factor 1, IF1
species: Escherichia coli [TaxId: 562]

Probab=83.93  E-value=0.45  Score=33.82  Aligned_cols=59  Identities=24%  Similarity=0.367  Sum_probs=45.1

Q ss_pred             EEEEEEEEEEeeceEE-EEEC-CEEEEEeecc-cCcccccCcccccCCCCEEEEEEEEEeCCCCeEE
Q 015066          266 SVVIGTVQSLKPYGAF-IDIG-GINGLLHVSQ-ISHDRVADIATVLQPGDTLKVMILSHDRERGRVS  329 (414)
Q Consensus       266 ~iv~g~V~~i~~~G~f-V~l~-gv~Glvh~se-ls~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~  329 (414)
                      ..+.|+|+...+.|.| |.+. |..-++|++- |...+     -.+.+||.|.+-+-..|.++++|.
T Consensus         6 ie~~G~V~e~lg~~~f~V~l~ng~~~~a~i~Gkmrk~r-----i~i~~GD~V~Vel~pyd~~kgrIi   67 (71)
T d1ah9a_           6 IEMQGTVLETLPNTMFRVELENGHVVTAHISGKMRKNY-----IRILTGDKVTVELTPYDLSKGRIV   67 (71)
T ss_dssp             EECCEEEEEECSSSEEEEEETTSCEEEEEECSSGGGTT-----CCCCTTCEECCEECSSCTTEEEEC
T ss_pred             EEEEEEEEEEcCCCEEEEEeCCCCEEEEEccchhheeE-----EEecCCCEEEEEECccCCCcEEEE
Confidence            4578999999998887 7887 7888888873 32222     247899999999888887777764

>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=82.03  E-value=2.5  Score=30.37  Aligned_cols=73  Identities=11%  Similarity=0.202  Sum_probs=50.5

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCC--CeeEEEcCc-cccccccCCccccCccCCcEEEEEEEEEeCCCCeEEEEeeeh
Q 015066           97 SELGTKVKGTVFCTDNRGALVDITA--KSSAYLPTQ-EACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (414)
Q Consensus        97 l~~G~iV~G~V~~v~~~G~~Vdig~--k~~g~lp~s-Els~~~~~~~~e~~~~vG~~v~v~Vl~id~~~~~i~LS~k~~  172 (414)
                      ..+|++.+|.|.- .++-++|.+.+  +.+|++-.. .+..+...+..+.  .+|..++++|+..|.-+|.+-++.++.
T Consensus         6 PnigdVtkGiVy~-kd~~fyV~L~dY~g~ea~l~dy~~~~~d~~~klk~k--LVGKtIkvqVIR~d~lKGYIDVr~~~~   81 (85)
T d1luza_           6 PNAGDVIKGRVYE-KDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDK--LVGKTVKVKVIRVDYTKGYIDVNYKRM   81 (85)
T ss_dssp             CCTTCEEEEEEEE-ETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHH--HTTCEEEEEEEEEETTTTEEEEEEEEE
T ss_pred             CCCCceeeeEEEE-eCCEEEEEecCCCCceEEeeehhhhhhHHHHHHHHH--hcCceEEEEEEEEcceeeEEEehhhhh
Confidence            3689999998764 44567788744  477776532 2222222233332  489999999999999999999988764

>d1wfqa_ b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Cold shock domain protein E1 (UNR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.72  E-value=6.3  Score=28.66  Aligned_cols=68  Identities=19%  Similarity=0.240  Sum_probs=48.6

Q ss_pred             ccEEEEEEEEEEeeceEEEEEC--CEEEEEeecccCcccccCcccccCCCCEEEEEEEEEeCCCCeEEEEEeeCC
Q 015066          264 IGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRVADIATVLQPGDTLKVMILSHDRERGRVSLSTKKLE  336 (414)
Q Consensus       264 ~G~iv~g~V~~i~~~G~fV~l~--gv~Glvh~sels~~~~~~~~~~~~~G~~V~vkVl~id~e~~ri~LS~K~~~  336 (414)
                      .+.-.+|+|...++--=||...  +-+-++|++++...     ...+++||.|...+..-++..+.....++.+.
T Consensus        15 ~~~r~~G~I~~~~~gfGFI~~~~~~~dvF~H~s~~~~~-----~~~l~~G~~VeF~v~~~~kg~k~~Av~V~~~~   84 (89)
T d1wfqa_          15 AALRETGVIEKLLTSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDRRTGKPIAVKLVKIS   84 (89)
T ss_dssp             CCCEEEEEEEEECSSEEEEEETTTTEEEEEETTTCSSC-----TTTCCTTCCEEEEEEECSSSCCEEEEEEEESS
T ss_pred             ccceEEEEEEEecCccceEEeCCCCceEEEEeehhhcc-----CCcccCCCEEEEEEEECCCCCceEEEEEEECC
Confidence            4566789999998633377765  47899999998532     34589999999987664433445666776664

>d2vnud2 b.40.4.5 (D:911-998) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome complex exonuclease RRP44
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=81.23  E-value=1.6  Score=32.18  Aligned_cols=54  Identities=19%  Similarity=0.260  Sum_probs=37.4

Q ss_pred             EEEEEEEEeeceEEEEEC--CEEEEEeecccCc-----cc------cc------CcccccCCCCEEEEEEEEE
Q 015066          268 VIGTVQSLKPYGAFIDIG--GINGLLHVSQISH-----DR------VA------DIATVLQPGDTLKVMILSH  321 (414)
Q Consensus       268 v~g~V~~i~~~G~fV~l~--gv~Glvh~sels~-----~~------~~------~~~~~~~~G~~V~vkVl~i  321 (414)
                      =+|.|.+|...|+.|-+.  |++|+|...+...     .+      ++      +-.-.|++=|.|+|+|-++
T Consensus         4 EegyV~~Vr~NGivVfVPkyGiEG~v~l~~~~~~~~~~~~De~~~~l~~~~~~~~~~~~~~vFD~V~V~is~v   76 (88)
T d2vnud2           4 ETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSV   76 (88)
T ss_dssp             EEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC--
T ss_pred             eEEEEEEEecccEEEEEeccceeEEEEEeccCCCCcceEEcchheEEEEecccCCCcEEEEecceEEEEEEEE
Confidence            369999999999999997  9999999975432     11      00      0122456668899988777

>d1wfqa_ b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Cold shock domain protein E1 (UNR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.24  E-value=8.1  Score=28.01  Aligned_cols=54  Identities=7%  Similarity=0.100  Sum_probs=41.1

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEcCccccccccCCccccCccCCcEEEEEEEE
Q 015066           98 ELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG  157 (414)
Q Consensus        98 ~~G~iV~G~V~~v~~~G~~Vdig~-k~~g~lp~sEls~~~~~~~~e~~~~vG~~v~v~Vl~  157 (414)
                      ..+...+|+|....+..=|+.-.+ ..+-|+|.+++...    ..  .+.+|+.|+|.+..
T Consensus        14 ~~~~r~~G~I~~~~~gfGFI~~~~~~~dvF~H~s~~~~~----~~--~l~~G~~VeF~v~~   68 (89)
T d1wfqa_          14 SAALRETGVIEKLLTSYGFIQCSERQARLFFHCSQYNGN----LQ--DLKVGDDVEFEVSS   68 (89)
T ss_dssp             SCCCEEEEEEEEECSSEEEEEETTTTEEEEEETTTCSSC----TT--TCCTTCCEEEEEEE
T ss_pred             CccceEEEEEEEecCccceEEeCCCCceEEEEeehhhcc----CC--cccCCCEEEEEEEE
Confidence            467889999999988666776644 46899999998432    11  26899999999866