Citrus Sinensis ID: 021034

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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-------32
Protein Sequence
MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVCL
Secondary Structure (PSIPRED)
cHHHHHHHHcccccccccccccccccHHHHHHHHHcccccccEEEEEEcccccHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccccccEEEEEEEEEEccEEEEEcccccEEEEEHHHHcccccccccccccccccEEEEEEEEEEcccccEEEEHHHHHHHHHHHHHHHHHccccEEEEEEEEEEccEEEEEEccEEEEEcccccccccccccccccEEEEEEEEEEcccccEEEEEHHHHHHHHHccccccEEEEEEEEEcccEEEEEccccccHHHHHHHccccccccccccccccEEEEEc
Secondary Structure Prediction (SSPRO)
cccHHHHHHcccccccccccccccccHcccccccccccccccEEEEEEccccccHHHHHHHHHHHHHHcHHHccccccHHccHHHHHHHHHHHHHHcccccEEEEEEEEEcccEEEEEEcccEEEEEEcHHccccccccccEEEEEcccEEEEEEEEEcccccEEEEEHHHcccccHHHHHHHHHHcccEEEEEEEEEEEcccEEEEcccEEEEEccccccccccccccccEEEEEEEEEcccccEEEEEHHHHccccHHHcccccEEEEEEEEEccccEEEEEccccEEEEEEHccHHcccccccEEEcccEEEEEc
Coil and Loop (DISEMBL)
matlaqqftglrcppishtrlsrRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCrtapmegvsFTLEEFHSALEkydfnselgtkvkgtvfctdnrgalVDITAkssaylptqEACIHKIKHveeagivpglkeeFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEglrgfvpfsqisskSTAEEllgkdlplkfvevdEEQSRLVLSNRKAMADSQAQLGIGSVVIGtvqslkpygafidigginGLLHVSQISHDRVADiatvlqpgdtlkvcl
Flexible Loop (DISEMBL)
matlaqqftglrcppishtrlsrrkSITQIQQKllnsrknktivsavaisnaetrerEELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIAtvlqpgdtlkvcl
Low Complexity Region (SEG)
MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDvvvkgkvvgankggvvaevegLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVCL
Disordered region (IsUnstruct)
******************************************IVSAVAI************QLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQI********LLGKDLPLKFVEV*******************AQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDT*****
Disordered Region (DISOPRED)
********T*********************************IV**VAISNAETREREELNQLFEEA*****************EFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVCL
Disordered Region (DISEMBL)
MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVCL
Disordered Region (DISPRO)
*****Q*FTGLRCP*************************NKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVCL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATLAQQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAIxxxxxxxxxxxxxxxxxxxxxCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVCL
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	318	2.2.26 [Sep-21-2011]
P29344	411	30S ribosomal protein S1,	N/A	no	0.984	0.761	0.799	1e-148
P73530	328	30S ribosomal protein S1	N/A	no	0.751	0.728	0.485	2e-65
P46228	307	30S ribosomal protein S1	yes	no	0.764	0.791	0.469	2e-59
P51345	263	30S ribosomal protein S1,	N/A	no	0.745	0.901	0.356	2e-39
Q1XDE2	263	30S ribosomal protein S1,	N/A	no	0.742	0.897	0.345	4e-39
O33698	295	30S ribosomal protein S1	no	no	0.764	0.823	0.360	6e-39
P74142	305	30S ribosomal protein S1	N/A	no	0.748	0.780	0.337	5e-37
P50889	429	30S ribosomal protein S1	N/A	no	0.761	0.564	0.337	8e-27
O06147	481	30S ribosomal protein S1	yes	no	0.713	0.471	0.319	5e-26
P38494	382	30S ribosomal protein S1	yes	no	0.676	0.562	0.347	1e-25

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

 Score =  524 bits (1349), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 255/319 (79%), Positives = 290/319 (90%), Gaps = 6/319 (1%)

Query: 1   MATLAQQFTG-LRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREE 59
           MA+LAQQ  G LRCPP+S++ LS+  S     +  L  R +  IVSAVA+SNA+TRER++
Sbjct: 1   MASLAQQLAGGLRCPPLSNSNLSKPFS----PKHTLKPRFS-PIVSAVAVSNAQTRERQK 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 RVADIATVLQPGDTLKVCL 318
           RV+DIATVLQPGDTLKV +
Sbjct: 296 RVSDIATVLQPGDTLKVMI 314

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 =  249 bits (636), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 117/241 (48%), Positives = 169/241 (70%), Gaps = 2/241 (0%)

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-LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVC 317
           +   L +  VV+G+V+ +KPYGAFIDIGG++GLLH+S+ISHD +    +V    D +KV 
Sbjct: 189 KMNGLEVAQVVVGSVRGIKPYGAFIDIGGVSGLLHISEISHDHIDTPHSVFNVNDEIKVM 248

Query: 318 L 318
           +
Sbjct: 249 I 249

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 =  229 bits (583), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 115/245 (46%), Positives = 171/245 (69%), Gaps = 2/245 (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 LKVCL 318
           +KV +
Sbjct: 246 VKVMI 250

Binds mRNA.

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

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

 Score =  163 bits (412), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 86/241 (35%), Positives = 142/241 (58%), Gaps = 4/241 (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 SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVC 317
           + + L +G+++ G +  + PYG FI  G + GL+H+S+I+  +V  I +  + GDT+K  
Sbjct: 185 ASSNLIVGNIIEGVINQITPYGLFIKAGNLKGLVHISEINVKQVERIPSQFKIGDTIKAV 244

Query: 318 L 318
           +
Sbjct: 245 I 245

Porphyra purpurea (taxid: 2787)

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

 Score =  162 bits (409), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 83/240 (34%), Positives = 142/240 (59%), Gaps = 4/240 (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 QAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318
            + L +G+++ G +  + PYG FI +G + GL+H+S+I+   +  I++  + GDT+K  +
Sbjct: 186 SSNLIVGNIIEGIINQITPYGLFIKVGNLKGLVHISEINIKNLEQISSQFKIGDTIKAVI 245

Porphyra yezoensis (taxid: 2788)

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

 Score =  161 bits (407), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 89/247 (36%), Positives = 143/247 (57%), Gaps = 4/247 (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  LHAVLDLE--AHLPKDEELEFLVIRDQNEDGQVTVSLRALALEQAWTRVAELQEGGQTVQ 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 DTLKVCL 318
           D ++  +
Sbjct: 240 DPIQALV 246

Binds mRNA.

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

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

 Score =  155 bits (391), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 81/240 (33%), Positives = 138/240 (57%), Gaps = 2/240 (0%)

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

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 =  121 bits (303), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 89/264 (33%), Positives = 142/264 (53%), Gaps = 22/264 (8%)

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 QISHDRVADIATVLQPGDTLKVCL 318
           +ISHDRV + A VL  GD + V +
Sbjct: 261 EISHDRVKNPADVLTKGDKVDVKI 284

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

Leuconostoc lactis (taxid: 1246)

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

 Score =  118 bits (296), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 79/247 (31%), Positives = 139/247 (56%), Gaps = 20/247 (8%)

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 PGDTLKV 316
            GD + V
Sbjct: 254 VGDEVTV 260

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

Mycobacterium tuberculosis (taxid: 1773)

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

 Score =  117 bits (293), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 80/230 (34%), Positives = 126/230 (54%), Gaps = 15/230 (6%)

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 VVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           V+ G VQ L  +GAF+DIGGI+GL+H+SQ+SH  V   + V++ G  +KV
Sbjct: 190 VLDGKVQRLTDFGAFVDIGGIDGLVHISQLSHSHVEKPSDVVEEGQEVKV 239

Plays a role in sporulation.

Bacillus subtilis (strain 168) (taxid: 224308)

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	318
133872	411	RecName: Full=30S ribosomal protein S1,	0.984	0.761	0.799	1e-146
225432062	410	PREDICTED: 30S ribosomal protein S1, chl	0.984	0.763	0.823	1e-143
255556496	412	tex protein-relatedtranscription accesso	0.990	0.764	0.821	1e-143
224099083	421	predicted protein [Populus trichocarpa]	0.990	0.748	0.801	1e-139
449459770	413	PREDICTED: 30S ribosomal protein S1, chl	0.987	0.760	0.788	1e-139
224112036	412	predicted protein [Populus trichocarpa]	0.990	0.764	0.783	1e-136
297813179	416	hypothetical protein ARALYDRAFT_489681 [	0.996	0.762	0.751	1e-133
30692346	416	small subunit ribosomal protein S1 [Arab	0.996	0.762	0.745	1e-132
227204349	378	AT5G30510 [Arabidopsis thaliana]	0.996	0.838	0.745	1e-132
358248430	412	uncharacterized protein LOC100812847 [Gl	0.902	0.696	0.766	1e-128

>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 =  524 bits (1349), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 255/319 (79%), Positives = 290/319 (90%), Gaps = 6/319 (1%)

Query: 1   MATLAQQFTG-LRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREE 59
           MA+LAQQ  G LRCPP+S++ LS+  S     +  L  R +  IVSAVA+SNA+TRER++
Sbjct: 1   MASLAQQLAGGLRCPPLSNSNLSKPFS----PKHTLKPRFS-PIVSAVAVSNAQTRERQK 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 RVADIATVLQPGDTLKVCL 318
           RV+DIATVLQPGDTLKV +
Sbjct: 296 RVSDIATVLQPGDTLKVMI 314

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 =  514 bits (1325), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 262/318 (82%), Positives = 287/318 (90%), Gaps = 5/318 (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 VADIATVLQPGDTLKVCL 318
           V+DIATVLQPGD LKV +
Sbjct: 296 VSDIATVLQPGDILKVMI 313

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 =  513 bits (1321), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 262/319 (82%), Positives = 291/319 (91%), Gaps = 4/319 (1%)

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 CRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVE 239
           CRQLQ+EDV+VKGKVVGANKGGVVA VE GLRGFVPFSQISSKSTAEELL K+LPLKFV+
Sbjct: 178 CRQLQAEDVIVKGKVVGANKGGVVAIVEGGLRGFVPFSQISSKSTAEELLEKELPLKFVD 237

Query: 240 VDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHD 299
           VDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHD
Sbjct: 238 VDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHD 297

Query: 300 RVADIATVLQPGDTLKVCL 318
           RV+DIATVLQPGDTLKV +
Sbjct: 298 RVSDIATVLQPGDTLKVMI 316

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 =  502 bits (1292), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 255/318 (80%), Positives = 282/318 (88%), Gaps = 3/318 (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 VADIATVLQPGDTLKVCL 318
           V+DIATVLQPGDTLKV +
Sbjct: 298 VSDIATVLQPGDTLKVMI 315

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 =  501 bits (1290), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 253/321 (78%), Positives = 286/321 (89%), Gaps = 7/321 (2%)

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 HDRVADIATVLQPGDTLKVCL 318
           HDR++DIATVLQPGD+LKV +
Sbjct: 297 HDRISDIATVLQPGDSLKVMI 317

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 =  490 bits (1261), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 249/318 (78%), Positives = 281/318 (88%), Gaps = 3/318 (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 VADIATVLQPGDTLKVCL 318
           V+DI+TVLQPGDTLKV +
Sbjct: 298 VSDISTVLQPGDTLKVMI 315

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 =  480 bits (1235), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 239/318 (75%), Positives = 282/318 (88%), Gaps = 1/318 (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 VADIATVLQPGDTLKVCL 318
           V+DIATVLQPGDTLKV +
Sbjct: 300 VSDIATVLQPGDTLKVMI 317

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 =  478 bits (1229), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 237/318 (74%), Positives = 284/318 (89%), Gaps = 1/318 (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 VADIATVLQPGDTLKVCL 318
           V+DIATVLQPGDTLKV +
Sbjct: 300 VSDIATVLQPGDTLKVMI 317

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|227204349|dbj|BAH57026.1| AT5G30510 [Arabidopsis thaliana]

 Score =  476 bits (1226), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 237/318 (74%), Positives = 284/318 (89%), Gaps = 1/318 (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 VADIATVLQPGDTLKVCL 318
           V+DIATVLQPGDTLKV +
Sbjct: 300 VSDIATVLQPGDTLKVMI 317

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 =  464 bits (1195), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 223/291 (76%), Positives = 256/291 (87%), Gaps = 4/291 (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 VIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318
           V G+VQSLKPYGAFIDIGGINGLLHVSQISHDRV DI+TVLQPGD LKV +
Sbjct: 265 VTGSVQSLKPYGAFIDIGGINGLLHVSQISHDRVTDISTVLQPGDILKVMI 315

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	318
TAIR|locus:2145860	416	RPS1 "ribosomal protein S1" [A	0.993	0.759	0.711	8.2e-115
TIGR_CMR|BA_1519	382	BA_1519 "ribosomal protein S1"	0.669	0.557	0.316	3.4e-22
UNIPROTKB|O06147	481	rpsA "30S ribosomal protein S1	0.748	0.494	0.284	1.3e-21
TIGR_CMR|SPO_0802	558	SPO_0802 "ribosomal protein S1	0.726	0.413	0.267	3.6e-17
TIGR_CMR|CPS_2335	553	CPS_2335 "ribosomal protein S1	0.704	0.405	0.235	7.9e-13
UNIPROTKB|Q9KQT3	556	VC_1915 "30S ribosomal protein	0.713	0.408	0.246	3.3e-12
TIGR_CMR|VC_1915	556	VC_1915 "ribosomal protein S1"	0.713	0.408	0.246	3.3e-12
TIGR_CMR|GSU_2603	586	GSU_2603 "ribosomal protein S1	0.704	0.382	0.261	8.5e-12
TIGR_CMR|SO_2402	555	SO_2402 "ribosomal protein S1"	0.707	0.405	0.240	1.3e-11
TIGR_CMR|GSU_1200	402	GSU_1200 "ribosomal protein S1	0.323	0.256	0.380	1.6e-11

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

 Score = 1132 (403.5 bits), Expect = 8.2e-115, P = 8.2e-115
 Identities = 227/319 (71%), Positives = 269/319 (84%)

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 RVADIATVLQPGDTLKVCL 318
             RV+DIATVLQPGDTLKV +
Sbjct:   299 RVSDIATVLQPGDTLKVMI 317

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 = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 73/231 (31%), Positives = 120/231 (51%)

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 SVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
              VV GTVQ L  +GAF+++GG++GL+H+SQISH+RV   + VL+ G  +KV
Sbjct:   190 DVVEGTVQRLTDFGAFVNVGGVDGLVHISQISHERVEQPSEVLEQGQKVKV 240

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 = 258 (95.9 bits), Expect = 1.3e-21, P = 1.3e-21
 Identities = 74/260 (28%), Positives = 132/260 (50%)

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 SHDRVADIATVLQPGDTLKV 316
             S   +   + V+Q GD + V
Sbjct:   241 SWKHIDHPSEVVQVGDEVTV 260

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 = 219 (82.2 bits), Expect = 3.6e-17, P = 3.6e-17
 Identities = 66/247 (26%), Positives = 116/247 (46%)

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 PGDTLKV 316
              G+T+KV
Sbjct:   241 IGETVKV 247

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 = 191 (72.3 bits), Expect = 7.9e-13, Sum P(2) = 7.9e-13
 Identities = 57/242 (23%), Positives = 113/242 (46%)

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 KV 316
             +V
Sbjct:   242 QV 243

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

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

 Score = 188 (71.2 bits), Expect = 3.3e-12, P = 3.3e-12
 Identities = 61/247 (24%), Positives = 113/247 (45%)

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 PGDTLKV 316
              GD + V
Sbjct:   237 VGDEILV 243

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 = 188 (71.2 bits), Expect = 3.3e-12, P = 3.3e-12
 Identities = 61/247 (24%), Positives = 113/247 (45%)

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 PGDTLKV 316
              GD + V
Sbjct:   237 VGDEILV 243

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

GO:0006412 "translation" evidence=ISS

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

 Score = 185 (70.2 bits), Expect = 8.5e-12, P = 8.5e-12
 Identities = 64/245 (26%), Positives = 110/245 (44%)

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 DTLKV 316
             D L V
Sbjct:   264 DKLSV 268

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 = 183 (69.5 bits), Expect = 1.3e-11, P = 1.3e-11
 Identities = 58/241 (24%), Positives = 110/241 (45%)

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 V 316
             V
Sbjct:   243 V 243

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

GO:0006412 "translation" evidence=ISS

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

 Score = 180 (68.4 bits), Expect = 1.6e-11, P = 1.6e-11
 Identities = 43/113 (38%), Positives = 63/113 (55%)

Query:   210 LRGFVPFSQISSKSTAE--ELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQ------ 261
             +R F P+SQIS +  A   E +G+ L  K VE  E    +VLS+R  + + + Q      
Sbjct:   139 VRAFCPYSQISLRRAANPAEFVGRQLLFKVVEFAERGRNIVLSHRAILEEEERQKREALK 198

Query:   262 --LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGD 312
               L  G+ + GTV  L P+GAF+DIGG+ GL+ +S+    RV +I  VL  G+
Sbjct:   199 DTLKEGTTLTGTVTRLMPFGAFVDIGGVEGLIPISEAGWSRVKEIGDVLSVGE 251

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P29344	RR1_SPIOL	No assigned EC number	0.7993	0.9842	0.7615	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	318
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	2e-88
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	3e-57
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	4e-47
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	8e-40
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	8e-39
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	1e-28
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	1e-25
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	5e-22
cd04465	67	cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec	9e-21
cd05692	69	cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: R	1e-20
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	2e-19
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	2e-19
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	2e-18
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	2e-16
cd05688	68	cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: R	1e-15
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	1e-13
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	1e-13
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	7e-13
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	1e-12
pfam00575	74	pfam00575, S1, S1 RNA binding domain	2e-12
cd04472	68	cd04472, S1_PNPase, S1_PNPase: Polynucleotide phos	2e-11
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	4e-11
TIGR00717	516	TIGR00717, rpsA, ribosomal protein S1	5e-11
cd05687	70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	8e-11
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	1e-10
cd05685	68	cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain	2e-10
pfam00575	74	pfam00575, S1, S1 RNA binding domain	3e-10
PRK08059	123	PRK08059, PRK08059, general stress protein 13; Val	4e-10
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	1e-09
pfam00575	74	pfam00575, S1, S1 RNA binding domain	3e-09
cd05708	77	cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12:	4e-09
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	5e-09
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	5e-09
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	5e-09
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	6e-09
COG1098	129	COG1098, VacB, Predicted RNA binding protein (cont	7e-09
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	2e-08
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	3e-08
cd05684	79	cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N	1e-07
PRK13806	491	PRK13806, rpsA, 30S ribosomal protein S1; Provisio	2e-07
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	2e-07
COG2183	780	COG2183, Tex, Transcriptional accessory protein [T	6e-07
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	7e-07
PRK08563	187	PRK08563, PRK08563, DNA-directed RNA polymerase su	8e-07
PRK05807	136	PRK05807, PRK05807, hypothetical protein; Provisio	2e-06
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	3e-06
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	4e-06
cd04460	99	cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-bindi	7e-06
cd05686	73	cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-b	1e-05
cd00164	65	cd00164, S1_like, S1_like: Ribosomal protein S1-li	3e-05
cd04452	76	cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha sub	3e-05
PRK07252	120	PRK07252, PRK07252, hypothetical protein; Provisio	4e-05
PRK12269	863	PRK12269, PRK12269, bifunctional cytidylate kinase	5e-05
COG1093	269	COG1093, SUI2, Translation initiation factor 2, al	5e-05
PRK08582	139	PRK08582, PRK08582, hypothetical protein; Provisio	7e-05
cd05687	70	cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec	9e-05
cd04453	88	cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase	2e-04
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	3e-04
COG1095	183	COG1095, RPB7, DNA-directed RNA polymerase, subuni	4e-04
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	6e-04
PRK03987	262	PRK03987, PRK03987, translation initiation factor	6e-04
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	8e-04
cd05698	70	cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs	0.001
cd04461	83	cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs	0.002
cd05690	69	cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: R	0.002
cd05691	73	cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: R	0.003

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

 Score =  267 bits (683), Expect = 2e-88
 Identities = 116/246 (47%), Positives = 172/246 (69%), Gaps = 2/246 (0%)

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 GDTLKV 316
            D +KV
Sbjct: 243 NDEMKV 248

Length = 318

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

 Score =  192 bits (491), Expect = 3e-57
 Identities = 86/248 (34%), Positives = 140/248 (56%), Gaps = 17/248 (6%)

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 QPGDTLKV 316
           + GD +KV
Sbjct: 237 KVGDEVKV 244

Length = 541

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

 Score =  162 bits (413), Expect = 4e-47
 Identities = 76/230 (33%), Positives = 128/230 (55%), Gaps = 12/230 (5%)

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 VVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           VV GTV  L  +GAF+DIGG++GL+H+S++SH+RV   + V+  G  ++V
Sbjct: 195 VVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVGQEVEV 244

Length = 390

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

 Score =  146 bits (371), Expect = 8e-40
 Identities = 73/246 (29%), Positives = 125/246 (50%), Gaps = 18/246 (7%)

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 GDTLKV 316
           GD +KV
Sbjct: 248 GDEVKV 253

Length = 565

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

 Score =  144 bits (365), Expect = 8e-39
 Identities = 77/246 (31%), Positives = 128/246 (52%), Gaps = 12/246 (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 TLKVCL 318
            +KV +
Sbjct: 526 EIKVYI 531

Length = 647

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

 Score =  114 bits (288), Expect = 1e-28
 Identities = 70/245 (28%), Positives = 118/245 (48%), Gaps = 18/245 (7%)

Query: 84  EEFHSALEK-YDFNSEL-GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE 141
           E F   LE+         G+ VKGTV   +     VD+  KS   +P +E     ++   
Sbjct: 1   ESFAQLLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAPLEIQV 60

Query: 142 EAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKG 201
              +   L       GE       VLS    Q    W +  +   E  +V+GK+VG  KG
Sbjct: 61  GDEVEVYLDRVEDRFGET------VLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKG 114

Query: 202 GVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVEVDEEQSRLVLS--------N 251
           G + ++ G+  F+P SQ+  K     + L+GK L  K +++D++++ +V+S         
Sbjct: 115 GFIVDLNGVEAFLPGSQVDVKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEER 174

Query: 252 RKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG 311
            +A  +    L  G VV G V+++  +GAF+D+GG++GLLH++ +S  RV   +  ++ G
Sbjct: 175 SQAREELLENLKEGDVVKGVVKNITDFGAFVDLGGVDGLLHITDMSWKRVKHPSEYVKVG 234

Query: 312 DTLKV 316
             +KV
Sbjct: 235 QEVKV 239

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 =  106 bits (266), Expect = 1e-25
 Identities = 80/250 (32%), Positives = 142/250 (56%), Gaps = 22/250 (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 VLQPGDTLKV 316
           V++ G  + V
Sbjct: 251 VVEVGQEVTV 260

Length = 486

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

 Score = 95.8 bits (239), Expect = 5e-22
 Identities = 63/232 (27%), Positives = 114/232 (49%), Gaps = 18/232 (7%)

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-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
             V G V +L  YGAF++I  G+ GL+HVS+IS  +    + V++ G  ++V
Sbjct: 279 DKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEV 330

Length = 541

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

 Score = 84.0 bits (209), Expect = 9e-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|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

 Score = 83.5 bits (207), Expect = 1e-20
 Identities = 32/53 (60%), Positives = 43/53 (81%), Gaps = 1/53 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           GSVV GTV  LKP+GAF+++G GI+GL+H+SQI+H RV D+  VL+ GD +KV
Sbjct: 1   GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKV 53

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

 Score = 88.1 bits (219), Expect = 2e-19
 Identities = 68/234 (29%), Positives = 116/234 (49%), Gaps = 25/234 (10%)

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-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +GS+V+G V  + P+GAF+++  G++GL+H+SQIS  R+     VL  G+ +K 
Sbjct: 562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKA 615

Length = 647

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

 Score = 88.2 bits (219), Expect = 2e-19
 Identities = 70/251 (27%), Positives = 110/251 (43%), Gaps = 28/251 (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 TVLQPGDTLKV 316
             +  GDT++V
Sbjct: 245 EAVSVGDTVRV 255

Length = 491

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

 Score = 84.5 bits (210), Expect = 2e-18
 Identities = 54/177 (30%), Positives = 95/177 (53%), Gaps = 12/177 (6%)

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-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +L  G V+ GTV+ L  +GAF+++  G+ GL+H+SQISH  +A  + VL+ G  +KV
Sbjct: 274 KLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKV 330

Length = 390

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

 Score = 79.0 bits (195), Expect = 2e-16
 Identities = 63/243 (25%), Positives = 119/243 (48%), Gaps = 17/243 (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 LKV 316
           ++V
Sbjct: 324 VEV 326

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 = 70.0 bits (172), Expect = 1e-15
 Identities = 25/53 (47%), Positives = 38/53 (71%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
            G VV GTV+S+  +GAF+D+GG++GLLH+S +S  RV   + V+  GD ++V
Sbjct: 1   EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEV 53

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

 Score = 70.8 bits (174), Expect = 1e-13
 Identities = 72/246 (29%), Positives = 123/246 (50%), Gaps = 16/246 (6%)

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 GDTLKV 316
           GD ++ 
Sbjct: 411 GDEVEA 416

Length = 541

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

 Score = 64.9 bits (159), Expect = 1e-13
 Identities = 26/56 (46%), Positives = 38/56 (67%), Gaps = 1/56 (1%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318
           +G VV GTV  + P GAF+D+G G+ GL+ +S++S  RV D   VL+ GD +KV +
Sbjct: 2   VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKV 57

Length = 72

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

 Score = 68.6 bits (168), Expect = 7e-13
 Identities = 71/241 (29%), Positives = 115/241 (47%), Gaps = 28/241 (11%)

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 V 316
           V
Sbjct: 346 V 346

Length = 491

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

 Score = 67.9 bits (167), Expect = 1e-12
 Identities = 52/203 (25%), Positives = 100/203 (49%), Gaps = 39/203 (19%)

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 SQISHDRVADIATVLQPGDTLKV 316
           S++S  +         P   + V
Sbjct: 317 SEMSWTKK-----NKHPSKVVSV 334

Length = 565

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

 Score = 61.1 bits (149), Expect = 2e-12
 Identities = 25/56 (44%), Positives = 35/56 (62%), Gaps = 1/56 (1%)

Query: 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
              G VV GTV  +   GAF+D+G G+ G + +S+IS DRV D   VL+ GD ++V
Sbjct: 2   PEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEV 57

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

 Score = 57.9 bits (141), Expect = 2e-11
 Identities = 22/53 (41%), Positives = 36/53 (67%), Gaps = 1/53 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           G +  G V  +K +GAF++I  G +GL+H+S++S +RV  +  VL+ GD +KV
Sbjct: 1   GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKV 53

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 = 63.5 bits (156), Expect = 4e-11
 Identities = 21/54 (38%), Positives = 36/54 (66%), Gaps = 1/54 (1%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +G +  G V  +  +GAF++I  G +GL+H+S+I+ +RV  +  VL+ GD +KV
Sbjct: 621 VGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKV 674

Length = 693

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

 Score = 62.8 bits (153), Expect = 5e-11
 Identities = 59/230 (25%), Positives = 104/230 (45%), Gaps = 16/230 (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-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           V G V  +K +GAF+++ GG+ GL+  S++S +R  D    ++ GD ++ 
Sbjct: 450 VKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEA 499

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

 Score = 56.8 bits (138), Expect = 8e-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|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 61.7 bits (151), Expect = 1e-10
 Identities = 21/54 (38%), Positives = 37/54 (68%), Gaps = 1/54 (1%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +G +  G V  +  +GAF++I  G +GL+H+S+I+++RV  +  VL+ GD +KV
Sbjct: 618 VGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKV 671

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|240190 cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa

 Score = 55.7 bits (135), Expect = 2e-10
 Identities = 19/53 (35%), Positives = 35/53 (66%), Gaps = 1/53 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           G V+ G V ++  +GAF+DIG   +GL+H+S+++   V+  + V+  GD ++V
Sbjct: 1   GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEV 53

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|216000 pfam00575, S1, S1 RNA binding domain

 Score = 55.0 bits (133), Expect = 3e-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|181215 PRK08059, PRK08059, general stress protein 13; Validated

 Score = 56.2 bits (136), Expect = 4e-10
 Identities = 26/58 (44%), Positives = 37/58 (63%), Gaps = 1/58 (1%)

Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +Q  +GSVV G V  ++PYGAF+ +     GL+H+S+I+H  V DI   L  GD +KV
Sbjct: 3   SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKV 60

Length = 123

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

 Score = 58.5 bits (142), Expect = 1e-09
 Identities = 64/230 (27%), Positives = 103/230 (44%), Gaps = 21/230 (9%)

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-IGGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           V G V+S+K  GAF++  GG+ GL+ +S++S D        L+ GD ++ 
Sbjct: 453 VKGKVKSVKDKGAFVELGGGVEGLIRLSELSRDV-------LKVGDEVEA 495

Length = 541

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

 Score = 52.3 bits (126), Expect = 3e-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|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 = 52.3 bits (126), Expect = 4e-09
 Identities = 24/54 (44%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 265 GSVVIGTVQSLKPYGAFIDIGGIN--GLLHVSQISHDRVADIATVLQPGDTLKV 316
           G  + GTV+ ++ YG FIDI G N  GL H S+IS +RVAD + + + GD ++ 
Sbjct: 3   GQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRA 56

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 = 56.7 bits (138), Expect = 5e-09
 Identities = 46/139 (33%), Positives = 70/139 (50%), Gaps = 13/139 (9%)

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 HDRVADIATVLQPGDTLKV 316
            DRV D   VL+ GD ++ 
Sbjct: 495 RDRVEDATEVLKVGDEVEA 513

Length = 565

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

 Score = 51.6 bits (124), Expect = 5e-09
 Identities = 18/50 (36%), Positives = 32/50 (64%), Gaps = 1/50 (2%)

Query: 268 VIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           V G V S+  +G F+++  G+ GL+H+S++S   V D + V + GD ++V
Sbjct: 1   VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEV 50

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

 Score = 56.8 bits (138), Expect = 5e-09
 Identities = 22/54 (40%), Positives = 37/54 (68%), Gaps = 1/54 (1%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +G V  GTV  +  +GAF+++  G +GL+H+SQ++ +RV  +  VL+ GD +KV
Sbjct: 619 VGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKV 672

Length = 692

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

 Score = 56.9 bits (138), Expect = 6e-09
 Identities = 53/178 (29%), Positives = 84/178 (47%), Gaps = 9/178 (5%)

Query: 83  LEEFHSALEKYDFNS-ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE 141
           LEE     ++  +NS E G  V+G V    + GA VDI       L   E    +++   
Sbjct: 460 LEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGG-VDGLLHVSEISWGRVEKPS 518

Query: 142 EAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKG 201
           +   V G + +  I+  ++ +  L LSL+ +     WE   +      +V GKVV     
Sbjct: 519 DVLKV-GDEIKVYILDIDKENKKLSLSLKKLL-PDPWENVEEKYPVGSIVLGKVVRIAPF 576

Query: 202 GVVAEVE-GLRGFVPFSQISSK--STAEELL--GKDLPLKFVEVDEEQSRLVLSNRKA 254
           G   E+E G+ G V  SQIS K     E++L  G+++  K +EVD E+ R+ LS ++ 
Sbjct: 577 GAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEV 634

Length = 647

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

 Score = 53.1 bits (128), Expect = 7e-09
 Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 1/58 (1%)

Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
             + +GS + G +  + PYGAF+++ GG  GL+H+S+I+   V DI   L+ G  +KV
Sbjct: 1   MSMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKV 58

Length = 129

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

 Score = 55.2 bits (134), Expect = 2e-08
 Identities = 41/139 (29%), Positives = 78/139 (56%), Gaps = 12/139 (8%)

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-VADIATVLQPGDTLKV 316
           D+   +   + + GD ++ 
Sbjct: 409 DKKGEEAVELYKKGDEVEA 427

Length = 565

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

 Score = 54.7 bits (131), Expect = 3e-08
 Identities = 62/240 (25%), Positives = 108/240 (45%), Gaps = 35/240 (14%)

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-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
            + + G+  VV G V  +  +GAFI++  GI GL H+S+ S      +    +P D +K+
Sbjct: 572 FENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSW-----VKKTSKPSDMVKI 626

Length = 863

>gnl|CDD|240189 cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 5/57 (8%)

Query: 265 GSVVIGTVQSLKPYGAFIDIGGIN----GLLHVSQISHD-RVADIATVLQPGDTLKV 316
           G +  G V S+  +G F+ + G+     GL+H+SQ+S + RVA+ + V++ G  +KV
Sbjct: 1   GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKV 57

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

 Score = 51.6 bits (124), Expect = 2e-07
 Identities = 42/150 (28%), Positives = 66/150 (44%), Gaps = 11/150 (7%)

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 INGLLHVSQISHDRVADIATVLQPGDTLKV 316
           + GLL  S IS          L+PGD++ +
Sbjct: 403 VTGLLPASVISRAGKPATYEKLKPGDSVTL 432

Length = 491

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

 Score = 52.4 bits (125), Expect = 2e-07
 Identities = 67/252 (26%), Positives = 112/252 (44%), Gaps = 44/252 (17%)

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 ATVLQPGDTLKV 316
              ++ G T+++
Sbjct: 534 REFVKKGQTIEL 545

Length = 863

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

 Score = 50.7 bits (122), Expect = 6e-07
 Identities = 24/56 (42%), Positives = 38/56 (67%), Gaps = 1/56 (1%)

Query: 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           L  G ++ GTV+++  +GAF+DIG   +GL+H+SQ+S   V D   V++ GD +KV
Sbjct: 656 LKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKV 711

Length = 780

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

 Score = 45.7 bits (109), Expect = 7e-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|236289 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E'; Provisional

 Score = 48.3 bits (116), Expect = 8e-07
 Identities = 17/36 (47%), Positives = 25/36 (69%)

Query: 267 VVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA 302
           VV G V  +  +GAF+ IG ++GLLH+SQI  D ++
Sbjct: 84  VVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYIS 119

Length = 187

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

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 21/55 (38%), Positives = 36/55 (65%)

Query: 262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           L  GS++ GTV ++  +GAF+++ G  GL+H+S+++   V DI   L+  D +KV
Sbjct: 3   LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKV 57

Length = 136

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

 Score = 48.1 bits (115), Expect = 3e-06
 Identities = 69/239 (28%), Positives = 116/239 (48%), Gaps = 43/239 (17%)

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-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
                IG +V G V  L P+GAF+ +  GI GL+H+S+++   V     V+Q GD + V
Sbjct: 288 ARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFV 346

Length = 486

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

 Score = 43.4 bits (103), Expect = 4e-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|239907 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding domain

 Score = 43.8 bits (104), Expect = 7e-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|240191 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-binding domain

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 2/49 (4%)

Query: 266 SVVIGTVQSLKPYGAFIDIGGI--NGLLHVSQISHDRVADIATVLQPGD 312
            +  G V S+  YGAF+ I G    GL+H S +S  RV D + V+  G+
Sbjct: 5   QIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGE 53

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

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

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 25/65 (38%), Positives = 37/65 (56%), Gaps = 5/65 (7%)

Query: 191 VKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKSTAEEL----LGKDLPLKFVEVDEEQS 245
           V GKVV   K GV  E+E G+ G V  S++S K   +      +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|239899 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 15/51 (29%), Positives = 31/51 (60%), Gaps = 3/51 (5%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPG 311
            G +V+ TV+S+   GA++ +   G I G++ +S++S  R+  I  +++ G
Sbjct: 3   EGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVG 53

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

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

 Score = 42.0 bits (99), Expect = 4e-05
 Identities = 20/54 (37%), Positives = 34/54 (62%), Gaps = 1/54 (1%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           IG  + GT+  +KPYGAF+ +  G  GL+H+S+I    + +I  +L+ G+ + V
Sbjct: 3   IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLV 56

Length = 120

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

 Score = 44.7 bits (105), Expect = 5e-05
 Identities = 36/128 (28%), Positives = 63/128 (49%), Gaps = 18/128 (14%)

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 QLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGD---- 792

Query: 308 LQPGDTLK 315
             PG+ L+
Sbjct: 793 --PGEALR 798

Length = 863

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

 Score = 43.5 bits (103), Expect = 5e-05
 Identities = 15/51 (29%), Positives = 31/51 (60%), Gaps = 3/51 (5%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPG 311
            G +V+GTV+ +  YGA++++    G  G +H+S+++   V +I   ++ G
Sbjct: 11  EGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEG 61

Length = 269

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

 Score = 41.9 bits (99), Expect = 7e-05
 Identities = 19/54 (35%), Positives = 35/54 (64%), Gaps = 1/54 (1%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +GS + G V  +  +GAF+++  G  GL+H+S+++ + V DI   L+ GD ++V
Sbjct: 5   VGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEV 58

Length = 139

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

 Score = 39.8 bits (94), Expect = 9e-05
 Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKVCL 318
           G +V GTV S+      +DIG    G++ +S+ S D + +    ++ GD ++V +
Sbjct: 1   GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYV 55

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 6/59 (10%)

Query: 264 IGSVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISH---DRVADIATVLQPGDTLKV 316
           +G++ +G V+ + P    AF+DIG G NG LH+S I      +   IA +L+ G  + V
Sbjct: 7   VGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILV 65

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

 Score = 41.8 bits (99), Expect = 3e-04
 Identities = 57/221 (25%), Positives = 93/221 (42%), Gaps = 40/221 (18%)

Query: 35  LNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYD 94
           L+  KN+ I+S  A+        EE     EE               +L+E         
Sbjct: 160 LDPEKNRVILSRRAV------VEEERAAKKEELLS------------SLKE--------- 192

Query: 95  FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFV 154
                G  V+GTV    + GA VDI       +   E    +++   E  +  G + E  
Sbjct: 193 -----GDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHERVEKPSEV-VSVGQEVEVK 245

Query: 155 IIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVG-ANKGGVVAEVEGLRGF 213
           ++  +   + + LSL+       WE   +   E  V++G V    + G  V  + G+ G 
Sbjct: 246 VLSIDWETERISLSLKDTLPG-PWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGL 304

Query: 214 VPFSQISSK--STAEELL--GKDLPLKFVEVDEEQSRLVLS 250
           V  SQIS K  +T  E+L  G+++ +K +EV+EE+ R+ LS
Sbjct: 305 VHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLS 345

Length = 390

>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription]

 Score = 40.4 bits (95), Expect = 4e-04
 Identities = 18/37 (48%), Positives = 25/37 (67%)

Query: 265 GSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV 301
           G VV G V  +  +GAF+ IG ++GL+HVSQI  D +
Sbjct: 82  GEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYI 118

Length = 183

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

 Score = 40.7 bits (96), Expect = 6e-04
 Identities = 34/177 (19%), Positives = 73/177 (41%), Gaps = 9/177 (5%)

Query: 89  ALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEAC-IHKIKHVEEAGIVP 147
             E++     +G  V+G V    + GA V++       +   +       +  E+     
Sbjct: 353 PWEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKK-- 410

Query: 148 GLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVG-ANKGGVVAE 206
           G + E  ++  ++  + + L ++ ++ E  WE   +   +  VVKGKV    +KG  V  
Sbjct: 411 GDEVEAKVLAVDKEKERISLGIKQLE-ESPWEEFSEKYKKGSVVKGKVKSVKDKGAFVEL 469

Query: 207 VEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLS-NRKAMADSQAQL 262
             G+ G +  S++S         G ++    V +D++  +++LS       + +  L
Sbjct: 470 GGGVEGLIRLSELSRDVLKV---GDEVEAVVVSIDKKNRKILLSIKALERKEEKEAL 523

Length = 541

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

 Score = 40.2 bits (95), Expect = 6e-04
 Identities = 16/50 (32%), Positives = 31/50 (62%), Gaps = 3/50 (6%)

Query: 265 GSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPG 311
           G +V+GTV+ +K +GAF+ +    G  G +H+S+++   V +I   ++ G
Sbjct: 9   GELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEG 58

Length = 262

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

 Score = 40.2 bits (95), Expect = 8e-04
 Identities = 20/63 (31%), Positives = 39/63 (61%), Gaps = 2/63 (3%)

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 KVC 317
           +V 
Sbjct: 70  EVY 72

Length = 390

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           G    GT+  +KP G  +     + G L  S++S   + D     + G  +KV
Sbjct: 1   GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKV 53

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|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 = 36.4 bits (85), Expect = 0.002
 Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           G VV G V+++ PYG F++  GG+ GL   S IS + V D +   + G ++  
Sbjct: 15  GMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTA 67

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 = 35.9 bits (83), Expect = 0.002
 Identities = 16/34 (47%), Positives = 26/34 (76%), Gaps = 1/34 (2%)

Query: 265 GSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQIS 297
           G+VV G ++S+  +G F+ + GGI+GL+H+S IS
Sbjct: 1   GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDIS 34

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           GS+V G V  +   GA + +G G+ G L  +++S DRV D     + GD ++ 
Sbjct: 1   GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEA 53

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	318
PRK07400	318	30S ribosomal protein S1; Reviewed	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	100.0
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	100.0
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	100.0
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	100.0
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	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
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	100.0
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	100.0
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.95
PRK07400	318	30S ribosomal protein S1; Reviewed	99.95
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.83
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.7
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.7
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.65
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.55
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.54
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.53
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.49
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.46
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.46
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.44
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.44
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	99.42
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.4
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.39
PRK07252	120	hypothetical protein; Provisional	99.39
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.38
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.38
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.37
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	99.36
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.36
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	99.36
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.35
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.35
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.33
PRK08582	139	hypothetical protein; Provisional	99.32
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	99.31
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	99.3
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.3
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	99.3
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.3
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.27
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.27
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.27
PHA02945	88	interferon resistance protein; Provisional	99.26
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	99.26
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.24
PRK08059	123	general stress protein 13; Validated	99.21
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	99.21
PRK05807	136	hypothetical protein; Provisional	99.21
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.21
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.21
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	99.21
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	99.21
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.2
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	99.2
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	99.2
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	99.2
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	99.19
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.19
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	99.19
PRK08582	139	hypothetical protein; Provisional	99.19
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.18
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	99.17
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.16
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	99.16
PRK09202	470	nusA transcription elongation factor NusA; Validat	99.16
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.15
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	99.14
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.14
PRK03987	262	translation initiation factor IF-2 subunit alpha;	99.13
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	99.12
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	99.1
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.1
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	99.1
PRK07252	120	hypothetical protein; Provisional	99.08
COG2183	780	Tex Transcriptional accessory protein [Transcripti	99.07
PRK05807	136	hypothetical protein; Provisional	99.07
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	99.06
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.06
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.06
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	99.05
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	99.05
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	99.04
PRK09202	470	nusA transcription elongation factor NusA; Validat	99.02
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	99.02
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	99.01
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	99.01
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	99.01
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.98
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.98
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.98
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.97
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.96
PHA02945	88	interferon resistance protein; Provisional	98.95
PRK08059	123	general stress protein 13; Validated	98.92
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.9
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	98.89
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.87
TIGR01953	341	NusA transcription termination factor NusA. This m	98.86
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.84
TIGR01953	341	NusA transcription termination factor NusA. This m	98.84
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	98.84
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.82
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.78
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	98.77
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	98.77
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.77
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.76
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.73
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.72
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.71
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	98.71
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.7
COG2183	780	Tex Transcriptional accessory protein [Transcripti	98.68
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.67
PRK12327	362	nusA transcription elongation factor NusA; Provisi	98.67
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.66
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.65
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.64
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.63
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	98.61
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	98.54
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.53
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.42
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	98.38
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.36
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	98.34
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	98.32
PRK12328	374	nusA transcription elongation factor NusA; Provisi	98.32
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	98.3
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.29
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.28
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	98.22
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.16
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	98.16
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.11
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.09
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	98.05
PRK12329	449	nusA transcription elongation factor NusA; Provisi	98.0
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	97.97
PRK12328	374	nusA transcription elongation factor NusA; Provisi	97.93
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	97.93
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.92
PRK11642	813	exoribonuclease R; Provisional	97.87
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.86
PRK11642	813	exoribonuclease R; Provisional	97.86
KOG2916	304	consensus Translation initiation factor 2, alpha s	97.86
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	97.86
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	97.81
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.73
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	97.66
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	97.63
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	97.63
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	97.6
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.57
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.54
PRK12329	449	nusA transcription elongation factor NusA; Provisi	97.35
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.3
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.22
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	97.13
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	97.05
PRK05054	644	exoribonuclease II; Provisional	96.94
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	96.91
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	96.86
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	96.74
PRK10811	1068	rne ribonuclease E; Reviewed	96.65
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	96.5
PRK11712	489	ribonuclease G; Provisional	96.44
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	96.41
PRK05054	644	exoribonuclease II; Provisional	96.38
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	96.28
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	96.19
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	96.18
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	96.12
PRK11712	489	ribonuclease G; Provisional	96.09
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	96.09
PRK10811	1068	rne ribonuclease E; Reviewed	96.09
KOG2916	304	consensus Translation initiation factor 2, alpha s	96.08
COG0557	706	VacB Exoribonuclease R [Transcription]	95.87
COG0557	706	VacB Exoribonuclease R [Transcription]	95.78
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	95.71
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	94.74
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	94.11
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	93.9
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	93.61
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	93.47
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	93.01
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	91.98
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	91.64
KOG4078	173	consensus Putative mitochondrial ribosomal protein	91.51
COG1530	487	CafA Ribonucleases G and E [Translation, ribosomal	90.94
KOG1004	230	consensus Exosomal 3'-5' exoribonuclease complex s	86.92
PRK12442	87	translation initiation factor IF-1; Reviewed	86.84
TIGR00008	68	infA translation initiation factor IF-1. This fami	86.6
PRK12442	87	translation initiation factor IF-1; Reviewed	86.33
TIGR00008	68	infA translation initiation factor IF-1. This fami	85.32
PRK15464	70	cold shock-like protein CspH; Provisional	84.96
PF00313	66	CSD: 'Cold-shock' DNA-binding domain; InterPro: IP	84.06
PRK10943	69	cold shock-like protein CspC; Provisional	83.36
PRK09937	74	stationary phase/starvation inducible regulatory p	82.89
PRK09507	69	cspE cold shock protein CspE; Reviewed	81.25
COG4044	247	Uncharacterized protein conserved in archaea [Func	80.7

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=3.6e-48  Score=361.37  Aligned_cols=245  Identities=47%  Similarity=0.855  Sum_probs=229.5

Q ss_pred             cCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEE
Q 021034           73 TAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEE  152 (318)
Q Consensus        73 ~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~  152 (318)
                      +.++....|++++|+++|++|+..++.|++++|+|+++.++|++|+++++.+||||.+|+++.++.++.++ +++|++++
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            44567789999999999999876799999999999999999999999999999999999999999999888 99999999


Q ss_pred             EEEEEEeCCCCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCcCCcchhcCCe
Q 021034          153 FVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKD  232 (318)
Q Consensus       153 v~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~~~~~~~vGq~  232 (318)
                      |+|++++++++++.||+|+......|+.+.++++.|.+|+|+|++++++|++|+++|++||||.||+++....+.++|+.
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            99999999999999999998777899999999989999999999999999999999999999999999864434469999


Q ss_pred             EeEEEEEEecccCeEeeehhhhhhh-hHhhcccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCcccccCCC
Q 021034          233 LPLKFVEVDEEQSRLVLSNRKAMAD-SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG  311 (318)
Q Consensus       233 v~~kVl~vd~~~~~i~lS~K~~l~~-~~~~l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~~~~~G  311 (318)
                      ++|+|+++|++++++.||+|+++.+ .+.++++|+++.|+|++|++||+||+++|+.||+|+++++|++..++.+.|++|
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            9999999999999999999988765 467899999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEC
Q 021034          312 DTLKVCL  318 (318)
Q Consensus       312 q~V~v~V  318 (318)
                      |.|+|+|
T Consensus       244 d~VkvkV  250 (318)
T PRK07400        244 DEMKVMI  250 (318)
T ss_pred             CEEEEEE
Confidence            9999986

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

Probab=100.00  E-value=1.4e-45  Score=357.79  Aligned_cols=282  Identities=25%  Similarity=0.386  Sum_probs=243.8

Q ss_pred             ccccccccCCCcc-cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHH
Q 021034            6 QQFTGLRCPPISH-TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLE   84 (318)
Q Consensus         6 ~~~~~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~   84 (318)
                      +++.|| .|-.|+ +|-....          ....|......++-.+..   |.++-..=..+++.-..           
T Consensus       126 ~gvr~F-lP~S~v~~r~v~d~----------~~~~Gk~~~~kiie~d~~---~n~vv~SrR~~~e~~~~-----------  180 (541)
T COG0539         126 EGVRAF-LPGSLVDVRPVRDL----------DPLIGKELEFKILELDKK---RNNVVLSRRAVLEEERS-----------  180 (541)
T ss_pred             CCEEEe-ccHHHhcccccccc----------cccCCceEEEEEEEEccc---cCcEEEEhHHHhhHHHH-----------
Confidence            368899 888888 6555443          456899999999999766   44433222223221111           


Q ss_pred             HHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCe
Q 021034           85 EFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS  164 (318)
Q Consensus        85 ~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~  164 (318)
                         +.-.....++++|++++|+|.+++++||||++++ ++|+||++||||.++.+|++. +++||+|+|+|+++|.+++|
T Consensus       181 ---~~r~e~~~~l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~~rv~~P~~v-vkvGd~VkvkVi~~D~e~~R  255 (541)
T COG0539         181 ---EQREELLNKLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISWKRVDHPSEV-VKVGDEVKVKVISLDEERGR  255 (541)
T ss_pred             ---HHHHHHHhcCCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccccccCCHHHh-cccCCEEEEEEEEEccCCCe
Confidence               1122222377899999999999999999999997 999999999999999999999 99999999999999999999


Q ss_pred             EEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcC--Ccchh--cCCeEeEEEEE
Q 021034          165 LVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS--TAEEL--LGKDLPLKFVE  239 (318)
Q Consensus       165 i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~--~~~~~--vGq~v~~kVl~  239 (318)
                      +.||+|+... .+|+.+.+.+++|+.+.|+|+++.++|+||++. |+.||+|.|+++|.+  .|+++  +||+|.|+|++
T Consensus       256 VsLSlK~l~~-dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~  334 (541)
T COG0539         256 VSLSLKQLEE-DPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLD  334 (541)
T ss_pred             EEEEehhccc-CcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEe
Confidence            9999999987 599999999999999999999999999999997 999999999999973  36776  69999999999


Q ss_pred             EecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEE
Q 021034          240 VDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTL  314 (318)
Q Consensus       240 vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V  314 (318)
                      +|++++||+||+|++..++|    ..+++|+.++|.|.++|++|+||.++ |++||+|.++++|.....+...|++|+.+
T Consensus       335 id~e~rRIsL~iKq~~~~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~le~gidG~vh~~d~sw~~~~~~~~~~k~Gd~v  414 (541)
T COG0539         335 IDPERRRISLGLKQLKENPWEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEV  414 (541)
T ss_pred             eCchhceEEeeehhhhcChhhhhhhhcCCCCeEEEEEeeecccceEEccCCCccceEEHHhcCccccCcHHHhhccCcEE
Confidence            99999999999999987764    45889999999999999999999999 79999999999999988888899999999


Q ss_pred             EEEC
Q 021034          315 KVCL  318 (318)
Q Consensus       315 ~v~V  318 (318)
                      +++|
T Consensus       415 ~~~v  418 (541)
T COG0539         415 EAKV  418 (541)
T ss_pred             EEEE
Confidence            9975

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

Probab=100.00  E-value=1.4e-44  Score=350.75  Aligned_cols=272  Identities=26%  Similarity=0.393  Sum_probs=250.1

Q ss_pred             cccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHH
Q 021034            7 QFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLE   84 (318)
Q Consensus         7 ~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~   84 (318)
                      ++.|| +|..||  .|+.||++         -|++|++|+++|+.+|..   |+++-..||++..               
T Consensus       214 GvdGL-lHiseiS~~rv~~P~~---------vvkvGd~VkvkVi~~D~e---~~RVsLSlK~l~~---------------  265 (541)
T COG0539         214 GVDGL-LHISEISWKRVDHPSE---------VVKVGDEVKVKVISLDEE---RGRVSLSLKQLEE---------------  265 (541)
T ss_pred             CeeeE-EehhhccccccCCHHH---------hcccCCEEEEEEEEEccC---CCeEEEEehhccc---------------
Confidence            79999 999999  99999999         999999999999999988   8888888887652               


Q ss_pred             HHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCe
Q 021034           85 EFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS  164 (318)
Q Consensus        85 ~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~  164 (318)
                         ..|+.....+.+|+.+.|+|+++.++||||+++.+++||+|+|||||.+...|+++ +++||+|+|+|+++|++++|
T Consensus       266 ---dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~ev-v~~Gq~V~V~Vl~id~e~rR  341 (541)
T COG0539         266 ---DPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEV-VKVGQEVEVKVLDIDPERRR  341 (541)
T ss_pred             ---CcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHh-cccCCEEEEEEEeeCchhce
Confidence               36776666778999999999999999999999999999999999999998889999 99999999999999999999


Q ss_pred             EEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcCC---cchh-cCCeEeEEEEE
Q 021034          165 LVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKST---AEEL-LGKDLPLKFVE  239 (318)
Q Consensus       165 i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~~---~~~~-vGq~v~~kVl~  239 (318)
                      +.||||++.. ++|+.+.+.++.|..++|+|++++++|+||.++ |++||+|.++++|...   ...| .|++++++|+.
T Consensus       342 IsL~iKq~~~-~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~le~gidG~vh~~d~sw~~~~~~~~~~k~Gd~v~~~vl~  420 (541)
T COG0539         342 ISLGLKQLKE-NPWEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLA  420 (541)
T ss_pred             EEeeehhhhc-ChhhhhhhhcCCCCeEEEEEeeecccceEEccCCCccceEEHHhcCccccCcHHHhhccCcEEEEEEEE
Confidence            9999999987 599999999999999999999999999999998 6999999999998732   2345 79999999999


Q ss_pred             EecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEE
Q 021034          240 VDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTL  314 (318)
Q Consensus       240 vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V  314 (318)
                      +|++++++.|+.|+...+++    ..++.|++++|+|+++.++|+||+++ ++.||++.++++.+       .|++||.|
T Consensus       421 vd~~~~~isLgiKql~~~p~~~~~~~~~~~~~v~~~v~~i~~~G~~v~l~~~v~G~i~~~~~~~~-------~~~~gd~v  493 (541)
T COG0539         421 VDKEKERISLGIKQLEESPWEEFSEKYKKGSVVKGKVKSVKDKGAFVELGGGVEGLIRLSELSRD-------VLKVGDEV  493 (541)
T ss_pred             EecccceeeeehhhhccCchhhhHhhccCCCeEEEEEEEEccCceEEEecCceeeeeecchhhhh-------hccCCCEE
Confidence            99999999999999876553    56899999999999999999999999 89999999999976       79999999


Q ss_pred             EEEC
Q 021034          315 KVCL  318 (318)
Q Consensus       315 ~v~V  318 (318)
                      +|+|
T Consensus       494 ~a~v  497 (541)
T COG0539         494 EAVV  497 (541)
T ss_pred             EEEE
Confidence            9985

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=6e-43  Score=341.03  Aligned_cols=235  Identities=31%  Similarity=0.543  Sum_probs=217.9

Q ss_pred             CHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCC
Q 021034           82 TLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA  161 (318)
Q Consensus        82 s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~  161 (318)
                      |.++|.++++++...++.|++|+|+|+++.++|++|+++++.+|+||.+|+++....+|++. +++|+.++|+|++++++
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            66788888877666799999999999999999999999989999999999999888888887 99999999999999999


Q ss_pred             CCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcchhcCCeEeEEEEE
Q 021034          162 DDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVE  239 (318)
Q Consensus       162 ~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~~vGq~v~~kVl~  239 (318)
                      ++++.||+|++.....|+.++++++.|++++|+|+++.++|++|++ |++||||.|++++.  .+++.++||+|+|+|++
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            9999999999987789999999998999999999999999999999 79999999999976  45667899999999999


Q ss_pred             EecccCeEeeehhhhhhh--------hHhhcccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCcccccCCC
Q 021034          240 VDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG  311 (318)
Q Consensus       240 vd~~~~~i~lS~K~~l~~--------~~~~l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~~~~~G  311 (318)
                      +|++++++.||+|..+.+        ....+++|+++.|+|+++++||+||+++|+.||||.|+++|.++.+|.+.|++|
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            999999999999976542        246899999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEC
Q 021034          312 DTLKVCL  318 (318)
Q Consensus       312 q~V~v~V  318 (318)
                      |.|+|+|
T Consensus       256 d~V~vkV  262 (486)
T PRK07899        256 QEVTVEV  262 (486)
T ss_pred             CEEEEEE
Confidence            9999986

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=1.3e-43  Score=349.35  Aligned_cols=282  Identities=23%  Similarity=0.343  Sum_probs=240.9

Q ss_pred             ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034            6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL   83 (318)
Q Consensus         6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~   83 (318)
                      ++..|| +|-.|+  -.+.+|+          .+ .|.++.|+|+.+++.   ++++-...+.+++.-.           
T Consensus       136 ~g~~~f-lP~s~~~~~~~~~~~----------~~-vG~~i~~~V~~id~~---~~~v~lSrk~~~~~~~-----------  189 (491)
T PRK13806        136 LGRRAF-CPVSQIDLRYVEDPE----------SY-VGQTFQFLITRVEEN---GRNIVVSRRALLEREQ-----------  189 (491)
T ss_pred             CCEEEE-EEHHHhccccCCChH----------Hc-CCCeEEEEEEEEECC---CCeEEEEeehhhhhhh-----------
Confidence            367888 888876  2244454          33 899999999999866   4444444333332211           


Q ss_pred             HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCC-
Q 021034           84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD-  162 (318)
Q Consensus        84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~-  162 (318)
                         .+.|+.+..++++|++++|+|+++.++|+||+++++.+||+|.+|+++.+..++.+. |++||.++|+|+++|.++ 
T Consensus       190 ---~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~-~~vGd~i~vkVl~id~~~~  265 (491)
T PRK13806        190 ---KEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEA-VSVGDTVRVKVLGIERAKK  265 (491)
T ss_pred             ---HHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHh-cCCCCEEEEEEEEEecccC
Confidence               245555555688999999999999999999999878999999999999999999888 999999999999999876 


Q ss_pred             ---CeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc---CCcchh--cCCeE
Q 021034          163 ---DSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEEL--LGKDL  233 (318)
Q Consensus       163 ---~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~---~~~~~~--vGq~v  233 (318)
                         +++.||+|++.. .+|..+.+.++.|++++|+|+++.++|+||+++ |++||+|.+++++.   .++.++  +||.|
T Consensus       266 ~~~~ri~lS~K~~~~-~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v  344 (491)
T PRK13806        266 GKGLRISLSIKQAGG-DPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAV  344 (491)
T ss_pred             CcceEEEEEehhhhc-ccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEE
Confidence               479999999865 589999888889999999999999999999996 99999999999973   234443  79999


Q ss_pred             eEEEEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCccccc
Q 021034          234 PLKFVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVL  308 (318)
Q Consensus       234 ~~kVl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~  308 (318)
                      +++|+++|++++++.||+|++..++|    .++++|++|+|+|+++++||+||++. |+.||||+|+++|.+..++.+.|
T Consensus       345 ~vkVl~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~~~~~~~~~~  424 (491)
T PRK13806        345 AVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKL  424 (491)
T ss_pred             EEEEEEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCcccccchhhcC
Confidence            99999999999999999999877664    57889999999999999999999998 99999999999999999999999


Q ss_pred             CCCCEEEEEC
Q 021034          309 QPGDTLKVCL  318 (318)
Q Consensus       309 ~~Gq~V~v~V  318 (318)
                      ++||+|+|+|
T Consensus       425 ~~Gd~v~~~V  434 (491)
T PRK13806        425 KPGDSVTLVV  434 (491)
T ss_pred             CCCCEEEEEE
Confidence            9999999986

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=4.6e-43  Score=341.83  Aligned_cols=278  Identities=23%  Similarity=0.330  Sum_probs=240.7

Q ss_pred             ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034            6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL   83 (318)
Q Consensus         6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~   83 (318)
                      ..+.|+ +|-.|+  .+..+|+.         .|++|.+|+|.|+..++.   ++++....+.+.               
T Consensus        57 ~k~eG~-Ip~~Els~~~~~~~~~---------~~~vGd~Ie~~V~~~~~~---~g~liLS~k~~~---------------  108 (486)
T PRK07899         57 YKTEGV-IPSRELSIKHDVDPNE---------VVEVGDEVEALVLQKEDK---EGRLILSKKRAQ---------------  108 (486)
T ss_pred             CCcEEE-EEHHHhcccccCChhh---------cCCCCCEEEEEEEEEECC---CCeEEEEehhhc---------------
Confidence            467899 999999  56788998         899999999999998766   445555555421               


Q ss_pred             HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC
Q 021034           84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD  163 (318)
Q Consensus        84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~  163 (318)
                        +...|+.++...+.|++++|+|+++.++|++|++  +.+||||.+++++.+..++.+   .+|++++|+|+++|.+++
T Consensus       109 --~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl--Gi~gflP~Sel~~~~~~~~~~---~vGq~V~vkVleid~~~~  181 (486)
T PRK07899        109 --YERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI--GLRGFLPASLVEMRRVRDLQP---YIGQEIEAKIIELDKNRN  181 (486)
T ss_pred             --ccchHHHHHHHhcCCCEEEEEEEEEECCeEEEEE--CCEEEEEhhHhcccccCChhh---cCCCEEEEEEEEEECCCC
Confidence              1246776654456899999999999999999999  389999999999887777654   489999999999999999


Q ss_pred             eEEEEeeehhh---hHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcchh--cCCeEeEE
Q 021034          164 SLVLSLRMIQY---ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEEL--LGKDLPLK  236 (318)
Q Consensus       164 ~i~lS~k~~~~---~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~~--vGq~v~~k  236 (318)
                      ++.||+|....   ...|+.+.+.++.|++++|+|+++.++|+||+++|++||||.++++|.  .++.++  +||.|+|+
T Consensus       182 ~ivLSrr~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v~~~~~~~kvGd~V~vk  261 (486)
T PRK07899        182 NVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVE  261 (486)
T ss_pred             EEEEEhHHHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCCHHHhcCCCCEEEEE
Confidence            99999997543   356777777778999999999999999999999999999999999986  345554  79999999


Q ss_pred             EEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCC
Q 021034          237 FVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPG  311 (318)
Q Consensus       237 Vl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~G  311 (318)
                      |+++|+++++|.||+|+...+++    ..+++|+++.|+|+++++||+||++. |+.||+|.+++++.++.++.+.|++|
T Consensus       262 Vl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvG  341 (486)
T PRK07899        262 VLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVG  341 (486)
T ss_pred             EEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCC
Confidence            99999999999999999877765    35778999999999999999999998 99999999999999999999999999


Q ss_pred             CEEEEEC
Q 021034          312 DTLKVCL  318 (318)
Q Consensus       312 q~V~v~V  318 (318)
                      |+|+|+|
T Consensus       342 d~V~VkI  348 (486)
T PRK07899        342 DEVFVKV  348 (486)
T ss_pred             CEEEEEE
Confidence            9999986

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=1.7e-42  Score=356.42  Aligned_cols=280  Identities=21%  Similarity=0.342  Sum_probs=244.5

Q ss_pred             ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034            6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL   83 (318)
Q Consensus         6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~   83 (318)
                      .++.|| ||..++  .+..+|+.         .|++|.+++|+|+..++.   ++++...++...    .          
T Consensus       514 ~Gv~Gf-vp~SeiS~~~v~~~~~---------~~kvGq~v~vkVi~iD~e---~~rI~LSlK~l~----~----------  566 (863)
T PRK12269        514 GGFDGL-LHVNDMSWGHVARPRE---------FVKKGQTIELKVIRLDQA---EKRINLSLKHFQ----P----------  566 (863)
T ss_pred             CCEEEE-EEchhccccccCCHHH---------hccCCCEEEEEEEEEecC---CCeEEEEEeccc----c----------
Confidence            478899 998887  56678876         789999999999999876   556666666542    1          


Q ss_pred             HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccc-ccccCccccCcCCCCEEEEEEEEEeCCC
Q 021034           84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI-HKIKHVEEAGIVPGLKEEFVIIGENEAD  162 (318)
Q Consensus        84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~-~~~~~~~~~~~~~G~~v~v~Vl~vd~~~  162 (318)
                          ..|..+...+++|++++|+|+++.++|+||+++.+.+|++|++|+++ ....+|.+. |++||+++|+|+++|+++
T Consensus       567 ----~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~-~kvGd~V~vkVl~iD~e~  641 (863)
T PRK12269        567 ----DPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDM-VKIGDEVECMILGYDIQA  641 (863)
T ss_pred             ----chhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHc-CCCCCEEEEEEEEEeccc
Confidence                35555555688999999999999999999999888999999999998 567888887 999999999999999999


Q ss_pred             CeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcCC---cch-h-cCCeEeEE
Q 021034          163 DSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKST---AEE-L-LGKDLPLK  236 (318)
Q Consensus       163 ~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~~---~~~-~-vGq~v~~k  236 (318)
                      +++.||+|+... .+|+.+.+.+++|++++|+|++++++|+||+++ |++||||.++++|..+   +++ + +||.|+|+
T Consensus       642 ~rIsLS~K~l~~-~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~kvGq~Vkvk  720 (863)
T PRK12269        642 GRVSLGLKQVTA-NPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECM  720 (863)
T ss_pred             CceEEEehhccc-CchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhccccccchhhccCCCCEEEEE
Confidence            999999999876 499999998999999999999999999999996 9999999999998532   332 4 89999999


Q ss_pred             EEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcc---ccc
Q 021034          237 FVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIA---TVL  308 (318)
Q Consensus       237 Vl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~---~~~  308 (318)
                      |+++|++++++.||+|+...+++    .++++|+++.|+|.+++++|+||++. |+.||+|.++++|++..++.   ..|
T Consensus       721 Vl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~GkV~~v~~~GvFVeL~~gVeGlI~~s~lsdd~~~~~~~~~~~f  800 (863)
T PRK12269        721 VIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRKY  800 (863)
T ss_pred             EEEEeccCCEEEEEecccccChHHHHHhhCCCCCEEEEEEEEEecCeEEEEcCCCeEEEEEHHHcCCcccccchhhcccc
Confidence            99999999999999998876665    34789999999999999999999998 99999999999998765543   469


Q ss_pred             CCCCEEEEEC
Q 021034          309 QPGDTLKVCL  318 (318)
Q Consensus       309 ~~Gq~V~v~V  318 (318)
                      ++||.|+|+|
T Consensus       801 ~vGD~V~v~V  810 (863)
T PRK12269        801 AVGDRVKAVI  810 (863)
T ss_pred             CCCCEEEEEE
Confidence            9999999986

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=2.4e-41  Score=325.62  Aligned_cols=279  Identities=24%  Similarity=0.353  Sum_probs=242.5

Q ss_pred             ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034            6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL   83 (318)
Q Consensus         6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~   83 (318)
                      .+++|+ +|..|+  .++.+|..         .|++|.+|+|+|+.++.+   ++++....+.+.    .          
T Consensus        40 ~~~~g~-lp~~e~~~~~~~~~~~---------~~~vGd~v~~~V~~v~~~---~~~i~lS~k~~~----~----------   92 (390)
T PRK06676         40 YKVEGV-IPISELSNDHIEDIND---------VVKVGDELEVYVLKVEDG---EGNLLLSKRRLE----A----------   92 (390)
T ss_pred             CCcEEE-EEHHHhccccccCccc---------ccCCCCEEEEEEEEEECC---CCCEEEEHHHhh----h----------
Confidence            368899 999998  56788887         899999999999999876   556666666542    1          


Q ss_pred             HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC
Q 021034           84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD  163 (318)
Q Consensus        84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~  163 (318)
                         ...|+++...++.|++++|+|.++.++|++|+++ +.+||+|.+|+++.+..++.+  + +|+++.|+|+++|.+++
T Consensus        93 ---~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~-G~~gflp~~el~~~~~~~~~~--~-vG~~v~~~Vl~~d~~~~  165 (390)
T PRK06676         93 ---EKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVE-GVRGFIPASLISTRFVEDFSD--F-KGKTLEVKIIELDPEKN  165 (390)
T ss_pred             ---hhhHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCccCCChHH--c-CCCEEEEEEEEEECCCC
Confidence               1456666556789999999999999999999996 479999999999988777764  3 89999999999999999


Q ss_pred             eEEEEeeehhhh---HHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcchh--cCCeEeEE
Q 021034          164 SLVLSLRMIQYE---LAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEEL--LGKDLPLK  236 (318)
Q Consensus       164 ~i~lS~k~~~~~---~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~~--vGq~v~~k  236 (318)
                      ++.||+|.....   ..|..+.+.++.|++++|+|+++.++|+||+++|++||+|.+++++.  .++.++  +|+.|+|+
T Consensus       166 ~i~lS~k~~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~  245 (390)
T PRK06676        166 RVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVGQEVEVK  245 (390)
T ss_pred             EEEEEeHHHhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCccccCCHHHhcCCCCEEEEE
Confidence            999999987542   46776666678999999999999999999999999999999999986  345443  79999999


Q ss_pred             EEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCC
Q 021034          237 FVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPG  311 (318)
Q Consensus       237 Vl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~G  311 (318)
                      |+++|++++++.||+|+.+.+++    +++++|++++|+|++++++|+||++. |+.||+|.|+++|.+..++.+.|++|
T Consensus       246 Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~G  325 (390)
T PRK06676        246 VLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEG  325 (390)
T ss_pred             EEEEeCCCCEEEEEEeecccCccccchhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccCChhhccCCC
Confidence            99999999999999998876554    56899999999999999999999998 99999999999999999999999999


Q ss_pred             CEEEEEC
Q 021034          312 DTLKVCL  318 (318)
Q Consensus       312 q~V~v~V  318 (318)
                      |.|+|+|
T Consensus       326 d~v~v~V  332 (390)
T PRK06676        326 QEVKVKV  332 (390)
T ss_pred             CEEEEEE
Confidence            9999986

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=3.2e-40  Score=331.66  Aligned_cols=283  Identities=23%  Similarity=0.377  Sum_probs=241.9

Q ss_pred             ccccccccCCCcccccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHH
Q 021034            6 QQFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEE   85 (318)
Q Consensus         6 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~   85 (318)
                      .++.|| ||-.|+.-  ++.+     .+  .+..|.++.|+|+.++..   ++++-...+.++.....            
T Consensus       135 ~g~~gf-ip~s~~~~--~~~~-----~~--~~~vG~~i~~~V~~~d~~---~~~i~lS~k~~~~~~~~------------  189 (565)
T PRK06299        135 NGVEAF-LPGSQVDV--RPVR-----DT--DPLEGKELEFKVIKLDKK---RNNIVVSRRAVLEEERA------------  189 (565)
T ss_pred             CCEEEE-EEHHHccC--cCCC-----Ch--HHhCCCEEEEEEEEEECC---CCEEEEEhHHhhhhhhh------------
Confidence            388999 99888731  1211     11  356999999999999866   55565555655533222            


Q ss_pred             HHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034           86 FHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL  165 (318)
Q Consensus        86 ~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i  165 (318)
                        ..|..+..++++|++++|+|.++.++|+||+++ +.+|++|.+|+++.++.+|.+. +++||++.|+|+++|++++++
T Consensus       190 --~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~-~kvG~~v~v~V~~~d~~~~~i  265 (565)
T PRK06299        190 --EEREELLENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEV-VNVGDEVKVKVLKFDKEKKRV  265 (565)
T ss_pred             --hHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhc-CCCCCEEEEEEEEEeCCCCeE
Confidence              244444447889999999999999999999998 7999999999999999999888 999999999999999999999


Q ss_pred             EEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc---CCcch-h-cCCeEeEEEEE
Q 021034          166 VLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEE-L-LGKDLPLKFVE  239 (318)
Q Consensus       166 ~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~---~~~~~-~-vGq~v~~kVl~  239 (318)
                      .||+|.... .+|+.+.+.++.|+++.|+|+++.++|+||+++ |+.||+|.++++|.   .++.+ + +||.|+|+|++
T Consensus       266 ~lS~k~~~~-~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~  344 (565)
T PRK06299        266 SLGLKQLGE-DPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLE  344 (565)
T ss_pred             EEEEEeccc-ChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEE
Confidence            999999876 599999888889999999999999999999997 99999999999975   23433 3 79999999999


Q ss_pred             EecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccc-cCcccccCCCCE
Q 021034          240 VDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV-ADIATVLQPGDT  313 (318)
Q Consensus       240 vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~-~~~~~~~~~Gq~  313 (318)
                      +|++++++.||+|++..+++    ..+++|++|.|+|++++++|+||+++ ++.||+|.++++|.+. .++.+.|++||.
T Consensus       345 id~~~~~i~ls~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~  424 (565)
T PRK06299        345 IDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDE  424 (565)
T ss_pred             EcCCCCEEEEehHHhccchhhhHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCE
Confidence            99999999999998866543    46889999999999999999999999 9999999999999876 889999999999


Q ss_pred             EEEEC
Q 021034          314 LKVCL  318 (318)
Q Consensus       314 V~v~V  318 (318)
                      |+|+|
T Consensus       425 v~v~I  429 (565)
T PRK06299        425 VEAVV  429 (565)
T ss_pred             EEEEE
Confidence            99986

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1.4e-39  Score=326.95  Aligned_cols=236  Identities=30%  Similarity=0.473  Sum_probs=215.1

Q ss_pred             CCCCHHHHHHHHhhhc--cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEE
Q 021034           79 VSFTLEEFHSALEKYD--FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVII  156 (318)
Q Consensus        79 ~~~s~~~~~~~~~~~~--~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl  156 (318)
                      ...+.++|+++++++.  .+++.|++++|+|+++.++|++|+++++.+||||.+|++...   +... +++|++++|+|+
T Consensus         8 ~~~~~~~f~~~l~~~~~~~~~~~G~~v~G~V~~v~~~~~~Vdig~k~~g~lp~~e~~~~~---~~~~-~~vG~~i~~~V~   83 (565)
T PRK06299          8 QNDMEESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQ---GELE-VKVGDEVEVYVE   83 (565)
T ss_pred             cccchHHHHHHHHhhcccccCCCCCEEEEEEEEEECCEEEEEeCCCeEEEEEHHHhcCcc---cccc-CCCCCEEEEEEE
Confidence            3445678999998875  568999999999999999999999998899999999998532   2233 899999999999


Q ss_pred             EEeCCCCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcchhcCCeEe
Q 021034          157 GENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLP  234 (318)
Q Consensus       157 ~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~~vGq~v~  234 (318)
                      ++++.++++.||+|++.....|+++.++++.|++++|+|.+++++|++|+++|++||||.+|+++.  .++..++||+++
T Consensus        84 ~~~~~~~~i~lS~k~~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~~~g~~gfip~s~~~~~~~~~~~~~vG~~i~  163 (565)
T PRK06299         84 RIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAFLPGSQVDVRPVRDTDPLEGKELE  163 (565)
T ss_pred             EEECCCCcEEEechHHHHHHHHHHHHHHhhCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHccCcCCCChHHhCCCEEE
Confidence            999989999999999988899999999999999999999999999999999999999999999986  345566999999


Q ss_pred             EEEEEEecccCeEeeehhhhhhh--------hHhhcccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCccc
Q 021034          235 LKFVEVDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIAT  306 (318)
Q Consensus       235 ~kVl~vd~~~~~i~lS~K~~l~~--------~~~~l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~  306 (318)
                      |+|+++|++++++.+|+|+++.+        .+.++++|+++.|+|++++++|+||+++|+.||+|.++++|.++.+|.+
T Consensus       164 ~~V~~~d~~~~~i~lS~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~g~~glv~~se~s~~~~~~~~~  243 (565)
T PRK06299        164 FKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVNHPSE  243 (565)
T ss_pred             EEEEEEECCCCEEEEEhHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEECCEEEEEEHHHhcccccCCHhh
Confidence            99999999999999999998743        2468999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCEEEEEC
Q 021034          307 VLQPGDTLKVCL  318 (318)
Q Consensus       307 ~~~~Gq~V~v~V  318 (318)
                      .|++||+|+|+|
T Consensus       244 ~~kvG~~v~v~V  255 (565)
T PRK06299        244 VVNVGDEVKVKV  255 (565)
T ss_pred             cCCCCCEEEEEE
Confidence            999999999986

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=100.00  E-value=1.8e-39  Score=312.66  Aligned_cols=234  Identities=34%  Similarity=0.605  Sum_probs=216.1

Q ss_pred             HHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEe-CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCC
Q 021034           83 LEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA  161 (318)
Q Consensus        83 ~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i-~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~  161 (318)
                      .++|+++++... ++++|++++|+|.+++++|++|++ +++.+|+||.+|+++....+|.+. +++|+.++|+|++++.+
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            467888887554 899999999999999999999999 878999999999999888888877 99999999999999998


Q ss_pred             CCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcchhcCCeEeEEEEE
Q 021034          162 DDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVE  239 (318)
Q Consensus       162 ~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~~vGq~v~~kVl~  239 (318)
                      ++++.||++++.....|+.+.++++.|++++|+|+++.++|++|+++|++||||.+|+++.  .+++.++|++++|+|++
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            8999999999887789999999999999999999999999999999999999999999976  45667799999999999


Q ss_pred             EecccCeEeeehhhhhhh--------hHhhcccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCcccccCCC
Q 021034          240 VDEEQSRLVLSNRKAMAD--------SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPG  311 (318)
Q Consensus       240 vd~~~~~i~lS~K~~l~~--------~~~~l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~~~~~G  311 (318)
                      +|++++++.||+|.++.+        .+.++++|+++.|+|.+++++|+||+++|+.||+|.++++|.++.++.+.|++|
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            999999999999987542        246789999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEEC
Q 021034          312 DTLKVCL  318 (318)
Q Consensus       312 q~V~v~V  318 (318)
                      |.|+|+|
T Consensus       240 d~i~~~V  246 (390)
T PRK06676        240 QEVEVKV  246 (390)
T ss_pred             CEEEEEE
Confidence            9999986

>TIGR00717 rpsA ribosomal protein S1

Probab=100.00  E-value=2e-40  Score=329.95  Aligned_cols=280  Identities=22%  Similarity=0.355  Sum_probs=241.3

Q ss_pred             ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034            6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL   83 (318)
Q Consensus         6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~   83 (318)
                      .++.|| +|-.++  .+..+|+.         .|++|.++.|+|+.+++.   ++++...++.+.    .          
T Consensus       208 ~g~~g~-lp~~e~s~~~~~~~~~---------~~~vG~~v~v~Vl~~d~~---~~~i~lS~k~~~----~----------  260 (516)
T TIGR00717       208 GGVDGL-LHITDMSWKRVKHPSE---------YVKVGQEVKVKVIKFDKE---KGRISLSLKQLG----E----------  260 (516)
T ss_pred             CCEEEE-EEHHHcCCCCCCCHHH---------hccCCCEEEEEEEEEECC---CCcEEEEEEecc----h----------
Confidence            478899 988887  45666765         799999999999999876   445544444321    1          


Q ss_pred             HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc-cccCccccCcCCCCEEEEEEEEEeCCC
Q 021034           84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH-KIKHVEEAGIVPGLKEEFVIIGENEAD  162 (318)
Q Consensus        84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~-~~~~~~~~~~~~G~~v~v~Vl~vd~~~  162 (318)
                          ..|+.+...+++|++++|+|+++.++|+||+++.+.+||+|.+|+++. ...+|.+. +++||.+.|+|+++|+++
T Consensus       261 ----~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~-~~vG~~v~v~V~~id~~~  335 (516)
T TIGR00717       261 ----DPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKV-VKKGDEVEVMILDIDPER  335 (516)
T ss_pred             ----hHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHh-ccCCCEEEEEEEEEcCCC
Confidence                345555446789999999999999999999998889999999999975 34566666 899999999999999999


Q ss_pred             CeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcC---Ccc-hh-cCCeEeEE
Q 021034          163 DSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS---TAE-EL-LGKDLPLK  236 (318)
Q Consensus       163 ~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~---~~~-~~-vGq~v~~k  236 (318)
                      +++.||+|.+.. .+|..+.+.+..|++++|+|++++++|+||+++ |++||+|.++++|..   ++. .+ +||.|+|+
T Consensus       336 ~~i~lS~k~~~~-~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~  414 (516)
T TIGR00717       336 RRLSLGLKQCKA-NPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAV  414 (516)
T ss_pred             CEEEEEehhccc-CcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEE
Confidence            999999998765 589888877789999999999999999999998 999999999999753   232 34 79999999


Q ss_pred             EEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCC
Q 021034          237 FVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPG  311 (318)
Q Consensus       237 Vl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~G  311 (318)
                      |+++|++++++.||+|++..+++    +++++|++++|+|++++++|+||++. ++.||+|.++++|++..++.+.|++|
T Consensus       415 Vl~vd~~~~~i~ls~K~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~G  494 (516)
T TIGR00717       415 VLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVG  494 (516)
T ss_pred             EEEEeCcCCEEEEeeccccCCchhhhhhccCcceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCccccccccccCCCC
Confidence            99999999999999999766554    56889999999999999999999998 89999999999999999999999999


Q ss_pred             CEEEEEC
Q 021034          312 DTLKVCL  318 (318)
Q Consensus       312 q~V~v~V  318 (318)
                      |.++|+|
T Consensus       495 d~v~~~V  501 (516)
T TIGR00717       495 DEVEAKV  501 (516)
T ss_pred             CEEEEEE
Confidence            9999986

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

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=100.00  E-value=6e-40  Score=337.53  Aligned_cols=281  Identities=20%  Similarity=0.300  Sum_probs=229.5

Q ss_pred             cccccccCCCcccccccccchhHHHHhhhhccCCceeEEEEEEeccch--hHHHHH----HHHHHHHHHHhhcCCCCCCC
Q 021034            7 QFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAET--REREEL----NQLFEEAYERCRTAPMEGVS   80 (318)
Q Consensus         7 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~----~~~i~e~~~~~~~~~~~~~~   80 (318)
                      ++.|| ||-.|+. +.+.+.      +  ..-.|.++++.|+..+...  +++.++    +..+++...           
T Consensus       423 ~~~gf-iP~se~~-~~~~~~------~--~~~vG~~ie~~V~~~~~~~~~~~~~~iVlSrr~~l~e~~~-----------  481 (863)
T PRK12269        423 GMMAF-LPISQSD-CQKVDA------P--ESLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERAR-----------  481 (863)
T ss_pred             CcEEE-EEHHHhc-cccccc------h--HHhCCCeEEEEEEEEecccccCCCCeEEEEHHHHHHHHHH-----------
Confidence            67889 9988861 212121      1  2238889999998765420  011111    222222110           


Q ss_pred             CCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeC
Q 021034           81 FTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENE  160 (318)
Q Consensus        81 ~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~  160 (318)
                             +.++++..++++|++++|+|.++.++|+||+++ +.+||+|.+++++.++.+|.+. +++||+++|+|+++|+
T Consensus       482 -------~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~-~kvGq~v~vkVi~iD~  552 (863)
T PRK12269        482 -------QAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREF-VKKGQTIELKVIRLDQ  552 (863)
T ss_pred             -------HHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEEC-CEEEEEEchhccccccCCHHHh-ccCCCEEEEEEEEEec
Confidence                   122222236789999999999999999999996 6999999999999999999887 8999999999999999


Q ss_pred             CCCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc---CCcchh--cCCeEe
Q 021034          161 ADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEEL--LGKDLP  234 (318)
Q Consensus       161 ~~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~---~~~~~~--vGq~v~  234 (318)
                      +++++.||+|.... .+|..+.+.++.|++++|+|+++.++|+||+++ |++||+|.|+++|.   .++.+.  +||+|+
T Consensus       553 e~~rI~LSlK~l~~-~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~  631 (863)
T PRK12269        553 AEKRINLSLKHFQP-DPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVE  631 (863)
T ss_pred             CCCeEEEEEecccc-chhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEE
Confidence            99999999999765 699999888899999999999999999999997 99999999999983   345553  799999


Q ss_pred             EEEEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccc-cCccccc
Q 021034          235 LKFVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV-ADIATVL  308 (318)
Q Consensus       235 ~kVl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~-~~~~~~~  308 (318)
                      |+|+++|++++++.||+|++..++|    +++++|++++|+|+++++||+||++. |+.||||.++++|.+. .+++..|
T Consensus       632 vkVl~iD~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~~~~~~~~~~~  711 (863)
T PRK12269        632 CMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHEL  711 (863)
T ss_pred             EEEEEEecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhccccccchhhcc
Confidence            9999999999999999999877654    56889999999999999999999998 9999999999999765 4456789


Q ss_pred             CCCCEEEEEC
Q 021034          309 QPGDTLKVCL  318 (318)
Q Consensus       309 ~~Gq~V~v~V  318 (318)
                      ++||.|+|+|
T Consensus       712 kvGq~VkvkV  721 (863)
T PRK12269        712 EVGKEIECMV  721 (863)
T ss_pred             CCCCEEEEEE
Confidence            9999999986

>TIGR00717 rpsA ribosomal protein S1

Probab=100.00  E-value=2.1e-38  Score=315.42  Aligned_cols=281  Identities=23%  Similarity=0.372  Sum_probs=234.4

Q ss_pred             cccccccCCCccc-ccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHH
Q 021034            7 QFTGLRCPPISHT-RLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEE   85 (318)
Q Consensus         7 ~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~   85 (318)
                      ++.|| +|-.|+. +..+ ..         ....|.++.+.|+.++..   ++++-...++++.....            
T Consensus       122 g~~~f-lP~s~~~~~~~~-~~---------~~~vG~~i~~~v~~~~~~---~~~iv~Srk~~l~~~~~------------  175 (516)
T TIGR00717       122 GVEAF-LPGSQVDVKPIK-DL---------DSLIGKTLKFKIIKLDQK---RNNIVVSRRAYLEEERS------------  175 (516)
T ss_pred             CEEEE-EeHHHhcCcccC-ch---------hhhCCCEEEEEEEEEECC---CCcEEEEHHHHHHHHHH------------
Confidence            67899 9988872 2111 11         456999999999999765   33443333333332221            


Q ss_pred             HHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034           86 FHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL  165 (318)
Q Consensus        86 ~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i  165 (318)
                        ..+.....++++|++++|+|.++.++|+||+++ +.+||+|.+|+++....++.+. +++||++.|+|+++|++++++
T Consensus       176 --~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~-g~~g~lp~~e~s~~~~~~~~~~-~~vG~~v~v~Vl~~d~~~~~i  251 (516)
T TIGR00717       176 --QAREELLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEY-VKVGQEVKVKVIKFDKEKGRI  251 (516)
T ss_pred             --HHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCCCCCCHHHh-ccCCCEEEEEEEEEECCCCcE
Confidence              233333346789999999999999999999997 5999999999999988888887 999999999999999999999


Q ss_pred             EEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc---CCcch-h-cCCeEeEEEEE
Q 021034          166 VLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEE-L-LGKDLPLKFVE  239 (318)
Q Consensus       166 ~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~---~~~~~-~-vGq~v~~kVl~  239 (318)
                      .+|+|.... .+|+.+.+.++.|++++|+|+++.++|+||+++ |++||+|.+++++.   .++.+ + +||.++|+|++
T Consensus       252 ~lS~k~~~~-~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~  330 (516)
T TIGR00717       252 SLSLKQLGE-DPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILD  330 (516)
T ss_pred             EEEEEecch-hHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEE
Confidence            999998865 689998887889999999999999999999996 99999999999974   23443 3 89999999999


Q ss_pred             EecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccc-cCcccccCCCCE
Q 021034          240 VDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV-ADIATVLQPGDT  313 (318)
Q Consensus       240 vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~-~~~~~~~~~Gq~  313 (318)
                      +|++++++.||+|++..+++    +++++|+++.|+|++++++|+||+++ |+.||+|.++++|.+. .++...|++||.
T Consensus       331 id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~  410 (516)
T TIGR00717       331 IDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDE  410 (516)
T ss_pred             EcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCE
Confidence            99999999999998766554    46889999999999999999999999 9999999999999764 467789999999


Q ss_pred             EEEEC
Q 021034          314 LKVCL  318 (318)
Q Consensus       314 V~v~V  318 (318)
                      |.|+|
T Consensus       411 V~~~V  415 (516)
T TIGR00717       411 IEAVV  415 (516)
T ss_pred             EEEEE
Confidence            99985

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=1.2e-37  Score=316.44  Aligned_cols=256  Identities=30%  Similarity=0.485  Sum_probs=228.6

Q ss_pred             HHHHHHHHHHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCc
Q 021034           61 NQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV  140 (318)
Q Consensus        61 ~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~  140 (318)
                      ..++++++..+++... -...+.+++.+.|+....++++|++++|+|.++.++|++|+++++.+|+||.+|+++....+|
T Consensus       265 ~~~i~~v~~~l~~~~~-~~~~~~~~~~~~~~~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~  343 (647)
T PRK00087        265 DWIIEEVIKKMSELDN-MEEVEENEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSL  343 (647)
T ss_pred             HHHHHHHHHHHHHhcc-ccccCHHHHHHHHHHHHhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccCCh
Confidence            5677777777765211 112334566666777667899999999999999999999999989999999999999888888


Q ss_pred             cccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccC
Q 021034          141 EEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQIS  220 (318)
Q Consensus       141 ~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls  220 (318)
                      .+. +++|+.++|+|++++++++++.||++.+.....|+.+.++++.|++++|+|+++.++|++|+++|++||||.+|++
T Consensus       344 ~~~-~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lggi~gfiP~sel~  422 (647)
T PRK00087        344 KES-VKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVE  422 (647)
T ss_pred             hhc-cCCCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHhC
Confidence            887 9999999999999999999999999999888899999999999999999999999999999999999999999999


Q ss_pred             Cc--CCcchhcCCeEeEEEEEEecccCe-Eeeehhhhhh--------hhHhhcccCeEEEEEEEEEEcceEEEEECCeEE
Q 021034          221 SK--STAEELLGKDLPLKFVEVDEEQSR-LVLSNRKAMA--------DSQAQLGIGSVVIGTVQSLKPYGAFIDIGGING  289 (318)
Q Consensus       221 ~~--~~~~~~vGq~v~~kVl~vd~~~~~-i~lS~K~~l~--------~~~~~l~~G~~v~G~V~~i~~~G~fV~i~gv~G  289 (318)
                      +.  .++.+++|+.+.|+|+++|+++++ +.+|+|..+.        ..++++++|+++.|+|.+++++|+||+++|+.|
T Consensus       423 ~~~~~d~~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~gv~G  502 (647)
T PRK00087        423 LGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDG  502 (647)
T ss_pred             ccccCCHHHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEECCEEE
Confidence            76  456667999999999999999888 9999999864        235789999999999999999999999999999


Q ss_pred             EEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          290 LLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       290 lv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      |+|.++++|.+..++.+.|++||.|+|+|
T Consensus       503 ll~~sels~~~~~~~~~~~~vGd~V~vkV  531 (647)
T PRK00087        503 LLHVSEISWGRVEKPSDVLKVGDEIKVYI  531 (647)
T ss_pred             EEEHHHcCccccCCHHHhcCCCCEEEEEE
Confidence            99999999999999999999999999986

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

Probab=100.00  E-value=2.7e-38  Score=321.01  Aligned_cols=279  Identities=28%  Similarity=0.391  Sum_probs=238.3

Q ss_pred             ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034            6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL   83 (318)
Q Consensus         6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~   83 (318)
                      ..++|+ +|..|+  .++++|+.         .|++|.+++++|+.++..   ++++..+.+...               
T Consensus       324 ~~~~G~-lp~~els~~~~~~~~~---------~~~vGd~V~v~V~~vd~~---~g~i~LS~k~~~---------------  375 (647)
T PRK00087        324 YKSEGV-IPLRELTLDEISSLKE---------SVKVGDEIEVKVLKLEDE---DGYVVLSKKEAD---------------  375 (647)
T ss_pred             CCeEEE-EEHHHhcccccCChhh---------ccCCCCEEEEEEEEEECC---CCcEEEEeehhc---------------
Confidence            356799 999988  56788887         899999999999999765   345555554331               


Q ss_pred             HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC
Q 021034           84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD  163 (318)
Q Consensus        84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~  163 (318)
                        ....|++....+++|+++.|+|.++.++|++|++++ .+||+|.+|+++.+..++++   .+|+++.|+|+++|++++
T Consensus       376 --~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lgg-i~gfiP~sel~~~~~~d~~~---~vG~~v~v~Vl~vd~e~~  449 (647)
T PRK00087        376 --REKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGG-VRAFLPASHVELGYVEDLSE---YKGQELEVKIIEFNRKRR  449 (647)
T ss_pred             --chhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHhCccccCCHHH---hCCCEEEEEEEEEEcCCC
Confidence              113555555467899999999999999999999986 99999999999988777764   389999999999999988


Q ss_pred             e-EEEEeeehhh---hHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcch-h-cCCeEeE
Q 021034          164 S-LVLSLRMIQY---ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEE-L-LGKDLPL  235 (318)
Q Consensus       164 ~-i~lS~k~~~~---~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~-~-vGq~v~~  235 (318)
                      + +.+|+|....   ...|....+.++.|++++|+|+++.++|+||+++|++||+|.+++++.  .++.+ + +|+.+++
T Consensus       450 ~~l~lS~k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~~~~~~~~~~~vGd~V~v  529 (647)
T PRK00087        450 KKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKVGDEIKV  529 (647)
T ss_pred             cEEEEEeHHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCccccCCHHHhcCCCCEEEE
Confidence            8 9999998753   234444444467999999999999999999999999999999999976  33443 3 7999999


Q ss_pred             EEEEEecccCeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCC
Q 021034          236 KFVEVDEEQSRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQP  310 (318)
Q Consensus       236 kVl~vd~~~~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~  310 (318)
                      +|+++|++++++.||+|+.+.+++    .++++|+++.|.|++++++|+||++. |+.||+|.++++|++..++.+.|++
T Consensus       530 kV~~id~~~~~I~lS~K~~~~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kv  609 (647)
T PRK00087        530 YILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSE  609 (647)
T ss_pred             EEEEEECCCCEEEEEeeccccChhhhhhhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCHhhcCCC
Confidence            999999999999999999876654    56889999999999999999999998 9999999999999999999999999


Q ss_pred             CCEEEEEC
Q 021034          311 GDTLKVCL  318 (318)
Q Consensus       311 Gq~V~v~V  318 (318)
                      ||.|+|+|
T Consensus       610 Gd~V~vkV  617 (647)
T PRK00087        610 GEEVKAKI  617 (647)
T ss_pred             CCEEEEEE
Confidence            99999986

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=100.00  E-value=1.5e-37  Score=306.38  Aligned_cols=274  Identities=26%  Similarity=0.362  Sum_probs=224.6

Q ss_pred             cccccccCCCcccccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHHH
Q 021034            7 QFTGLRCPPISHTRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEF   86 (318)
Q Consensus         7 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~~   86 (318)
                      .+.|+ +|-.++.. ...+.         .+.+|.++.+.|+..+++.     +  .+...+.  ..          ..+
T Consensus        57 k~eg~-ip~~e~~~-~~~~~---------~~~~G~~i~~~Vi~~~~~~-----~--~lS~~~~--~~----------~~~  106 (491)
T PRK13806         57 KVDGV-VDRAELLD-ADGEL---------TVAVGDEVELYVVSVNGQE-----I--RLSKALS--GQ----------GGA  106 (491)
T ss_pred             CcEEE-EEHHHhcC-ccccc---------cccCCCEEEEEEEEEcCCE-----E--EEEhHHh--hh----------hhH
Confidence            45777 77666431 11122         6889999999999886541     1  1111111  00          112


Q ss_pred             HHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034           87 HSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV  166 (318)
Q Consensus        87 ~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~  166 (318)
                      +.+++    .++.|++++|+|.++.++|++|+++ +.+||||.+++++.+..++++   .+|++++|+|+++|++++++.
T Consensus       107 ~~l~~----~~~~g~~v~g~V~~~~~~G~~V~i~-g~~~flP~s~~~~~~~~~~~~---~vG~~i~~~V~~id~~~~~v~  178 (491)
T PRK13806        107 AMLEE----AYENGVPVEGKVTGTCKGGFNVEVL-GRRAFCPVSQIDLRYVEDPES---YVGQTFQFLITRVEENGRNIV  178 (491)
T ss_pred             HHHHH----HHhCCCEEEEEEEEEEcCCEEEEEC-CEEEEEEHHHhccccCCChHH---cCCCeEEEEEEEEECCCCeEE
Confidence            23333    4468999999999999999999998 599999999999988888765   389999999999999999999


Q ss_pred             EEeeehhh---hHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcchh--cCCeEeEEEE
Q 021034          167 LSLRMIQY---ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEEL--LGKDLPLKFV  238 (318)
Q Consensus       167 lS~k~~~~---~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl  238 (318)
                      ||+|....   ...|+.+.+.++.|++++|+|+++.++|+||+++ |++||+|.+|+++.  .++.++  +||.|+|+|+
T Consensus       179 lSrk~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl  258 (491)
T PRK13806        179 VSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVL  258 (491)
T ss_pred             EEeehhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEE
Confidence            99998864   3577777667789999999999999999999996 99999999999986  356664  8999999999


Q ss_pred             EEeccc----CeEeeehhhhhhhhH----hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCc-ccccCccccc
Q 021034          239 EVDEEQ----SRLVLSNRKAMADSQ----AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH-DRVADIATVL  308 (318)
Q Consensus       239 ~vd~~~----~~i~lS~K~~l~~~~----~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~-~~~~~~~~~~  308 (318)
                      ++|.++    +++.||+|++..++|    .++++|+++.|+|+++++||+||+++ |+.||+|.|+++| .++.+|.+.|
T Consensus       259 ~id~~~~~~~~ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~  338 (491)
T PRK13806        259 GIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVV  338 (491)
T ss_pred             EEecccCCcceEEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcC
Confidence            999876    479999999977765    47889999999999999999999998 9999999999999 5678899999


Q ss_pred             CCCCEEEEEC
Q 021034          309 QPGDTLKVCL  318 (318)
Q Consensus       309 ~~Gq~V~v~V  318 (318)
                      ++||.|+|+|
T Consensus       339 ~~Gd~v~vkV  348 (491)
T PRK13806        339 APGDAVAVKI  348 (491)
T ss_pred             CCCCEEEEEE
Confidence            9999999986

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

Probab=99.95  E-value=1.6e-28  Score=252.26  Aligned_cols=284  Identities=19%  Similarity=0.258  Sum_probs=243.8

Q ss_pred             ccccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCH
Q 021034            6 QQFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTL   83 (318)
Q Consensus         6 ~~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~   83 (318)
                      .+|.|+ +|+.|+  .++|+|++         +|..|+.++||||++|..   |.....+++.++.+...          
T Consensus       532 ~ni~g~-lp~~hlsd~~~~~p~~---------~f~v~~~~k~RVl~~~~~---~~~v~l~~K~slv~~~~----------  588 (1710)
T KOG1070|consen  532 GNIKGV-LPKEHLSDHPLQPPLR---------DFKVGSGVKLRVLSVNRD---RNRVALTLKKSLVNTQL----------  588 (1710)
T ss_pred             Cceeee-cChHhhhhcccccccc---------eeeeccccEEEEEEEEcc---CCeeEEEechhhhcccC----------
Confidence            469999 999999  88999999         999999999999999876   78899999999988843          


Q ss_pred             HHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC
Q 021034           84 EEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD  163 (318)
Q Consensus        84 ~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~  163 (318)
                          +.-.+|+ ++.+|+++.|+|..+.++||||.|.+++.||+|.++|++.++.+++++ |.+||++.+.|+++|+++.
T Consensus       589 ----plp~d~~-~~~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~eh-f~vGqTv~~~i~nvd~ek~  662 (1710)
T KOG1070|consen  589 ----PLPSDFE-QAIPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEH-FPVGQTVRAKIVNVDDEKR  662 (1710)
T ss_pred             ----CCccchh-hcCCCceEEEEEeeeccCCeEEEecCccccccchhhhhhhhhcChhhh-cccccEEEEEEEecCchhc
Confidence                3445555 677999999999999999999999999999999999999999999999 9999999999999999999


Q ss_pred             eEEEEeeehhh-hHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcC---------C----cc-
Q 021034          164 SLVLSLRMIQY-ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKS---------T----AE-  226 (318)
Q Consensus       164 ~i~lS~k~~~~-~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~---------~----~~-  226 (318)
                      ++.+|||.+.. ........+.+..|.+.++.+...+++.++|++.  |+.|.+-..||.|..         +    .+ 
T Consensus       663 rm~l~~r~s~~~~a~~~~~~e~~~~g~v~s~~~~~~tkd~viVei~~~~~~~v~~~~~L~dg~v~~~~~~~~kl~~~t~~  742 (1710)
T KOG1070|consen  663 RMPLGLRASSCARACVKRSVENFVKGGVKSLKSIDKTKDSVIVEIVDQGITGVGVFGELVDGSVVVNKVLENKLRKNTSL  742 (1710)
T ss_pred             eeehhhhhhhhHHHHHHHHHHHhhccccccceeehhccccEEEEccCcceEEEEEEEEEccCceEEccchhhhhhhcchh
Confidence            99999999874 3333444444557788999999999999999995  799999999999751         1    11 


Q ss_pred             -hh-cCCeEeEEEEEEecccCeEeeehhhhhhhh----------------------------------------------
Q 021034          227 -EL-LGKDLPLKFVEVDEEQSRLVLSNRKAMADS----------------------------------------------  258 (318)
Q Consensus       227 -~~-vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~----------------------------------------------  258 (318)
                       .+ +||...++|++++..+.-+.+|.++-|...                                              
T Consensus       743 ~~lv~gq~~~~~i~~isl~k~lv~~s~~~~L~~~~~~l~k~~~~~~~v~~is~~~~~~a~~~~~i~~v~~s~~v~s~~~d  822 (1710)
T KOG1070|consen  743 LHLVVGQVTVGVILSISLKKSLVLISLCTDLPNNATKLLKGSYALALVRSISKEGKFVAFVSNLIALVKVSHLVDSELDD  822 (1710)
T ss_pred             heeeecceeEEEEEEeehhhhhhhccccccccchHHHHhcCchhHHHHHhhhhheeheeecccccceeeccccccccccc
Confidence             12 599999999999987777777765422100                                              


Q ss_pred             ---------------------------------------------------------HhhcccCeEEEEEEEEEEcceEE
Q 021034          259 ---------------------------------------------------------QAQLGIGSVVIGTVQSLKPYGAF  281 (318)
Q Consensus       259 ---------------------------------------------------------~~~l~~G~~v~G~V~~i~~~G~f  281 (318)
                                                                               ..++..|++++++|++|.|+++-
T Consensus       823 ~~~~~y~Q~v~~~~~st~~~~~~~~~a~e~p~~K~~~~~~~~~~~~~d~~Vd~a~k~~~~~~igsiv~a~v~svKp~~L~  902 (1710)
T KOG1070|consen  823 LTKAEYGQSVTVKLLSTEPKVVKDLKAVEKPKKKKEKKFIKVSSNDSDNEVDLAIKSTEDLSIGSIVRAYVKSVKPDQLN  902 (1710)
T ss_pred             cceeeeecccceEEEecChhHHHHHHhhcchhhccceeEEEeccccCCCccccccccccceeeeeEEEEEEeeecccceE
Confidence                                                                     15788999999999999999999


Q ss_pred             EEEC-CeEEEEecCCcCcc--cccCcccccCCCCEEEEEC
Q 021034          282 IDIG-GINGLLHVSQISHD--RVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       282 V~i~-gv~Glv~~s~ls~~--~~~~~~~~~~~Gq~V~v~V  318 (318)
                      |.++ ++.|-+|+|++-++  -+.+|.+.|++||.|.|||
T Consensus       903 v~l~~~~~gri~isev~d~~~eitDp~~k~~vG~~I~vrv  942 (1710)
T KOG1070|consen  903 VLLAANHHGRIHISEVLDNLHEITDPLDKFKVGDGIFVRV  942 (1710)
T ss_pred             EeccccccCceehHHhhccccccCChhhhcccCCeEEEEE
Confidence            9999 99999999999886  4678999999999999986

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.95  E-value=1.1e-26  Score=217.10  Aligned_cols=212  Identities=22%  Similarity=0.290  Sum_probs=169.5

Q ss_pred             cccccccCCCcc--cccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHH
Q 021034            7 QFTGLRCPPISH--TRLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLE   84 (318)
Q Consensus         7 ~~~~~~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~   84 (318)
                      ...|| +|-.++  .+..+|+.         .|++|.+|.|.|+..+++   .+++..-++++.    .           
T Consensus        54 k~~g~-lp~sEis~~~~~~~~~---------~~~~G~~v~~~Vi~~~~~---~~~i~lS~k~~~----~-----------  105 (318)
T PRK07400         54 KTAAF-MPIQEMSINRVEGPEE---------VLQPNETREFFILSDENE---DGQLTLSIRRIE----Y-----------  105 (318)
T ss_pred             CeEEE-EEHHHhccccccCHHH---------ccCCCCEEEEEEEEEeCC---CCeEEEehhhhh----h-----------
Confidence            35788 776666  22345554         799999999999998765   344444444431    1           


Q ss_pred             HHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCe
Q 021034           85 EFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDS  164 (318)
Q Consensus        85 ~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~  164 (318)
                        ...|++.....+.|++++|+|+++.++|++|+++ +++||+|.+++++.+..   +  ..+|+.+.|+|+++|+++++
T Consensus       106 --~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~-Gv~gfip~s~ls~~~~~---~--~~vG~~i~~kVl~id~~~~~  177 (318)
T PRK07400        106 --MRAWERVRQLQKEDATVRSEVFATNRGGALVRIE-GLRGFIPGSHISTRKPK---E--ELVGEELPLKFLEVDEERNR  177 (318)
T ss_pred             --hhHHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCccCCc---c--ccCCCEEEEEEEEEEcccCE
Confidence              1356666545567999999999999999999996 69999999999985422   2  35999999999999999999


Q ss_pred             EEEEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCcC--Ccch-h-cCCeEeEEEEEE
Q 021034          165 LVLSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS--TAEE-L-LGKDLPLKFVEV  240 (318)
Q Consensus       165 i~lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~~--~~~~-~-vGq~v~~kVl~v  240 (318)
                      +.||+|++..+..    .+.++.|+++.|+|+++.++|+||+++|+.||+|.+++++..  ++.+ + +||.++|+|+++
T Consensus       178 i~lS~K~~~~~~~----~~~~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~i  253 (318)
T PRK07400        178 LVLSHRRALVERK----MNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDL  253 (318)
T ss_pred             EEEEhhHhhhhhh----hccCCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccccccChhhccCCCCEEEEEEEEE
Confidence            9999997765322    233579999999999999999999999999999999999873  3444 3 799999999999


Q ss_pred             ecccCeEeeehhhhhhhh
Q 021034          241 DEEQSRLVLSNRKAMADS  258 (318)
Q Consensus       241 d~~~~~i~lS~K~~l~~~  258 (318)
                      |.+++++.||+|+...++
T Consensus       254 D~e~~rI~LS~K~l~~~P  271 (318)
T PRK07400        254 DAERGRISLSTKQLEPEP  271 (318)
T ss_pred             eCCCCEEEEEEeccccCh
Confidence            999999999999976554

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

Probab=99.83  E-value=8.9e-20  Score=188.50  Aligned_cols=259  Identities=21%  Similarity=0.264  Sum_probs=213.1

Q ss_pred             ccccccchhHHHHhhhhccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHHHHHHHhhhccCCCC
Q 021034           20 RLSRRKSITQIQQKLLNSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSEL   99 (318)
Q Consensus        20 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~   99 (318)
                      -|-+||+         +|+.|..+.|-|+.-+..            ..+.++                 -..+.++...+
T Consensus      1026 ~le~~e~---------~F~~g~al~~~V~~~~~~------------~tv~~i-----------------G~~~~~k~~s~ 1067 (1710)
T KOG1070|consen 1026 VLELPES---------LFPLGKALDEYVVRNDKS------------KTVRAI-----------------GFSKSDKNPSP 1067 (1710)
T ss_pred             hhhCchh---------hcccccceeeEEecccce------------eEEEec-----------------ccccCCCCCCc
Confidence            3778999         999999999999977422            010000                 01222335569


Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEe-CcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh----
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLP-TQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY----  174 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp-~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~----  174 (318)
                      |+++-|+|.++.+++++++++.+..|-.. +.+|++.+..+|.++ |..++.+-+.++.++..++.+.||++.+..    
T Consensus      1068 G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~~~~P~~~-f~~~~~v~~~~L~vs~~n~~leLslr~sr~~~t~ 1146 (1710)
T KOG1070|consen 1068 GDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSYSMTPVEH-FTKIQIVYVCVLSVSALNKGLELSLRESRTKITP 1146 (1710)
T ss_pred             chhhcceeeeeccceeEEecCCccccceEEeeehhccccCChHHh-cccccEEEEEEEEEecccccceeecccccccCcc
Confidence            99999999999999999999888888444 558888888899888 999999999999999887779999994332    


Q ss_pred             ----hHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCCeEeEEEEEEecccC
Q 021034          175 ----ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGKDLPLKFVEVDEEQS  245 (318)
Q Consensus       175 ----~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq~v~~kVl~vd~~~~  245 (318)
                          +.....+++ ++.|+++.|.|.++.+.|+|+.++ ++.||+|.+++++.  +.+++ + +||.+.++|+.+++..+
T Consensus      1147 ~~~kd~~iks~eD-lk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~ 1225 (1710)
T KOG1070|consen 1147 VDSKDGSIKSIED-LKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSK 1225 (1710)
T ss_pred             ccccCCcccchhh-cccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCc
Confidence                112233444 469999999999999999999998 99999999999976  33443 4 79999999999999999


Q ss_pred             eEeeehhhhhhh-------hHhhcccCeEEEEEEEEEEcceEEEEEC-C--eEEEEecCCcCcccccCcccccCCCCEEE
Q 021034          246 RLVLSNRKAMAD-------SQAQLGIGSVVIGTVQSLKPYGAFIDIG-G--INGLLHVSQISHDRVADIATVLQPGDTLK  315 (318)
Q Consensus       246 ~i~lS~K~~l~~-------~~~~l~~G~~v~G~V~~i~~~G~fV~i~-g--v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~  315 (318)
                      |+.||+|++-..       .+.++++|+...|+|.+..++|+||++. +  +.|++|.++.++.+..+....|+.|+.|.
T Consensus      1226 riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~g~~~~~e~~d~~~e~it~~~~~~~~V~ 1305 (1710)
T KOG1070|consen 1226 RIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMVGLCHISEEADDRGENITALYYAGDRVK 1305 (1710)
T ss_pred             eEEEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEEEecCcceecccccceeecchhhhhcccceeccceee
Confidence            999999986332       2478999999999999999999999998 3  69999999999999999999999999999


Q ss_pred             EEC
Q 021034          316 VCL  318 (318)
Q Consensus       316 v~V  318 (318)
                      |.+
T Consensus      1306 a~~ 1308 (1710)
T KOG1070|consen 1306 ACV 1308 (1710)
T ss_pred             eEe
Confidence            864

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

Probab=99.70  E-value=2.7e-15  Score=133.23  Aligned_cols=192  Identities=19%  Similarity=0.166  Sum_probs=155.0

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCe-EEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKS-SAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~-~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      +..+|++..+.|.+..++|+|++-+... .-+||.++..+.        ...+||+|++.|.  -+.++++++|.+.+..
T Consensus         2 ~~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~~--------e~evGdev~vFiY--~D~~~rl~aTt~~p~~   71 (287)
T COG2996           2 MIKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEED--------ELEVGDEVTVFIY--VDSEDRLIATTREPKA   71 (287)
T ss_pred             cccccceEEEEEEEeeceeEEEecCCCceEEeccccCCcCC--------ccccCcEEEEEEE--ECCCCceeheeecceE
Confidence            4679999999999999999999986543 678888876332        1679999999994  3567899999998876


Q ss_pred             hHHHHHHhhhcCCCcEEEEEEEEEE-cCeEEEEEC-CEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeeehh
Q 021034          175 ELAWERCRQLQSEDVVVKGKVVGAN-KGGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNR  252 (318)
Q Consensus       175 ~~~~~~~~~~~~~G~iv~g~V~~v~-~~G~~V~i~-gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K  252 (318)
                                 ..|..-.++|++++ +-|+|+++| .-+.++|.+++...+.++.-+|+.+-|.+ .+|.+ +|+.-.++
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 -----------TVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLKSLWPQKGDKLLVYL-YVDKK-GRIWGTLA  138 (287)
T ss_pred             -----------eecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccccccCCCCCCEEEEEE-EEccC-CcEEEEec
Confidence                       48999999999998 889999998 78999999999976665556899998884 57754 57776654


Q ss_pred             hh--hhhhHhhcc---cCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          253 KA--MADSQAQLG---IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       253 ~~--l~~~~~~l~---~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .-  +.+......   .|+.|+|+|++....|.||-.. +.-||||.||....        ++.||.+++||
T Consensus       139 ~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~--------prlG~~l~~rV  202 (287)
T COG2996         139 IEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAE--------PRLGERLTARV  202 (287)
T ss_pred             chhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhccc--------ccCCceEEEEE
Confidence            32  222222222   2999999999999999999998 99999999997644        78999999986

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.70  E-value=3.1e-17  Score=151.35  Aligned_cols=121  Identities=18%  Similarity=0.168  Sum_probs=110.9

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeC--CCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhh
Q 021034           98 ELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE  175 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~--~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~  175 (318)
                      ++|++|.|+|.++.++|+||++.  ++.+||||.||+|+.++.+++++ +++||++.|+|+++|++++++.||+|+...+
T Consensus        16 ~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~-vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~~   94 (319)
T PTZ00248         16 EEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKL-IRVGRHEVVVVLRVDKEKGYIDLSKKRVSPE   94 (319)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHh-cCCCCEEEEEEEEEeCCCCEEEEEeeecccc
Confidence            37999999999999999999994  57999999999999999999998 9999999999999999999999999999886


Q ss_pred             HHHHHHhhhcCCCcEEEEEEEEEE-cCeEEEE-------ECCEEEEEeCcccC
Q 021034          176 LAWERCRQLQSEDVVVKGKVVGAN-KGGVVAE-------VEGLRGFVPFSQIS  220 (318)
Q Consensus       176 ~~~~~~~~~~~~G~iv~g~V~~v~-~~G~~V~-------i~gl~gfip~s~ls  220 (318)
                       +|..+.+.++.|++++|+|..+. +.|++++       +.+.++|.|..+..
T Consensus        95 -pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af  146 (319)
T PTZ00248         95 -DIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDAL  146 (319)
T ss_pred             -hHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHH
Confidence             99999999999999999999994 5899987       34788888877654

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.65  E-value=2.9e-17  Score=151.59  Aligned_cols=128  Identities=17%  Similarity=0.282  Sum_probs=112.7

Q ss_pred             CCcEEEEEEEEEEcCeEEEEE---CCEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhhhhhhhH
Q 021034          187 EDVVVKGKVVGANKGGVVAEV---EGLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRKAMADSQ  259 (318)
Q Consensus       187 ~G~iv~g~V~~v~~~G~~V~i---~gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~~  259 (318)
                      .|++|.|+|+++.++|+||+|   +|+.||||.|+++++  .+++++  +||++.|+|+++|+++++|.||.|+...++|
T Consensus        17 ~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~~pw   96 (319)
T PTZ00248         17 EDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSPEDI   96 (319)
T ss_pred             CCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecccchH
Confidence            799999999999999999999   489999999999987  566665  7999999999999999999999999877665


Q ss_pred             ----hhcccCeEEEEEEEEEEc-ceEEEE------EC-CeEEEEecCCcCcccccCcccccC---CCCEE
Q 021034          260 ----AQLGIGSVVIGTVQSLKP-YGAFID------IG-GINGLLHVSQISHDRVADIATVLQ---PGDTL  314 (318)
Q Consensus       260 ----~~l~~G~~v~G~V~~i~~-~G~fV~------i~-gv~Glv~~s~ls~~~~~~~~~~~~---~Gq~V  314 (318)
                          ..++.|++++|.|+++.+ +|+|++      .. .+.++.|..++....+.+|.+.|.   +++.+
T Consensus        97 ~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af~~~v~~~~evl~~l~i~~ev  166 (319)
T PTZ00248         97 EACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDNVFEGLDIPEEV  166 (319)
T ss_pred             HHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHhcCchhhhccCCCCHHH
Confidence                678899999999999965 999998      33 789999999998888888887776   55543

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

Probab=99.55  E-value=7.1e-15  Score=115.66  Aligned_cols=77  Identities=18%  Similarity=0.349  Sum_probs=73.7

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      .+++|++++|+|+.++++||||++.++..|++|+||+++.++++..++ +++||.|.|+|+++|. +|++.||+|.+..
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            578999999999999999999999988999999999999999999999 9999999999999997 9999999999876

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

Probab=99.54  E-value=8.5e-14  Score=102.48  Aligned_cols=73  Identities=22%  Similarity=0.338  Sum_probs=69.2

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      ++.|+++.|+|.++.++|+||+++++.+||||.+|+++.+..++.+. +++||++.|+|+++|.+++++.+|+|
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            57899999999999999999999988999999999999888888887 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 ....

>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=99.53  E-value=5.6e-14  Score=103.74  Aligned_cols=71  Identities=13%  Similarity=0.138  Sum_probs=65.1

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCc---cccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV---EEAGIVPGLKEEFVIIGENEADDSLVLS  168 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~---~~~~~~~G~~v~v~Vl~vd~~~~~i~lS  168 (318)
                      +++|+++.|+|.++.++|+||+++.+.+||+|++|+++.++.++   .+. |++||.++|+|+++|++++++.||
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            47899999999999999999999989999999999999886665   356 999999999999999999999886

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.

>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=99.49  E-value=1.2e-13  Score=104.17  Aligned_cols=79  Identities=15%  Similarity=0.165  Sum_probs=72.3

Q ss_pred             HHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034           89 ALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (318)
Q Consensus        89 ~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS  168 (318)
                      ++..+. ++++|+++.|+|.++.++|+||+++++.+||+|.+++++.+..++.+. |++||+++|+|+++|.+++++.||
T Consensus         5 l~~~~~-~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~-~~~Gd~v~vkV~~id~~~~~i~ls   82 (83)
T cd04461           5 LPTNFS-DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFG-FKKGQSVTAKVTSVDEEKQRFLLS   82 (83)
T ss_pred             chhhHH-hCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHh-cCCCCEEEEEEEEEcCCCCEEEEe
Confidence            444554 789999999999999999999999888999999999999988888887 999999999999999999999998


Q ss_pred             e
Q 021034          169 L  169 (318)
Q Consensus       169 ~  169 (318)
                      +
T Consensus        83 l   83 (83)
T cd04461          83 L   83 (83)
T ss_pred             C
Confidence            5

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

>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=99.46  E-value=6.1e-13  Score=98.13  Aligned_cols=71  Identities=18%  Similarity=0.250  Sum_probs=64.4

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC-CCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~-~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      +++.|+++.|+|.++.++|+||+++ ++..||+|.+|+++.      +. +++||.+.|+|+++|++++++.||+|+..
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            4689999999999999999999997 579999999999875      23 89999999999999999999999999764

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

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

Probab=99.46  E-value=3.9e-13  Score=97.85  Aligned_cols=70  Identities=24%  Similarity=0.356  Sum_probs=65.9

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      |+++.|+|.++.++|+||+++++.+||+|.+++++.+..++.+. +++||.++|+|+++|++++++.||+|
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            78999999999999999999888999999999998888888877 99999999999999999999999985

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

>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=99.44  E-value=6.7e-13  Score=97.73  Aligned_cols=70  Identities=20%  Similarity=0.254  Sum_probs=65.2

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccc--ccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK--IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~--~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      |++++|+|.++.++|++|.++.+++|++|.+++++..  ..++.+. |++||.++|+|+++|++++++.||.+
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            7899999999999999999988899999999999763  6778777 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.

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

Probab=99.44  E-value=7.4e-14  Score=109.96  Aligned_cols=58  Identities=36%  Similarity=0.714  Sum_probs=56.0

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .+++|++++|+|++|++||+||+|. |-+||||+|++++.++.++.+.+++||.|+|+|
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKV   60 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKV   60 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEE
Confidence            4789999999999999999999998 899999999999999999999999999999986

>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=99.42  E-value=3e-13  Score=99.83  Aligned_cols=57  Identities=23%  Similarity=0.346  Sum_probs=53.1

Q ss_pred             cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCc---ccccCCCCEEEEEC
Q 021034          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADI---ATVLQPGDTLKVCL  318 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~---~~~~~~Gq~V~v~V  318 (318)
                      +++|++|.|+|++++++|+||+++ ++.|++|.+++||.++.+|   .+.|++||.|+|+|
T Consensus         1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kV   61 (74)
T cd05705           1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKV   61 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEE
Confidence            578999999999999999999998 9999999999999987765   58999999999986

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.

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

Probab=99.40  E-value=2.2e-12  Score=93.96  Aligned_cols=70  Identities=33%  Similarity=0.444  Sum_probs=66.1

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      |+++.|+|.++.++|++|+++++.+|+||.+|+++.+..++.+. +++||.++|+|++++++++++.||++
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            78999999999999999999888999999999999888888887 99999999999999988899999985

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.

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

Probab=99.39  E-value=2.3e-12  Score=93.15  Aligned_cols=65  Identities=40%  Similarity=0.775  Sum_probs=59.4

Q ss_pred             CcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCc--CCcchhcCCeEeEEEEEEecccCeEeeehh
Q 021034          188 DVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSK--STAEELLGKDLPLKFVEVDEEQSRLVLSNR  252 (318)
Q Consensus       188 G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~--~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K  252 (318)
                      |++++|+|+++.++|++|+++|++||+|.+|+++.  .++..++||.++|+|+++|.+++++.||+|
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            68999999999999999999999999999999965  345556999999999999999999999986

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.

>PRK07252 hypothetical protein; Provisional

Probab=99.39  E-value=2.5e-12  Score=103.59  Aligned_cols=81  Identities=21%  Similarity=0.263  Sum_probs=74.8

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHH
Q 021034           98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELA  177 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~  177 (318)
                      ++|+++.|+|+++.++|+||+++++..|++|.+++++.+..++.+. +++||.+.|+|+++|.+.+++.+|++....+..
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~-~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~~   80 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQL-LKVGEEVLVQVVDFDEYTGKASLSLRTLEEEKQ   80 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhc-cCCCCEEEEEEEEEeCCCCEEEEEEeecccCcc
Confidence            5799999999999999999999888999999999999888888777 999999999999999999999999999988656


Q ss_pred             HH
Q 021034          178 WE  179 (318)
Q Consensus       178 ~~  179 (318)
                      |.
T Consensus        81 ~~   82 (120)
T PRK07252         81 HF   82 (120)
T ss_pred             cc
Confidence            64

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

Probab=99.38  E-value=2.7e-12  Score=93.22  Aligned_cols=69  Identities=28%  Similarity=0.430  Sum_probs=64.5

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~  169 (318)
                      |+++.|+|.++.++|++|+++++.+||+|.+++++.+..++.+. +++||.++|+|+++|.+++++.||+
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            78999999999999999999888999999999999887777776 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 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=99.38  E-value=5.5e-12  Score=92.58  Aligned_cols=73  Identities=16%  Similarity=0.142  Sum_probs=67.3

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      +++|+++.|+|.++.++|++|++..+.+|++|.+++++.+..++.+. |++||.++++|+++|.+++++.||++
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            46899999999999999999999988999999999998877777776 99999999999999999999999975

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.

>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=99.37  E-value=3.4e-12  Score=93.72  Aligned_cols=71  Identities=20%  Similarity=0.179  Sum_probs=65.5

Q ss_pred             CCCCCEEEEEEEEEEC-CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034           97 SELGTKVKGTVFCTDN-RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~-~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      +++|+++.|+|.++.+ .|++++++.+.+|++|++++++.+..++.+. +++||.++|+|++++.  +++.||+|
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 7999999989999999999999999998887 9999999999999974  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.

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

Probab=99.36  E-value=7.6e-12  Score=91.99  Aligned_cols=68  Identities=31%  Similarity=0.600  Sum_probs=61.4

Q ss_pred             cCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcc-hh-cCCeEeEEEEEEecccCeEeeehh
Q 021034          185 QSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAE-EL-LGKDLPLKFVEVDEEQSRLVLSNR  252 (318)
Q Consensus       185 ~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~-~~-vGq~v~~kVl~vd~~~~~i~lS~K  252 (318)
                      ++.|++++|+|.+++++|+||+++ +++||||.+++++.  .++. .+ +||++.|+|+++|++++++.||+|
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 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence            368999999999999999999998 99999999999986  3333 34 799999999999999999999987

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 ....

>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=99.36  E-value=4.7e-12  Score=92.65  Aligned_cols=69  Identities=22%  Similarity=0.233  Sum_probs=63.7

Q ss_pred             CCEEE-EEEEEE-ECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034          100 GTKVK-GTVFCT-DNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (318)
Q Consensus       100 G~iv~-G~V~~i-~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~  169 (318)
                      |++++ |+|+++ .++|+||++.++.+||+|.+++++....++.+. +++||.++++|+++|+.++++.||+
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 699999999878999999999998887877776 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.

>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=99.36  E-value=4.3e-12  Score=93.61  Aligned_cols=67  Identities=22%  Similarity=0.362  Sum_probs=60.9

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcCCcchh-cCCeEeEEEEEEecccCeEeeehhhhh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVEVDEEQSRLVLSNRKAM  255 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~vd~~~~~i~lS~K~~l  255 (318)
                      +.|+++.|+|+++.++|+||+++  |+.||+|.+++++.   ..+ +||.+.|+|+++|++++++.||+|+..
T Consensus         3 ~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~---~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~   72 (74)
T cd05694           3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF---SKLKVGQLLLCVVEKVKDDGRVVSLSADPSK   72 (74)
T ss_pred             CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc---cccCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence            58999999999999999999996  89999999999986   333 799999999999999999999998753

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). 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=99.35  E-value=4e-12  Score=92.09  Aligned_cols=68  Identities=18%  Similarity=0.191  Sum_probs=64.1

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS  168 (318)
                      |+++.|+|.++.++|+||+++++.+||+|.+++++.+..++.+. +++||.++|+|+++|++++++.||
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            78999999999999999999888999999999999888888887 999999999999999999999876

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.

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

Probab=99.35  E-value=9e-12  Score=92.03  Aligned_cols=73  Identities=22%  Similarity=0.236  Sum_probs=67.6

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeCC--CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034           98 ELGTKVKGTVFCTDNRGALVDITA--KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~~--~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~  171 (318)
                      +.|+++.|+|.++.++|+||++.+  +.+|++|.+++++.+..++.+. |++||.+.++|+++|.+++++.||+|+
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  4899999999999988888887 999999999999999989999999874

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

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

Probab=99.33  E-value=1.1e-11  Score=90.78  Aligned_cols=72  Identities=22%  Similarity=0.318  Sum_probs=67.6

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      |+++.|+|.++.++|++|+++++.+|++|.+++++.+..++.+. |++||.++|+|+++|.+++++.||+|..
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            78999999999999999999888999999999999888888887 9999999999999999889999999874

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.

>PRK08582 hypothetical protein; Provisional

Probab=99.32  E-value=1.3e-11  Score=101.98  Aligned_cols=82  Identities=20%  Similarity=0.332  Sum_probs=74.0

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE  175 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~  175 (318)
                      .+++|+++.|+|+++.++|+||+++++..|++|++++++.++.++.+. +++||.|+|+|++++. ++++.||++++...
T Consensus         2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~-l~vGD~VkvkV~~id~-~gkI~LSlk~~~~~   79 (139)
T PRK08582          2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDH-LKVGDEVEVKVLNVED-DGKIGLSIKKAKDR   79 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccc-cCCCCEEEEEEEEECC-CCcEEEEEEecccC
Confidence            467999999999999999999999988999999999999888888777 9999999999999986 58999999998653


Q ss_pred             HHHHH
Q 021034          176 LAWER  180 (318)
Q Consensus       176 ~~~~~  180 (318)
                       +|..
T Consensus        80 -~~~~   83 (139)
T PRK08582         80 -PKRQ   83 (139)
T ss_pred             -chhh
Confidence             6653

>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=99.31  E-value=3.8e-12  Score=95.94  Aligned_cols=64  Identities=30%  Similarity=0.501  Sum_probs=59.4

Q ss_pred             hhhhHhhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          255 MADSQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       255 l~~~~~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +...+.++++|+++.|+|.+++++|+||+++ ++.||+|.+++++++..++.+.|++||+|+|+|
T Consensus         5 l~~~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV   69 (83)
T cd04461           5 LPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKV   69 (83)
T ss_pred             chhhHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEE
Confidence            3445678999999999999999999999998 999999999999999999999999999999986

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.

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

Probab=99.30  E-value=1.8e-11  Score=88.35  Aligned_cols=67  Identities=30%  Similarity=0.470  Sum_probs=60.7

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      |++++|+|.++.++|++|++ ++.+||+|.++++..+..++.+   .+||.++|+|+++|.+++++.||+|
T Consensus         1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~~~~~---~vG~~i~~~i~~vd~~~~~i~lS~k   67 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDE---YVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCChHH---hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            78999999999999999999 5799999999999877666654   4899999999999998999999985

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.

>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=99.30  E-value=2.4e-11  Score=89.81  Aligned_cols=74  Identities=19%  Similarity=0.304  Sum_probs=68.0

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034           98 ELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      ++|+++.|+|.++.++|+||++.+ +.+|++|.+++++.+..++.+. |++||.++|+|+++|.+++++.+|+|.+
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            369999999999999999999974 7999999999998887777777 9999999999999999999999999875

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.

>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=99.30  E-value=1.4e-11  Score=90.73  Aligned_cols=65  Identities=31%  Similarity=0.421  Sum_probs=58.0

Q ss_pred             CcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc----CCcc-hh-cCCeEeEEEEEEecccCeEeeehh
Q 021034          188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK----STAE-EL-LGKDLPLKFVEVDEEQSRLVLSNR  252 (318)
Q Consensus       188 G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~----~~~~-~~-vGq~v~~kVl~vd~~~~~i~lS~K  252 (318)
                      |++++|+|+++.++|+||+++ +++||+|.+++++.    .++. .+ +||.++|+|+++|++++++.||+|
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            689999999999999999996 99999999999864    2333 34 899999999999999999999986

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=99.30  E-value=3.8e-12  Score=93.42  Aligned_cols=57  Identities=25%  Similarity=0.538  Sum_probs=54.1

Q ss_pred             cccCeEEEEEEEEEEc-ceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          262 LGIGSVVIGTVQSLKP-YGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~-~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +++|++|.|+|.++.+ +|+||+++ |.+|++|+|+++|++..+|.+.|++||.|+|+|
T Consensus         1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV   59 (72)
T cd05704           1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCI   59 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEE
Confidence            4689999999999996 89999998 999999999999999999999999999999986

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

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

Probab=99.27  E-value=3.6e-11  Score=88.44  Aligned_cols=70  Identities=24%  Similarity=0.305  Sum_probs=63.5

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034           98 ELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~  169 (318)
                      +.|++++|+|.++.++|+||++.+ +.+|++|++|+++.+..++.+. +++||++.|+|+++|.++ ++.||+
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            579999999999999999999954 3799999999999888888887 999999999999999865 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.

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

Probab=99.27  E-value=2.5e-11  Score=87.48  Aligned_cols=66  Identities=17%  Similarity=0.092  Sum_probs=58.6

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS  168 (318)
                      |++++|+|.++.++|++|++.++.+||+|.+|++.....  .+. |++|+.++|+|+++|++++++.||
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            789999999999999999997779999999999765433  344 999999999999999999998886

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.

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

Probab=99.27  E-value=3e-11  Score=86.94  Aligned_cols=69  Identities=22%  Similarity=0.355  Sum_probs=64.3

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      |+++.|+|.++.++|+||+++.+.+||+|.+++++.+..++.+. +++||.+.++|++++. ++++.+|+|
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            78999999999999999999988999999999998888888777 9999999999999998 899999985

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.

>PHA02945 interferon resistance protein; Provisional

Probab=99.26  E-value=4.1e-11  Score=89.12  Aligned_cols=74  Identities=15%  Similarity=0.222  Sum_probs=67.5

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEe--CCCeEEEEeCccc--ccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034           97 SELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEA--CIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i--~~~~~g~lp~sEl--s~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      .++|+++.|+|.. .++|+||++  +++.+||+|.||.  +..++++ .++ + .||++.|+|+.+|+.+|.+-||+|+.
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            4789999999999 999999999  5589999999965  9999999 887 7 99999999999999999999999986


Q ss_pred             hh
Q 021034          173 QY  174 (318)
Q Consensus       173 ~~  174 (318)
                      ..
T Consensus        85 ~~   86 (88)
T PHA02945         85 CR   86 (88)
T ss_pred             cc
Confidence            53

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

Probab=99.26  E-value=1.5e-11  Score=90.41  Aligned_cols=56  Identities=36%  Similarity=0.570  Sum_probs=52.9

Q ss_pred             ccCeEEEEEEEEEEcceEEEEECC--eEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIGG--INGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~g--v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ..|+++.|.|.++++||+||++.|  .+||+|.++++|.+..++.+.|++||+|+|+|
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv   59 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKV   59 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEE
Confidence            479999999999999999999975  79999999999999999999999999999985

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.

>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=99.24  E-value=2.6e-11  Score=94.70  Aligned_cols=76  Identities=14%  Similarity=0.156  Sum_probs=67.4

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc-------------------cCccccCcCCCCEEEEEEEE
Q 021034           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI-------------------KHVEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~-------------------~~~~~~~~~~G~~v~v~Vl~  157 (318)
                      +++|+++.|+|.++.+.|++|++.++..||+|.+++++.+.                   .++.+. |++||.+.|+|++
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            46899999999999999999999888999999999998653                   235566 9999999999999


Q ss_pred             EeCC---CCeEEEEeeehh
Q 021034          158 ENEA---DDSLVLSLRMIQ  173 (318)
Q Consensus       158 vd~~---~~~i~lS~k~~~  173 (318)
                      +|++   ++++.||+|+..
T Consensus        80 ~d~~~~~~~~i~LSlr~~~   98 (100)
T cd05693          80 LDKSKSGKKRIELSLEPEL   98 (100)
T ss_pred             ccCCcCCCcEEEEEecHHH
Confidence            9987   789999999864

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.

>PRK08059 general stress protein 13; Validated

Probab=99.21  E-value=1.1e-10  Score=94.69  Aligned_cols=78  Identities=19%  Similarity=0.300  Sum_probs=72.3

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      ++++|+++.|+|.++.++|++|+++.+.+|++|.++++..+..++.+. +++||.+.|+|+++|.+++++.+|++....
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            467999999999999999999999988999999999998888777776 899999999999999999999999999865

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

Probab=99.21  E-value=2.8e-11  Score=107.30  Aligned_cols=77  Identities=21%  Similarity=0.271  Sum_probs=73.4

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEe--CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034           97 SELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i--~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      .+.|++|-|||.++.++|+||.+  +++.+||+|+||++..++++..++ +++||.+-|+|+++|+++|.+-||+|+...
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            57899999999999999999998  678999999999999999999999 999999999999999999999999999876

>PRK05807 hypothetical protein; Provisional

Probab=99.21  E-value=1.2e-10  Score=95.86  Aligned_cols=75  Identities=20%  Similarity=0.312  Sum_probs=69.1

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      .+++|++++|+|..+.++|+||++. +..|++|++|+++.++.++.+. +++||.++|+|++++. ++++.||+|...
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            4578999999999999999999994 6899999999999999888877 9999999999999987 799999999975

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

Probab=99.21  E-value=7.5e-11  Score=89.40  Aligned_cols=76  Identities=21%  Similarity=0.170  Sum_probs=66.0

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccc----ccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI----HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~----~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~  171 (318)
                      .+++|+++.|+|+++.++|++|+++++.+|+||.+|+++    .+..+..+. +++||.+.|+|++++++ +++.||++.
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            457999999999999999999999989999999999985    333455555 89999999999999865 899999988


Q ss_pred             hh
Q 021034          172 IQ  173 (318)
Q Consensus       172 ~~  173 (318)
                      ..
T Consensus        81 ~~   82 (86)
T cd05789          81 LK   82 (86)
T ss_pred             cc
Confidence            64

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".

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

Probab=99.21  E-value=9.2e-11  Score=88.16  Aligned_cols=75  Identities=21%  Similarity=0.198  Sum_probs=68.2

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      ..++|+++.|+|+++.+++++|+++++.+|++|.++++..+..+..+. +++||.+.|+|++++++ +++.||++..
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            357999999999999999999999999999999999998777777776 99999999999999876 8999999874

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".

>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=99.21  E-value=2.6e-11  Score=87.76  Aligned_cols=54  Identities=28%  Similarity=0.517  Sum_probs=52.1

Q ss_pred             CeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       265 G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      |+++.|+|+++.++|+||++. ++.||+|.+++++++..++.+.|++||.++|+|
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v   55 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKI   55 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEE
Confidence            789999999999999999998 899999999999999999999999999999986

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.

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

Probab=99.21  E-value=1.2e-10  Score=83.89  Aligned_cols=72  Identities=28%  Similarity=0.422  Sum_probs=65.7

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034           98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      ++|+++.|+|.++.++|++|+++++..|++|.+++...+..++.+. +++||.+.|+|++++.+++++.+|++
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            3699999999999999999999988999999999998876666666 99999999999999988899999975

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

Probab=99.20  E-value=7.9e-11  Score=85.27  Aligned_cols=68  Identities=18%  Similarity=0.317  Sum_probs=61.5

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccc-ccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI-HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~-~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS  168 (318)
                      |+++.|+|.++.++|+||++.++.+|++|.+++++ ....++.+. |++||.+.|+|+++|.+++++.||
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            78999999999999999999888999999999985 456677776 999999999999999999998775

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.

>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=99.20  E-value=4.8e-11  Score=87.55  Aligned_cols=57  Identities=16%  Similarity=0.416  Sum_probs=53.9

Q ss_pred             cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +++|+++.|+|++++++|+||+++ +++|++|.++++|++..++.+.|++||.++|+|
T Consensus         1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V   58 (73)
T cd05706           1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACV   58 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEE
Confidence            468999999999999999999999 999999999999998888899999999999986

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.

>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=99.20  E-value=7.5e-11  Score=85.74  Aligned_cols=65  Identities=29%  Similarity=0.552  Sum_probs=58.1

Q ss_pred             CcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCCeEeEEEEEEecccCeEeeehh
Q 021034          188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGKDLPLKFVEVDEEQSRLVLSNR  252 (318)
Q Consensus       188 G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq~v~~kVl~vd~~~~~i~lS~K  252 (318)
                      |+++.|+|+++.++|+||+++ ++.||+|.+++++.  .++.+ + +||.++|+|+++|++++++.||+|
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            689999999999999999996 89999999999865  34444 3 799999999999999999999975

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.

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

Probab=99.20  E-value=9.1e-11  Score=84.58  Aligned_cols=63  Identities=19%  Similarity=0.330  Sum_probs=55.6

Q ss_pred             CcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc-CCcchh-cCCeEeEEEEEEecccCeEeee
Q 021034          188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK-STAEEL-LGKDLPLKFVEVDEEQSRLVLS  250 (318)
Q Consensus       188 G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~-~~~~~~-vGq~v~~kVl~vd~~~~~i~lS  250 (318)
                      |++++|+|+++.++|++|++. +++||+|.+|++.. ...+.+ +|++++|+|+++|++++++.||
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 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCcccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            689999999999999999995 89999999999854 224455 8999999999999999999887

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.

>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=99.19  E-value=1.1e-10  Score=84.83  Aligned_cols=64  Identities=25%  Similarity=0.466  Sum_probs=56.8

Q ss_pred             CcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcc-hh-cCCeEeEEEEEEecccCeEeeeh
Q 021034          188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAE-EL-LGKDLPLKFVEVDEEQSRLVLSN  251 (318)
Q Consensus       188 G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~-~~-vGq~v~~kVl~vd~~~~~i~lS~  251 (318)
                      |++++|+|+++.++|++|+++ +++||+|.+++++.  .++. .+ +||.++|+|+++|++++++.||+
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            689999999999999999996 89999999999976  2333 34 79999999999999999999984

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.19  E-value=6.1e-11  Score=122.41  Aligned_cols=125  Identities=17%  Similarity=0.164  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHHHH-hhcCCCCCCC---CCHHHHHHH---HhhhccCCCCCCEEE-EEEEEEECCeEEEEeCCCeEEEEeC
Q 021034           58 EELNQLFEEAYER-CRTAPMEGVS---FTLEEFHSA---LEKYDFNSELGTKVK-GTVFCTDNRGALVDITAKSSAYLPT  129 (318)
Q Consensus        58 ~~~~~~i~e~~~~-~~~~~~~~~~---~s~~~~~~~---~~~~~~~~~~G~iv~-G~V~~i~~~G~~V~i~~~~~g~lp~  129 (318)
                      +.|++|+++.-.. ++-.+.+.+.   .+.+.++.+   ++.+..+.++|+++. |+|+++.++|+||++..+.+||||+
T Consensus       705 ktIk~I~eetg~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHI  784 (891)
T PLN00207        705 KKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHI  784 (891)
T ss_pred             hhHHHHHHHHCCCccCcCCCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEh
Confidence            5889999997666 4444444443   233333333   455545788999996 6999999999999998889999999


Q ss_pred             cccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHHHhhhc
Q 021034          130 QEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCRQLQ  185 (318)
Q Consensus       130 sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~~~~  185 (318)
                      +|+++.++.++++. +++||.|+|+|+++|. ++++.||+|.... .+|+...+..
T Consensus       785 SeLs~~rv~~~~dv-~kvGD~V~VkVi~ID~-~grI~LSlK~l~~-~Pw~~~~~~~  837 (891)
T PLN00207        785 SELSSNWLAKPEDA-FKVGDRIDVKLIEVND-KGQLRLSRRALLP-EANSEKSSQK  837 (891)
T ss_pred             hhcCCccccCHHHh-cCCCCEEEEEEEEECC-CCcEEEEEecccc-Cchhhhhhhh
Confidence            99999999999888 9999999999999997 7899999999765 5999886643

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

Probab=99.19  E-value=3.7e-11  Score=87.00  Aligned_cols=54  Identities=33%  Similarity=0.735  Sum_probs=50.6

Q ss_pred             CeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCc-ccccCcccccCCCCEEEEEC
Q 021034          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH-DRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       265 G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~-~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      |+++.|+|.++++||+||++. +++||+|.++++| .+..++.+.|++||+|+|+|
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v   56 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVV   56 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEE
Confidence            789999999999999999998 9999999999997 57788999999999999985

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.

>PRK08582 hypothetical protein; Provisional

Probab=99.19  E-value=5e-11  Score=98.54  Aligned_cols=57  Identities=33%  Similarity=0.689  Sum_probs=54.9

Q ss_pred             cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +++|++|.|+|++|+++|+||+|+ +++||||.++++|+++.++.+.|++||.|+|+|
T Consensus         3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV   60 (139)
T PRK08582          3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKV   60 (139)
T ss_pred             CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEE
Confidence            678999999999999999999998 999999999999999999999999999999986

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

Probab=99.18  E-value=4.1e-11  Score=91.39  Aligned_cols=58  Identities=36%  Similarity=0.649  Sum_probs=54.3

Q ss_pred             hcccCeEEEEEEEEEEcc--eEEEEEC-CeEEEEecCCcCc---ccccCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPY--GAFIDIG-GINGLLHVSQISH---DRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~--G~fV~i~-gv~Glv~~s~ls~---~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .+++|+++.|.|++|.++  |+||+++ |..||+|.|+++|   .++.++.+.+++||.|.|+|
T Consensus         4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV   67 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQV   67 (88)
T ss_pred             cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEE
Confidence            467899999999999997  9999999 9999999999999   77889999999999999986

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

>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=99.17  E-value=1.3e-10  Score=84.99  Aligned_cols=64  Identities=28%  Similarity=0.349  Sum_probs=55.9

Q ss_pred             CcEEE-EEEEEE-EcCeEEEEEC-CEEEEEeCcccCCc--CC-cchh-cCCeEeEEEEEEecccCeEeeeh
Q 021034          188 DVVVK-GKVVGA-NKGGVVAEVE-GLRGFVPFSQISSK--ST-AEEL-LGKDLPLKFVEVDEEQSRLVLSN  251 (318)
Q Consensus       188 G~iv~-g~V~~v-~~~G~~V~i~-gl~gfip~s~ls~~--~~-~~~~-vGq~v~~kVl~vd~~~~~i~lS~  251 (318)
                      |++++ |+|+++ .++|+||++. |++||+|.|++++.  .+ .+.+ +||.++++|+++|+.++++.||+
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            67888 999998 6999999996 89999999999865  22 3345 89999999999999999999985

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.

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

Probab=99.16  E-value=1.5e-10  Score=83.06  Aligned_cols=68  Identities=24%  Similarity=0.316  Sum_probs=62.8

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS  168 (318)
                      |+++.|+|.++.++|+||+++.+..|++|.+++++.+..++.+. +++||.+.|+|+++|.+++++.||
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            78999999999999999999888999999999998877777776 899999999999999988998876

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

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

Probab=99.16  E-value=1.9e-10  Score=82.68  Aligned_cols=68  Identities=24%  Similarity=0.331  Sum_probs=62.6

Q ss_pred             CCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034           99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (318)
Q Consensus        99 ~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS  168 (318)
                      +|+++.|+|.++.++|++|+++ +.+|++|.+|+++.+..++.+. |++||.+.|+|+++|.+++++.||
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            4899999999999999999997 5999999999998878788777 999999999999999988998876

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=99.16  E-value=4.4e-10  Score=109.96  Aligned_cols=122  Identities=14%  Similarity=0.121  Sum_probs=91.4

Q ss_pred             eEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHH-----HHHHhhhcC--CCcEEEEEE
Q 021034          123 SSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELA-----WERCRQLQS--EDVVVKGKV  195 (318)
Q Consensus       123 ~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~-----~~~~~~~~~--~G~iv~g~V  195 (318)
                      ..+.+|++++...   +|.   +.+|+.+.+.|...+  -+|+.++..+....+.     ++.+.+.|+  .|++|+|+|
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---DPD---AEVGDYIEEEIESVD--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVV  142 (470)
T ss_pred             CcceeeHHHHhhh---Ccc---ccCCCeEEEEEcccc--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEE
Confidence            4477777766432   232   789999999997765  4454444333322223     345666665  899999999


Q ss_pred             EEEEcCeEEEEECCEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccC--eEeeehhhh
Q 021034          196 VGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQS--RLVLSNRKA  254 (318)
Q Consensus       196 ~~v~~~G~~V~i~gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~--~i~lS~K~~  254 (318)
                      .++.++|++|+++|+.||||.++++.+..+  .+|+.++++|++++++++  .|.||++..
T Consensus       143 ~ri~~~giiVDLggvea~LP~sE~ip~E~~--~~GdrIka~I~~Vd~~~kg~qIilSRt~p  201 (470)
T PRK09202        143 KRVERGNIIVDLGRAEAILPRKEQIPRENF--RPGDRVRAYVYEVRKEARGPQIILSRTHP  201 (470)
T ss_pred             EEEecCCEEEEECCeEEEecHHHcCCCccC--CCCCEEEEEEEEEecCCCCCeEEEEeCcH
Confidence            999999999999999999999999744221  289999999999998877  899999875

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

Probab=99.15  E-value=1e-10  Score=85.59  Aligned_cols=57  Identities=30%  Similarity=0.629  Sum_probs=51.9

Q ss_pred             cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcc-cccCcccccCCCCEEEEEC
Q 021034          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHD-RVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~-~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +++|+++.|.|.+++++|+||++. +++||+|.++++|. +..++.+.|++||+|+|+|
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v   59 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMV   59 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEE
Confidence            468999999999999999999998 89999999999985 5557888999999999985

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.

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

Probab=99.14  E-value=2.6e-10  Score=82.05  Aligned_cols=68  Identities=21%  Similarity=0.312  Sum_probs=62.8

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~  169 (318)
                      |+++.|+|.++.++|+||+++.+..||+|.+++++.+..++.+. +++||.+.|+|.++|+ ++++.+|+
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            78999999999999999999888999999999998887777776 9999999999999998 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.

>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=99.14  E-value=3.9e-10  Score=84.10  Aligned_cols=72  Identities=15%  Similarity=0.271  Sum_probs=64.9

Q ss_pred             CCEEEEEEEEEECCeEEEEeC---CCeEEEEeCcccccccc-cCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034          100 GTKVKGTVFCTDNRGALVDIT---AKSSAYLPTQEACIHKI-KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~---~~~~g~lp~sEls~~~~-~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      |+++.|+|.++.++|+||+++   .+..||+|.+++++.+. .++.+. |++||.+.|+|+++|  ++++.+|+|....
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            789999999999999999997   35899999999998875 788777 999999999999998  7899999998653

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.

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

Probab=99.13  E-value=3.5e-10  Score=102.96  Aligned_cols=84  Identities=21%  Similarity=0.276  Sum_probs=74.7

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEeCC--CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034           97 SELGTKVKGTVFCTDNRGALVDITA--KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i~~--~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      +++|+++.|+|.++.++|+||++..  +.+||||.+|++..+..++.+. +++||.+.|+|+++|.+++++.||+|....
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            5789999999999999999999953  6999999999999888888887 999999999999999999999999998776


Q ss_pred             hHHHHHH
Q 021034          175 ELAWERC  181 (318)
Q Consensus       175 ~~~~~~~  181 (318)
                      .+.|+.+
T Consensus        85 ~e~~~~~   91 (262)
T PRK03987         85 HQRREKI   91 (262)
T ss_pred             chHHHHH
Confidence            5444433

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

Probab=99.12  E-value=3.8e-09  Score=94.36  Aligned_cols=146  Identities=20%  Similarity=0.178  Sum_probs=114.3

Q ss_pred             CCCCCCEEEEEEEEEE-CCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034           96 NSELGTKVKGTVFCTD-NRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~-~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      .+.+|+.-.++|+.+. +.|+|||.|-.-+.++|.+|+....     +.=+++|+.+-|.+. +| .++|+..+++... 
T Consensus        70 ~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~-----~~wpq~Gd~l~v~l~-~D-kk~Ri~g~~a~~~-  141 (287)
T COG2996          70 KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLK-----SLWPQKGDKLLVYLY-VD-KKGRIWGTLAIEK-  141 (287)
T ss_pred             eEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhccccc-----ccCCCCCCEEEEEEE-Ec-cCCcEEEEecchh-
Confidence            5678999999999999 7899999998899999999986421     111578999998873 44 4668887776543 


Q ss_pred             hHHHHHHhh-hcC--CCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeee
Q 021034          175 ELAWERCRQ-LQS--EDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLS  250 (318)
Q Consensus       175 ~~~~~~~~~-~~~--~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS  250 (318)
                        ..+.+.. .+.  .++.++|+|.+....|.||-.+ +..||||.|+..-..    .+|+.++++|+.+.+ .+++.||
T Consensus       142 --~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~p----rlG~~l~~rVi~~re-Dg~lnLS  214 (287)
T COG2996         142 --ILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAEP----RLGERLTARVIGVRE-DGKLNLS  214 (287)
T ss_pred             --HHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhcccc----cCCceEEEEEEEEcc-CCeeecc
Confidence              2222222 221  3789999999999999999986 999999999865432    389999999999987 8999999


Q ss_pred             hhhhhh
Q 021034          251 NRKAMA  256 (318)
Q Consensus       251 ~K~~l~  256 (318)
                      .++...
T Consensus       215 l~p~~~  220 (287)
T COG2996         215 LRPRAH  220 (287)
T ss_pred             cccccH
Confidence            998643

>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=2.1e-10  Score=84.69  Aligned_cols=56  Identities=27%  Similarity=0.482  Sum_probs=53.0

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC---CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~---gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ++|+++.|+|.++.++|+||++.   |+.||+|.++++|++..++.+.|++||.|+|+|
T Consensus         2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv   60 (76)
T cd04452           2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKV   60 (76)
T ss_pred             CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEE
Confidence            57999999999999999999995   599999999999999999999999999999985

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

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

Probab=99.10  E-value=5.6e-10  Score=85.10  Aligned_cols=75  Identities=17%  Similarity=0.170  Sum_probs=64.7

Q ss_pred             CCCCCCEEEEEEEEEECC--eEEEEeCCCeEEEEeCccccc---ccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034           96 NSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACI---HKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~--G~~V~i~~~~~g~lp~sEls~---~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      .++.|+++.|+|+++.++  ||||+++.+.+||||.+|+++   .++.++.+. +++||.+.|.|++....+....||.+
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  999999988999999999998   556677776 99999999999998766666777765


Q ss_pred             e
Q 021034          171 M  171 (318)
Q Consensus       171 ~  171 (318)
                      -
T Consensus        83 ~   83 (88)
T cd04453          83 I   83 (88)
T ss_pred             E
Confidence            4

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

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

Probab=99.10  E-value=6.3e-10  Score=81.31  Aligned_cols=70  Identities=19%  Similarity=0.253  Sum_probs=61.2

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc-cccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034           98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH-KIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~-~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS  168 (318)
                      .+|+++.|+|.++.++|+||++..+.+|++|.+++++. ...++.+. +++||.+.|+|+++|.+++++.+|
T Consensus         2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~-~~~Gd~v~v~v~~id~~~~~i~~~   72 (72)
T cd05689           2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKV-VSLGDEVEVMVLDIDEERRRISLG   72 (72)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccE-eCCCCEEEEEEEEeeCCcCEEeCC
Confidence            58999999999999999999998789999999999864 33355555 899999999999999988888764

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.

>PRK07252 hypothetical protein; Provisional

Probab=99.08  E-value=2.8e-10  Score=91.72  Aligned_cols=56  Identities=36%  Similarity=0.725  Sum_probs=53.7

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ++|+++.|+|.+|+++|+||++. ++.||+|.+++++++..++.+.|++||.|+|+|
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI   58 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQV   58 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEE
Confidence            57999999999999999999998 899999999999999999999999999999986

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=99.07  E-value=4.1e-10  Score=113.55  Aligned_cols=112  Identities=22%  Similarity=0.224  Sum_probs=89.3

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccccc
Q 021034           59 ELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK  138 (318)
Q Consensus        59 ~~~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~  138 (318)
                      .+++|+.+.....++...++-.++-   .+-..+.. ++++|++++|+|.++.++|+||++|-+.+|++|+|++++.+++
T Consensus       622 Tl~dIi~eL~kp~rdpR~~f~~~~~---~~~v~~i~-dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~  697 (780)
T COG2183         622 TLEDIILELEKPGRDPRDEFHTPTL---DEGVESIT-DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVK  697 (780)
T ss_pred             hHHHHHHHhhcCCCCCcccccccch---hhhhhhHh-hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcC
Confidence            3455555555555554333222222   22223333 8999999999999999999999999999999999999999999


Q ss_pred             CccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhh
Q 021034          139 HVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE  175 (318)
Q Consensus       139 ~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~  175 (318)
                      +|.+. +++||.|+|+|+++|..++++.||++.....
T Consensus       698 ~P~~v-v~vGdiV~v~V~~vD~~r~rI~Lsmr~~~~~  733 (780)
T COG2183         698 DPNEV-VKVGDIVKVKVIEVDTARKRIALSMRLDEEE  733 (780)
T ss_pred             ChHHh-cccCCEEEEEEEEEecccCeeeeEeeccCCc
Confidence            99988 9999999999999999999999999988753

>PRK05807 hypothetical protein; Provisional

Probab=99.07  E-value=3.9e-10  Score=92.92  Aligned_cols=57  Identities=37%  Similarity=0.670  Sum_probs=54.7

Q ss_pred             cccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +++|++|.|+|+.|+++|+||++.+..||+|++++++.++.++.+.|++||.|+|+|
T Consensus         3 ~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV   59 (136)
T PRK05807          3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKV   59 (136)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCccccCCCCCEEEEEE
Confidence            678999999999999999999999899999999999999999999999999999986

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

Probab=99.06  E-value=3.7e-10  Score=81.17  Aligned_cols=54  Identities=59%  Similarity=1.037  Sum_probs=51.8

Q ss_pred             CeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       265 G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      |+++.|+|.+++++|+||+++ +..||+|.+++++++..++.+.|++||.++|+|
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v   55 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKV   55 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEE
Confidence            789999999999999999999 999999999999999999999999999999985

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.06  E-value=2.3e-10  Score=115.84  Aligned_cols=120  Identities=19%  Similarity=0.183  Sum_probs=93.6

Q ss_pred             eEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCC---CHHHHHHH---Hhhhcc--CCCCCCEEEEEEEEEECCe
Q 021034           43 IVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSF---TLEEFHSA---LEKYDF--NSELGTKVKGTVFCTDNRG  114 (318)
Q Consensus        43 ~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~---s~~~~~~~---~~~~~~--~~~~G~iv~G~V~~i~~~G  114 (318)
                      -|-+-++...+    +.|+.++++.=..++-.+.+.+.+   +.+....+   ++.+..  .+++|++++|+|+++.++|
T Consensus       587 ~ki~~vIG~gG----k~I~~i~~~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfG  662 (719)
T TIGR02696       587 DKIGEVIGPKG----KMINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFG  662 (719)
T ss_pred             HHhhheeCCCc----HhHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECce
Confidence            34455666555    699999999877777766666543   33333332   333333  4789999999999999999


Q ss_pred             EEEEeCCCeEEEEeCcccc----cccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034          115 ALVDITAKSSAYLPTQEAC----IHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (318)
Q Consensus       115 ~~V~i~~~~~g~lp~sEls----~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS  168 (318)
                      +||++..+.+||||+||++    +.++.++.+. +++||.|+|+|+++|. ++++.|+
T Consensus       663 aFVel~~G~eGLvHISeisdls~~~rv~~~~dv-~kvGd~V~VKVl~ID~-~gKI~L~  718 (719)
T TIGR02696       663 AFVSLLPGKDGLLHISQIRKLAGGKRVENVEDV-LSVGQKIQVEIADIDD-RGKLSLV  718 (719)
T ss_pred             EEEEecCCceEEEEhhhccccccccCcCCHHHc-CCCCCEEEEEEEEECC-CCCeeec
Confidence            9999988899999999996    4678899988 9999999999999995 7788775

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=99.06  E-value=8.7e-10  Score=113.32  Aligned_cols=113  Identities=17%  Similarity=0.235  Sum_probs=91.4

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCCC---HHHHH---HHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcc
Q 021034           58 EELNQLFEEAYERCRTAPMEGVSFT---LEEFH---SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQE  131 (318)
Q Consensus        58 ~~~~~~i~e~~~~~~~~~~~~~~~s---~~~~~---~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sE  131 (318)
                      ..|++|+++.-..++-.+.+.+..+   .+..+   ++++.+..++++|+++.|+|+++.++|+||++.++.+|++|+++
T Consensus       574 ~~ik~I~~~~~~~idi~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSe  653 (693)
T PRK11824        574 KTIREITEETGAKIDIEDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISE  653 (693)
T ss_pred             hhHHHHHHHHCCccccCCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeee
Confidence            5789999987665555444444332   23332   23344445788999999999999999999999888999999999


Q ss_pred             cccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034          132 ACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus       132 ls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      +++.++.++.+. +++||.++|+|+++|++ +++.||+|..
T Consensus       654 ls~~~v~~~~~v-~kvGD~V~VkV~~iD~~-grI~LS~k~~  692 (693)
T PRK11824        654 IADERVEKVEDV-LKEGDEVKVKVLEIDKR-GRIRLSRKAV  692 (693)
T ss_pred             ccCccccCccce-eCCCCEEEEEEEEECCC-CcEEEEEEec
Confidence            999999999888 99999999999999976 9999999874

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

Probab=99.05  E-value=1.1e-09  Score=79.49  Aligned_cols=65  Identities=28%  Similarity=0.584  Sum_probs=57.9

Q ss_pred             CcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCCeEeEEEEEEecccCeEeeehh
Q 021034          188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGKDLPLKFVEVDEEQSRLVLSNR  252 (318)
Q Consensus       188 G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq~v~~kVl~vd~~~~~i~lS~K  252 (318)
                      |++++|+|.++.++|++|+++ +..|++|.+++++.  .++.+ + +||.++++|+++|++++++.||+|
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            689999999999999999997 89999999999975  34544 3 799999999999988899999975

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.

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

Probab=99.05  E-value=1.4e-09  Score=78.54  Aligned_cols=64  Identities=25%  Similarity=0.336  Sum_probs=55.5

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCC--CeEEEEe
Q 021034           98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD--DSLVLSL  169 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~--~~i~lS~  169 (318)
                      ..|++++|+|.++.++|+||++++ .+||||.+|++.      .+. +++|+.+++.|.++++++  +++.||+
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            469999999999999999999976 999999999963      334 899999999999998654  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.

>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=99.04  E-value=5.9e-10  Score=87.02  Aligned_cols=71  Identities=31%  Similarity=0.494  Sum_probs=61.9

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcC---------------------Ccch-h-cCCeEeEEEEEEe
Q 021034          186 SEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS---------------------TAEE-L-LGKDLPLKFVEVD  241 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~---------------------~~~~-~-vGq~v~~kVl~vd  241 (318)
                      ..|++|.|+|+++.+.|++|.+. |+.||+|.+++++.+                     ++.+ + +||.++|+|+++|
T Consensus         2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d   81 (100)
T cd05693           2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLD   81 (100)
T ss_pred             CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEcc
Confidence            58999999999999999999996 999999999999731                     1333 3 7999999999999


Q ss_pred             cc---cCeEeeehhhhhh
Q 021034          242 EE---QSRLVLSNRKAMA  256 (318)
Q Consensus       242 ~~---~~~i~lS~K~~l~  256 (318)
                      ++   ++++.||+|+++.
T Consensus        82 ~~~~~~~~i~LSlr~~~v   99 (100)
T cd05693          82 KSKSGKKRIELSLEPELV   99 (100)
T ss_pred             CCcCCCcEEEEEecHHHC
Confidence            87   7899999998764

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=99.02  E-value=7e-09  Score=101.60  Aligned_cols=117  Identities=18%  Similarity=0.262  Sum_probs=91.1

Q ss_pred             hccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeE
Q 021034           36 NSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGA  115 (318)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~  115 (318)
                      .+..|..+...+...+.+   |..+...-...++.+++.          +.+.++++|  .-+.|++++|+|.++.++|+
T Consensus        86 ~~~vGD~ie~~I~~~~fg---Ria~q~aKq~i~Qkire~----------ere~i~~ey--k~~~GeIV~G~V~ri~~~gi  150 (470)
T PRK09202         86 DAEVGDYIEEEIESVDFG---RIAAQTAKQVIVQKIREA----------ERERVYEEY--KDRVGEIITGVVKRVERGNI  150 (470)
T ss_pred             cccCCCeEEEEEccccCC---hHHHHHHHHHHHHHHHHH----------HHHHHHHHH--HhhcCCEEEEEEEEEecCCE
Confidence            567999999999887755   533333323344555552          344566666  23489999999999999999


Q ss_pred             EEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC--eEEEEeeehhhh
Q 021034          116 LVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD--SLVLSLRMIQYE  175 (318)
Q Consensus       116 ~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~--~i~lS~k~~~~~  175 (318)
                      +|+++ +.+||||.+|++      |.+. |++|++++|+|++++.+.+  +++||++.+...
T Consensus       151 iVDLg-gvea~LP~sE~i------p~E~-~~~GdrIka~I~~Vd~~~kg~qIilSRt~p~~l  204 (470)
T PRK09202        151 IVDLG-RAEAILPRKEQI------PREN-FRPGDRVRAYVYEVRKEARGPQIILSRTHPEFL  204 (470)
T ss_pred             EEEEC-CeEEEecHHHcC------CCcc-CCCCCEEEEEEEEEecCCCCCeEEEEeCcHHHH
Confidence            99996 599999999985      5566 9999999999999998766  899999998763

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

Probab=99.02  E-value=1.6e-09  Score=79.17  Aligned_cols=67  Identities=25%  Similarity=0.508  Sum_probs=59.1

Q ss_pred             CcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCCeEeEEEEEEecccCeEeeehhhh
Q 021034          188 DVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGKDLPLKFVEVDEEQSRLVLSNRKA  254 (318)
Q Consensus       188 G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq~v~~kVl~vd~~~~~i~lS~K~~  254 (318)
                      |+++.|+|+++.++|++|+++ +++||+|.+++++.  .++.+ + +||.++|+|+++|.+++++.||+|..
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 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK   72 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence            689999999999999999996 99999999999976  33433 3 79999999999999999999998753

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=99.01  E-value=2.1e-09  Score=79.32  Aligned_cols=68  Identities=22%  Similarity=0.412  Sum_probs=60.2

Q ss_pred             CCcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcC--Ccch-h-cCCeEeEEEEEEecccCeEeeehhhh
Q 021034          187 EDVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKS--TAEE-L-LGKDLPLKFVEVDEEQSRLVLSNRKA  254 (318)
Q Consensus       187 ~G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~--~~~~-~-vGq~v~~kVl~vd~~~~~i~lS~K~~  254 (318)
                      .|+++.|+|+++.++|+||++.  +..|++|.+++++..  ++.+ + +||.++|+|+++|++++++.+|+|++
T Consensus         2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~~   75 (77)
T cd05708           2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS   75 (77)
T ss_pred             CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEee
Confidence            6899999999999999999996  699999999999763  3333 3 79999999999999999999999875

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

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

Probab=99.01  E-value=7.8e-10  Score=82.44  Aligned_cols=54  Identities=31%  Similarity=0.602  Sum_probs=50.7

Q ss_pred             CeEEEEEEEEEEcceEEEEEC----CeEEEEecCCcCcccc-cCcccccCCCCEEEEEC
Q 021034          265 GSVVIGTVQSLKPYGAFIDIG----GINGLLHVSQISHDRV-ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       265 G~~v~G~V~~i~~~G~fV~i~----gv~Glv~~s~ls~~~~-~~~~~~~~~Gq~V~v~V  318 (318)
                      |+++.|.|.++++||+||+++    +..||+|.++++|.+. .++.+.|++||.|+|+|
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v   59 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKV   59 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEE
Confidence            789999999999999999998    6899999999999986 89999999999999975

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.

>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=99.01  E-value=5.8e-10  Score=80.00  Aligned_cols=54  Identities=35%  Similarity=0.669  Sum_probs=51.5

Q ss_pred             CeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       265 G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      |+++.|+|.+++++|+||+++ +..||+|.+++++.+..++.+.|++||.++|+|
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i   55 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKV   55 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEE
Confidence            689999999999999999999 999999999999998889999999999999985

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=98.98  E-value=1.2e-09  Score=78.53  Aligned_cols=55  Identities=45%  Similarity=0.819  Sum_probs=52.3

Q ss_pred             cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +|+++.|+|.+++++|+||+++++.|++|.++++|.+..++.+.|++||.|+|+|
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i   55 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKV   55 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccccCHhHEECCCCEEEEEE
Confidence            4899999999999999999999999999999999999989999999999999985

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.

>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=98.98  E-value=2.9e-09  Score=77.53  Aligned_cols=63  Identities=19%  Similarity=0.127  Sum_probs=56.7

Q ss_pred             CCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccc--ccCccccCcCCCCEEEEEEEEEeCCCC
Q 021034          100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK--IKHVEEAGIVPGLKEEFVIIGENEADD  163 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~--~~~~~~~~~~~G~~v~v~Vl~vd~~~~  163 (318)
                      |+++.|+|+++.++|++|+++.+.+|++|.+++++.+  ..++.+. |++||.+.|+|++++.++.
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            7899999999999999999998999999999999874  6677676 9999999999999987653

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=98.98  E-value=2e-09  Score=76.00  Aligned_cols=65  Identities=18%  Similarity=0.240  Sum_probs=58.8

Q ss_pred             EEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEE
Q 021034          103 VKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLS  168 (318)
Q Consensus       103 v~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS  168 (318)
                      +.|+|.++.++|++|+++.+.+|++|.+++++.+..++.+. +++||.+.|+|+++|.+++++.||
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            47999999999999999988999999999998877777776 999999999999999988888775

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.

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

Probab=98.97  E-value=1.3e-09  Score=79.37  Aligned_cols=54  Identities=22%  Similarity=0.410  Sum_probs=51.1

Q ss_pred             CeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCccc--ccCcccccCCCCEEEEEC
Q 021034          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR--VADIATVLQPGDTLKVCL  318 (318)
Q Consensus       265 G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~--~~~~~~~~~~Gq~V~v~V  318 (318)
                      |++|.|+|.++.++|+||+++ |++|++|.+++++++  ..++.+.|++||.|+|+|
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kV   57 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARV   57 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEE
Confidence            789999999999999999998 999999999999884  788999999999999986

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.

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

Probab=98.96  E-value=1.8e-09  Score=77.63  Aligned_cols=54  Identities=41%  Similarity=0.766  Sum_probs=51.3

Q ss_pred             CeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       265 G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      |+++.|+|.++.++|+||+++ +..||+|.+++++.+..++.+.|++||.++|+|
T Consensus         1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v   55 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKV   55 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEE
Confidence            689999999999999999998 899999999999999889999999999999985

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.

>PHA02945 interferon resistance protein; Provisional

Probab=98.95  E-value=3.3e-09  Score=78.97  Aligned_cols=69  Identities=17%  Similarity=0.214  Sum_probs=60.6

Q ss_pred             cCCCcEEEEEEEEEEcCeEEEEEC---CEEEEEeCccc--CCc--CCcchh-cCCeEeEEEEEEecccCeEeeehhhhh
Q 021034          185 QSEDVVVKGKVVGANKGGVVAEVE---GLRGFVPFSQI--SSK--STAEEL-LGKDLPLKFVEVDEEQSRLVLSNRKAM  255 (318)
Q Consensus       185 ~~~G~iv~g~V~~v~~~G~~V~i~---gl~gfip~s~l--s~~--~~~~~~-vGq~v~~kVl~vd~~~~~i~lS~K~~l  255 (318)
                      -+.|+++-|+|.. .++|+||.+.   |++||+|.|+.  +.+  ++ +++ .||++.|+|+.+|+.++.|-||+|..-
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-RDKLVGKTVKVKVIRVDYTKGYIDVNYKRMC   85 (88)
T ss_pred             CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEecCCEEEEEEEEECCCCCEEEeEeeEcc
Confidence            3689999999999 9999999983   99999999966  755  56 555 799999999999999999999999753

>PRK08059 general stress protein 13; Validated

Probab=98.92  E-value=2e-09  Score=87.29  Aligned_cols=59  Identities=44%  Similarity=0.780  Sum_probs=55.8

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +++++|+++.|.|.+++++|+||+++ ++.|++|.+++++++..++.+.|++||.|+|+|
T Consensus         3 ~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI   62 (123)
T PRK08059          3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKV   62 (123)
T ss_pred             ccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEE
Confidence            45889999999999999999999999 999999999999999999999999999999986

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.90  E-value=4.4e-09  Score=106.72  Aligned_cols=58  Identities=36%  Similarity=0.647  Sum_probs=54.3

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcC----cccccCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQIS----HDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls----~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .+++|+++.|+|++|++||+||++. |++||+|+|+++    |.++.++.+.|++||.|+|+|
T Consensus       644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKV  706 (719)
T TIGR02696       644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEI  706 (719)
T ss_pred             cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEE
Confidence            4789999999999999999999998 999999999996    468999999999999999986

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.

>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=98.89  E-value=7.4e-09  Score=74.93  Aligned_cols=63  Identities=19%  Similarity=0.383  Sum_probs=54.9

Q ss_pred             CcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCc--CC---cchh-cCCeE-eEEEEEEecccCeEeeehh
Q 021034          188 DVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSK--ST---AEEL-LGKDL-PLKFVEVDEEQSRLVLSNR  252 (318)
Q Consensus       188 G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~--~~---~~~~-vGq~v-~~kVl~vd~~~~~i~lS~K  252 (318)
                      |++|+|+|.++++++++|+++  |++||+|..||+|.  ++   ++++ +||++ ++.|+  +..++.+.+|.|
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            679999999999999999995  89999999999995  22   4455 89999 88888  888899999976

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.

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

Probab=98.87  E-value=1.4e-08  Score=72.93  Aligned_cols=66  Identities=35%  Similarity=0.625  Sum_probs=58.4

Q ss_pred             CCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcC--Ccch-h-cCCeEeEEEEEEecccCeEeeehh
Q 021034          187 EDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKS--TAEE-L-LGKDLPLKFVEVDEEQSRLVLSNR  252 (318)
Q Consensus       187 ~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~--~~~~-~-vGq~v~~kVl~vd~~~~~i~lS~K  252 (318)
                      .|+++.|+|.++++.|++++++ ++.||+|.+++.+..  ++.+ + +||.++|+|++++++++++.+|++
T Consensus         2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316        2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence            6899999999999999999998 999999999999762  2222 4 799999999999998899999875

>TIGR01953 NusA transcription termination factor NusA

Probab=98.86  E-value=8.1e-08  Score=90.60  Aligned_cols=116  Identities=19%  Similarity=0.267  Sum_probs=86.6

Q ss_pred             hccCCceeEEEEEEeccchhHHHHHHHHHHHHH-HHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCe
Q 021034           36 NSRKNKTIVSAVAISNAETREREELNQLFEEAY-ERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRG  114 (318)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~-~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G  114 (318)
                      .+..|..+...+-.-+.+   | ..-.+.+..+ +.+++.          +.+.++++|.  -+.|++++|+|.++.++|
T Consensus        83 ~~~vGD~I~~~I~~~~fg---R-~aaq~aKqvi~Qkire~----------ere~i~~ey~--~k~GeiV~G~V~~v~~~g  146 (341)
T TIGR01953        83 DVQIGDEVKKEIPPENFG---R-IAAQTAKQVILQKIREA----------ERERVYDEFS--SKEGEIISGTVKRVNRRG  146 (341)
T ss_pred             ccccCCEEEEEecccCCC---H-HHHHHHHHHHHHHHHHH----------HHHHHHHHHH--hhcCCEEEEEEEEEecCC
Confidence            567899998887555444   4 3333333322 444442          3456777773  368999999999999987


Q ss_pred             -EEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCC--CCeEEEEeeehhhh
Q 021034          115 -ALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA--DDSLVLSLRMIQYE  175 (318)
Q Consensus       115 -~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~--~~~i~lS~k~~~~~  175 (318)
                       ++|+++ +.+||||.+|+.      |.+. |++|++++|.|++++..  ..++.||++.+...
T Consensus       147 ~v~VdiG-~~ea~LP~~E~i------p~E~-~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~~~v  202 (341)
T TIGR01953       147 NLYVELG-KTEGILPKKEQI------PGEK-FRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFV  202 (341)
T ss_pred             cEEEEEC-CeEEEecHHHcC------CCcC-CCCCCEEEEEEEEEEcCCCCCeEEEEeCcHHHH
Confidence             699996 799999999986      3445 89999999999999854  35899999998763

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.

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

Probab=98.84  E-value=2.6e-08  Score=74.49  Aligned_cols=70  Identities=10%  Similarity=0.145  Sum_probs=59.2

Q ss_pred             CCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCccccccccc-----------CccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034           99 LGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADDSLV  166 (318)
Q Consensus        99 ~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~-----------~~~~~~~~~G~~v~v~Vl~vd~~~~~i~  166 (318)
                      .|+++.|+|+++.++|+||+++. +.+|++|.+++++.+..           ..... +++||.++|+|.++|.+++++.
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            38999999999999999999986 79999999999864321           22234 8999999999999998889998


Q ss_pred             EEe
Q 021034          167 LSL  169 (318)
Q Consensus       167 lS~  169 (318)
                      +++
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.

>TIGR01953 NusA transcription termination factor NusA

Probab=98.84  E-value=1.2e-08  Score=96.18  Aligned_cols=105  Identities=18%  Similarity=0.211  Sum_probs=79.2

Q ss_pred             cCCCCEEEEEEEEEeCCCCeEEEEeeeh-h----hhHHHHHHhhhc--CCCcEEEEEEEEEEcCe-EEEEECCEEEEEeC
Q 021034          145 IVPGLKEEFVIIGENEADDSLVLSLRMI-Q----YELAWERCRQLQ--SEDVVVKGKVVGANKGG-VVAEVEGLRGFVPF  216 (318)
Q Consensus       145 ~~~G~~v~v~Vl~vd~~~~~i~lS~k~~-~----~~~~~~~~~~~~--~~G~iv~g~V~~v~~~G-~~V~i~gl~gfip~  216 (318)
                      +.+|+.+.+.+...  +-++..++..+. .    .+..++.+.+.|  +.|++|+|+|.++.++| ++|++++..||||.
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 VQIGDEVKKEIPPE--NFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGILPK  161 (341)
T ss_pred             cccCCEEEEEeccc--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEECCeEEEecH
Confidence            78999999888432  234544433333 1    134555555555  48999999999999977 69999999999999


Q ss_pred             cccCCcCCcchh-cCCeEeEEEEEEeccc--CeEeeehhhh
Q 021034          217 SQISSKSTAEEL-LGKDLPLKFVEVDEEQ--SRLVLSNRKA  254 (318)
Q Consensus       217 s~ls~~~~~~~~-vGq~v~~kVl~vd~~~--~~i~lS~K~~  254 (318)
                      +++..+..   + +|+++++.|++++.+.  ..+.||++..
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            99886533   4 7999999999999553  5799999875

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.

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

Probab=98.84  E-value=5.5e-09  Score=79.11  Aligned_cols=57  Identities=23%  Similarity=0.341  Sum_probs=51.7

Q ss_pred             cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCc----ccccCcccccCCCCEEEEEC
Q 021034          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISH----DRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~----~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .++|++|.|+|.+++++|+||+++ ++.|++|.+++++    .+..++.+.|++||.++|+|
T Consensus         4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V   65 (86)
T cd05789           4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEV   65 (86)
T ss_pred             CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEE
Confidence            468999999999999999999999 9999999999997    44567778899999999986

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".

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

Probab=98.82  E-value=4.8e-08  Score=72.49  Aligned_cols=64  Identities=16%  Similarity=0.166  Sum_probs=57.5

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~  169 (318)
                      +++.|+.+.|+|.++.++|+||++.++..|++|.+++.        +. ++.||.++++|.++ .+++++.+|.
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            57799999999999999999999988899999999973        22 89999999999999 7889998874

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.78  E-value=1.8e-07  Score=88.88  Aligned_cols=117  Identities=19%  Similarity=0.163  Sum_probs=90.5

Q ss_pred             hccCCceeEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeE
Q 021034           36 NSRKNKTIVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGA  115 (318)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~  115 (318)
                      ....|..+...+-..+.+   |..+...-....+.+++.          +.+.++++|  .-+.|++++|+|.++.++|+
T Consensus        86 ~~~vGD~i~~~I~~~~fg---R~aaq~akqvI~Qkire~----------ere~v~~ef--~~k~GeiV~G~V~~~~~~~~  150 (362)
T PRK12327         86 AYELGDVIEIEVTPKDFG---RIAAQTAKQVIMQRLREA----------EREIIYNEF--SEREGDIVTGVVQRRDNRFV  150 (362)
T ss_pred             cccCCCEEEEecCcCCCC---hHHHHHHHHHHHHHHHHH----------HHHHHHHHH--HHhcCCEEEEEEEEEeCCcE
Confidence            456899998888766666   655555555556666653          344677777  34689999999999999999


Q ss_pred             EEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC--eEEEEeeehhhh
Q 021034          116 LVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD--SLVLSLRMIQYE  175 (318)
Q Consensus       116 ~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~--~i~lS~k~~~~~  175 (318)
                      +|++++ .+||||.+|+.      |.+. |++|++++|+|++++.+.+  ++.||+..+...
T Consensus       151 ~Vdlg~-vEa~LP~~E~i------p~e~-~~~Gd~Ika~V~~V~~~~kgp~IivSRt~p~~v  204 (362)
T PRK12327        151 YVNLGK-IEAVLPPAEQI------PGET-YKHGDRIKVYVVKVEKTTKGPQIFVSRTHPGLV  204 (362)
T ss_pred             EEEeCC-eEEEecHHHcC------CCCC-CCCCCEEEEEEEEEecCCCCCeEEEEeCCHHHH
Confidence            999975 99999998874      3455 8999999999999986543  699999887653

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=98.77  E-value=2.5e-08  Score=103.43  Aligned_cols=100  Identities=19%  Similarity=0.372  Sum_probs=75.9

Q ss_pred             CCeEEEEeeehhh-hHHHHHHhhh---cCCCcEEE-EEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCC
Q 021034          162 DDSLVLSLRMIQY-ELAWERCRQL---QSEDVVVK-GKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGK  231 (318)
Q Consensus       162 ~~~i~lS~k~~~~-~~~~~~~~~~---~~~G~iv~-g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq  231 (318)
                      ++.+.+....... +...+.++++   .+.|+++. |+|+++.++|+||++. |++||+|.|++++.  .++.+ + +||
T Consensus       724 dg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD  803 (891)
T PLN00207        724 DGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGD  803 (891)
T ss_pred             CeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCC
Confidence            4555555444333 3333334333   46899995 6999999999999996 99999999999986  34444 3 799


Q ss_pred             eEeEEEEEEecccCeEeeehhhhhhhhHhhc
Q 021034          232 DLPLKFVEVDEEQSRLVLSNRKAMADSQAQL  262 (318)
Q Consensus       232 ~v~~kVl~vd~~~~~i~lS~K~~l~~~~~~l  262 (318)
                      .|+|+|+++|+ ++++.||+|+.+.++|+..
T Consensus       804 ~V~VkVi~ID~-~grI~LSlK~l~~~Pw~~~  833 (891)
T PLN00207        804 RIDVKLIEVND-KGQLRLSRRALLPEANSEK  833 (891)
T ss_pred             EEEEEEEEECC-CCcEEEEEeccccCchhhh
Confidence            99999999997 7899999999887776433

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

Probab=98.77  E-value=2.2e-08  Score=74.95  Aligned_cols=55  Identities=27%  Similarity=0.601  Sum_probs=48.3

Q ss_pred             cCeEEEEEEEEEEcceEEEEEC--CeEEEEecCCcCccccc-----------CcccccCCCCEEEEEC
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVCL  318 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~--gv~Glv~~s~ls~~~~~-----------~~~~~~~~Gq~V~v~V  318 (318)
                      +|+++.|+|++++++|+||++.  |+.|++|.+++++++..           ++...|++||.|+|+|
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v   68 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRV   68 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEE
Confidence            3899999999999999999998  79999999999986422           4567899999999986

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.

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

Probab=98.77  E-value=5.1e-08  Score=70.37  Aligned_cols=63  Identities=19%  Similarity=0.355  Sum_probs=54.0

Q ss_pred             CCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCcCCcchhcCCeEeEEEEEEeccc--CeEeeeh
Q 021034          187 EDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQ--SRLVLSN  251 (318)
Q Consensus       187 ~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~--~~i~lS~  251 (318)
                      .|++++|+|.+++++|++|++++..||||.+++++...+  .+|+++++.|++++.++  ..+.||+
T Consensus         3 ~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~~~~~--~~Gd~v~v~v~~v~~~~~~~~i~lSr   67 (67)
T cd04455           3 EGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPGESY--RPGDRIKAYVLEVRKTSKGPQIILSR   67 (67)
T ss_pred             CCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCCCCcC--CCCCEEEEEEEEEecCCCCCEEEEeC
Confidence            689999999999999999999999999999999864221  28999999999998654  4688885

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.

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=98.76  E-value=1.9e-08  Score=87.61  Aligned_cols=79  Identities=22%  Similarity=0.324  Sum_probs=66.2

Q ss_pred             EEEEecccCeEeeehhhhhhhhHhhcccCeEEEEEEEEEEcceEEEEEC-----------CeEEEEecCCcCcccccCcc
Q 021034          237 FVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIG-----------GINGLLHVSQISHDRVADIA  305 (318)
Q Consensus       237 Vl~vd~~~~~i~lS~K~~l~~~~~~l~~G~~v~G~V~~i~~~G~fV~i~-----------gv~Glv~~s~ls~~~~~~~~  305 (318)
                      ++++|.+++++.+...   ......+++|++|.|+|++++++|+||+++           ++.|++|.+++++.+..++.
T Consensus        40 ~~~id~~~~~Isv~P~---~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~  116 (189)
T PRK09521         40 KVFIDDINRKISVIPF---KKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLT  116 (189)
T ss_pred             EEEEcCCCCEEEEecC---cCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHH
Confidence            4567877778877532   222346679999999999999999999994           58899999999999888999


Q ss_pred             cccCCCCEEEEEC
Q 021034          306 TVLQPGDTLKVCL  318 (318)
Q Consensus       306 ~~~~~Gq~V~v~V  318 (318)
                      +.|++||.|.|+|
T Consensus       117 ~~~~~GD~V~akV  129 (189)
T PRK09521        117 DAFKIGDIVRAKV  129 (189)
T ss_pred             hccCCCCEEEEEE
Confidence            9999999999986

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.73  E-value=2.4e-08  Score=102.57  Aligned_cols=107  Identities=16%  Similarity=0.224  Sum_probs=84.4

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCC---CHHHHHH---HHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcc
Q 021034           58 EELNQLFEEAYERCRTAPMEGVSF---TLEEFHS---ALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQE  131 (318)
Q Consensus        58 ~~~~~~i~e~~~~~~~~~~~~~~~---s~~~~~~---~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sE  131 (318)
                      +.|+.+++++=..++-.+.+.+..   ..+....   .++.....+++|+++.|+|+++.++|+||++.++.+||||+++
T Consensus       571 k~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSe  650 (684)
T TIGR03591       571 KVIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISE  650 (684)
T ss_pred             HHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHH
Confidence            577888888766666555444422   3333333   3344445678999999999999999999999888999999999


Q ss_pred             cccccccCccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034          132 ACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV  166 (318)
Q Consensus       132 ls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~  166 (318)
                      +++.++.++.+. +++||.+.|+|+++|. ++++.
T Consensus       651 i~~~~v~~~~~~-~kvGD~V~VkVi~id~-~gki~  683 (684)
T TIGR03591       651 IANERVEKVEDV-LKEGDEVKVKVLEIDK-QGRIK  683 (684)
T ss_pred             cCCCcccChhhc-cCCCCEEEEEEEEECC-CCCcc
Confidence            999999999888 9999999999999997 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).

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

Probab=98.72  E-value=2.2e-08  Score=89.09  Aligned_cols=71  Identities=24%  Similarity=0.410  Sum_probs=64.2

Q ss_pred             cCCCcEEEEEEEEEEcCeEEEEEC---CEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhhhh
Q 021034          185 QSEDVVVKGKVVGANKGGVVAEVE---GLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRKAM  255 (318)
Q Consensus       185 ~~~G~iv~g~V~~v~~~G~~V~i~---gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~~l  255 (318)
                      -+.|++|-|+|.++.++|+||.+.   |++||+|.|+++.+  ++..++  .||.+-|+||.+|++++.|-||+|..-
T Consensus         9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~   86 (269)
T COG1093           9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVT   86 (269)
T ss_pred             CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCC
Confidence            368999999999999999999984   89999999999966  677776  599999999999999999999999753

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

Probab=98.71  E-value=4.7e-08  Score=72.56  Aligned_cols=51  Identities=29%  Similarity=0.592  Sum_probs=46.6

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .++++|+.+.|.|.+++++|+||++. +..||+|.+++.        +.|++||+++++|
T Consensus        12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------~~~~iGd~v~v~I   63 (77)
T cd04473          12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQV   63 (77)
T ss_pred             hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------CcCCCCCEEEEEE
Confidence            56889999999999999999999998 899999999863        4599999999985

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.

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=98.71  E-value=4.3e-08  Score=85.38  Aligned_cols=80  Identities=23%  Similarity=0.187  Sum_probs=68.1

Q ss_pred             HHhhhccCCCCCCEEEEEEEEEECCeEEEEeC----------CCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEE
Q 021034           89 ALEKYDFNSELGTKVKGTVFCTDNRGALVDIT----------AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE  158 (318)
Q Consensus        89 ~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~----------~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~v  158 (318)
                      .|..+...+++|++|.|+|+++.++|++|+++          .+.+|++|.+++++.+..++.+. |++||.+.|+|+++
T Consensus        54 P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~-~~~GD~V~akV~~i  132 (189)
T PRK09521         54 PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDA-FKIGDIVRAKVISY  132 (189)
T ss_pred             cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhc-cCCCCEEEEEEEec
Confidence            35444457789999999999999999999995          24789999999998777777776 99999999999998


Q ss_pred             eCCCCeEEEEeeeh
Q 021034          159 NEADDSLVLSLRMI  172 (318)
Q Consensus       159 d~~~~~i~lS~k~~  172 (318)
                      +   +++.||++..
T Consensus       133 ~---~~i~LS~k~~  143 (189)
T PRK09521        133 T---DPLQLSTKGK  143 (189)
T ss_pred             C---CcEEEEEecC
Confidence            7   6899999853

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

Probab=98.70  E-value=7.7e-08  Score=72.18  Aligned_cols=67  Identities=15%  Similarity=0.132  Sum_probs=58.5

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCCeEeEEEEEEecccCeEeeehhh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGKDLPLKFVEVDEEQSRLVLSNRK  253 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq~v~~kVl~vd~~~~~i~lS~K~  253 (318)
                      +.|++|.|+|+++.+.+++|+++ +..|++|.++++..  .++.+ + +|+.+.|+|+++|.+ +++.||++.
T Consensus         5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~   76 (82)
T cd04454           5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD   76 (82)
T ss_pred             CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence            58999999999999999999997 89999999999864  23333 3 799999999999986 899999875

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=98.68  E-value=1.4e-08  Score=102.59  Aligned_cols=59  Identities=41%  Similarity=0.671  Sum_probs=57.7

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .+|++|+++.|+|+|+++||+||+++ ..+||+|+|++++.++.+|.+++++||.|+|+|
T Consensus       654 ~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V  713 (780)
T COG2183         654 TDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKV  713 (780)
T ss_pred             hhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEE
Confidence            69999999999999999999999999 999999999999999999999999999999986

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.67  E-value=1.3e-07  Score=85.08  Aligned_cols=75  Identities=23%  Similarity=0.209  Sum_probs=66.3

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc----cCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI----KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~----~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~  171 (318)
                      ..++|++|.|+|+++.+++++|+++....|+||.+++++.+.    .++.+. |++||.|.|+|++++++ +.+.||++.
T Consensus        60 ~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~-~~~GDlV~akV~~i~~~-~~~~LS~k~  137 (235)
T PRK04163         60 IPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKY-LDIGDYIIAKVKDVDRT-RDVVLTLKG  137 (235)
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhh-CCCCCEEEEEEEEECCC-CcEEEEEcC
Confidence            568999999999999999999999988999999999998765    666666 99999999999999864 459999975


Q ss_pred             h
Q 021034          172 I  172 (318)
Q Consensus       172 ~  172 (318)
                      .
T Consensus       138 ~  138 (235)
T PRK04163        138 K  138 (235)
T ss_pred             C
Confidence            3

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=98.67  E-value=4.7e-08  Score=92.73  Aligned_cols=106  Identities=13%  Similarity=0.122  Sum_probs=74.5

Q ss_pred             cCCCCEEEEEEEEEeCCCCeEEEEeeehhh----hHHHHHHhhhc--CCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcc
Q 021034          145 IVPGLKEEFVIIGENEADDSLVLSLRMIQY----ELAWERCRQLQ--SEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQ  218 (318)
Q Consensus       145 ~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~----~~~~~~~~~~~--~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~  218 (318)
                      ..+|+.+.+.+...+-. +....+.|+...    +...+.+.+.|  +.|++++|+|.++.++|++|+++++.||||.++
T Consensus        87 ~~vGD~i~~~I~~~~fg-R~aaq~akqvI~Qkire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP~~E  165 (362)
T PRK12327         87 YELGDVIEIEVTPKDFG-RIAAQTAKQVIMQRLREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLGKIEAVLPPAE  165 (362)
T ss_pred             ccCCCEEEEecCcCCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeCCeEEEecHHH
Confidence            78999999887543321 212222222221    11223333333  689999999999999999999999999999888


Q ss_pred             cCCcCCcchh-cCCeEeEEEEEEecccC--eEeeehhhh
Q 021034          219 ISSKSTAEEL-LGKDLPLKFVEVDEEQS--RLVLSNRKA  254 (318)
Q Consensus       219 ls~~~~~~~~-vGq~v~~kVl~vd~~~~--~i~lS~K~~  254 (318)
                      +..+.   .+ +|+++++.|++++.+++  .+.||+...
T Consensus       166 ~ip~e---~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~p  201 (362)
T PRK12327        166 QIPGE---TYKHGDRIKVYVVKVEKTTKGPQIFVSRTHP  201 (362)
T ss_pred             cCCCC---CCCCCCEEEEEEEEEecCCCCCeEEEEeCCH
Confidence            76532   23 79999999999996554  599998654

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=98.66  E-value=4.5e-08  Score=100.78  Aligned_cols=59  Identities=37%  Similarity=0.704  Sum_probs=56.6

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .++++|+++.|+|+++.+||+||++. |.+||+|+|+++|+++.++.+.|++||.|+|+|
T Consensus       617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV  676 (693)
T PRK11824        617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKV  676 (693)
T ss_pred             ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEE
Confidence            56889999999999999999999998 999999999999999999999999999999986

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

Probab=98.65  E-value=2.4e-08  Score=99.57  Aligned_cols=123  Identities=15%  Similarity=0.216  Sum_probs=98.8

Q ss_pred             EEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCCHHHHH------HHHhhhccCCCCCCEEEEEEEEEECCeEEE
Q 021034           44 VSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFTLEEFH------SALEKYDFNSELGTKVKGTVFCTDNRGALV  117 (318)
Q Consensus        44 ~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s~~~~~------~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V  117 (318)
                      |-+-.+.+++    +.+++++++.=..++..+.+.+..+..+-+      +.++.+...+++|+++.|+|+++.++|+||
T Consensus       562 KI~dvIG~gG----k~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv  637 (692)
T COG1185         562 KIRDVIGPGG----KTIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFV  637 (692)
T ss_pred             HHhhccCCcc----cchhhhhhhhCcEEEecCCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEE
Confidence            4455566555    688999999777777766666533332211      234555568899999999999999999999


Q ss_pred             EeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034          118 DITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus       118 ~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      .+.++-+|++|++++++.++.+.++. ++.||.+.|+++.+|+ .+++.+|++..
T Consensus       638 ~l~~gkdgl~hiS~~~~~rv~kv~dv-lk~Gd~v~Vkv~~iD~-~Gri~ls~~~~  690 (692)
T COG1185         638 ELLPGKDGLVHISQLAKERVEKVEDV-LKEGDEVKVKVIEIDK-QGRIRLSIKAV  690 (692)
T ss_pred             EecCCcceeEEehhhhhhhhhcccce-eecCceEEEEEeeecc-cCCccceehhc
Confidence            99989999999999999988888888 9999999999999984 68999998864

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

Probab=98.64  E-value=1e-07  Score=86.85  Aligned_cols=70  Identities=23%  Similarity=0.393  Sum_probs=61.8

Q ss_pred             cCCCcEEEEEEEEEEcCeEEEEEC---CEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhhh
Q 021034          185 QSEDVVVKGKVVGANKGGVVAEVE---GLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRKA  254 (318)
Q Consensus       185 ~~~G~iv~g~V~~v~~~G~~V~i~---gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~~  254 (318)
                      .+.|++|.|+|+++.++|+||++.   |+.||+|.|++++.  .++.+.  +||.+.|+|+++|++++++.||+|..
T Consensus         6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v   82 (262)
T PRK03987          6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRV   82 (262)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEec
Confidence            468999999999999999999994   79999999999965  344443  79999999999999999999999854

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

Probab=98.63  E-value=5.7e-08  Score=68.37  Aligned_cols=51  Identities=35%  Similarity=0.713  Sum_probs=47.9

Q ss_pred             EEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          268 VIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       268 v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +.|+|.++.++|+||+++ +..|++|.+++++.+..++.+.|++||.|+|+|
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v   52 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKV   52 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEE
Confidence            479999999999999999 999999999999988888889999999999986

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=98.61  E-value=1.2e-07  Score=97.54  Aligned_cols=59  Identities=37%  Similarity=0.709  Sum_probs=56.3

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ...++|+++.|+|+++.+||+||++. |.+||+|+|+++|.++.++.+.|++||.|+|+|
T Consensus       614 ~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkV  673 (684)
T TIGR03591       614 AEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKV  673 (684)
T ss_pred             cccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEE
Confidence            46788999999999999999999998 999999999999999999999999999999986

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).

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

Probab=98.54  E-value=1.8e-07  Score=93.47  Aligned_cols=80  Identities=28%  Similarity=0.596  Sum_probs=66.8

Q ss_pred             EEEecccCeEeeehhhhh---------hhhHhhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccc
Q 021034          238 VEVDEEQSRLVLSNRKAM---------ADSQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATV  307 (318)
Q Consensus       238 l~vd~~~~~i~lS~K~~l---------~~~~~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~  307 (318)
                      ++++ +.+.+.++-...-         ...-.++++|+++.|+|+++.+||+||.|. |-.||||+|++++.++.+.++.
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            4555 5677666544321         112368899999999999999999999998 9999999999999999999999


Q ss_pred             cCCCCEEEEEC
Q 021034          308 LQPGDTLKVCL  318 (318)
Q Consensus       308 ~~~Gq~V~v~V  318 (318)
                      +++||.+.|+|
T Consensus       664 lk~Gd~v~Vkv  674 (692)
T COG1185         664 LKEGDEVKVKV  674 (692)
T ss_pred             eecCceEEEEE
Confidence            99999999985

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

Probab=98.53  E-value=5.5e-07  Score=70.04  Aligned_cols=78  Identities=18%  Similarity=0.110  Sum_probs=63.2

Q ss_pred             CEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCc-----------cccCcCCCCEEEEEEEEEeCCC-----Ce
Q 021034          101 TKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV-----------EEAGIVPGLKEEFVIIGENEAD-----DS  164 (318)
Q Consensus       101 ~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~-----------~~~~~~~G~~v~v~Vl~vd~~~-----~~  164 (318)
                      +++.|+|+++.++|+||++.+ .+|++|.++++..+....           .+. |++||.+.++|.++|.+.     ++
T Consensus         1 ~vv~g~V~~i~~~GifV~l~~-v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~Gd~v~vkI~~vd~~~~~~~~~~   78 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIGP-VDGLLHISQIMDDYISYDPKNKRLIGEETKRV-LKVGDVVRARIVAVSLKERRPRESK   78 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEcC-eEEEEEEEEccCCceEechhheeecccCcCCE-ECCCCEEEEEEEEEeHHHCcCCCce
Confidence            478999999999999999984 999999999987654432           244 899999999999999764     57


Q ss_pred             EEEEeeehhhhHHHHHH
Q 021034          165 LVLSLRMIQYELAWERC  181 (318)
Q Consensus       165 i~lS~k~~~~~~~~~~~  181 (318)
                      +.||.+.... -+|.-+
T Consensus        79 i~ls~k~~~~-g~~~~~   94 (99)
T cd04460          79 IGLTMRQPGL-GKLEWI   94 (99)
T ss_pred             EEEEEecCCC-CcHHHh
Confidence            9999998876 344444

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

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

Probab=98.42  E-value=4.1e-07  Score=88.48  Aligned_cols=78  Identities=17%  Similarity=0.209  Sum_probs=69.4

Q ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      .+++.|-+++|+|.++.+.|++|.++++..|+||++|++..++.+|++. +.+||.++++.++.|+..+ +.+|.|..+.
T Consensus       664 ~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~-levGq~I~vk~ie~d~~g~-~~ls~ralLp  741 (760)
T KOG1067|consen  664 QDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDL-LEVGQEIQVKYIERDPRGG-IMLSSRALLP  741 (760)
T ss_pred             cceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHH-HhhcceeEEEEEeecCccc-eeehhhhhcC
Confidence            4788999999999999999999999999999999999999999999999 9999999999999997555 5555555544

>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=98.38  E-value=1.4e-06  Score=63.10  Aligned_cols=69  Identities=19%  Similarity=0.212  Sum_probs=56.4

Q ss_pred             CCEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccc-cCcCCCCEE-EEEEEEEeCCCCeEEEEee
Q 021034          100 GTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEE-AGIVPGLKE-EFVIIGENEADDSLVLSLR  170 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~-~~~~~G~~v-~v~Vl~vd~~~~~i~lS~k  170 (318)
                      |++|+|+|....+++++|++.+ ++.|+||..++++..-++... ..+++||++ ++.|+  +...+.+.+|.|
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            7899999999999999999955 899999999999943333222 137899999 99998  677788888875

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.

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

Probab=98.36  E-value=1e-06  Score=68.49  Aligned_cols=53  Identities=40%  Similarity=0.684  Sum_probs=46.9

Q ss_pred             eEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccC-----------cccccCCCCEEEEEC
Q 021034          266 SVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVAD-----------IATVLQPGDTLKVCL  318 (318)
Q Consensus       266 ~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~-----------~~~~~~~Gq~V~v~V  318 (318)
                      +++.|+|.++.++|+||++.++.|++|.+++++++...           +...|++||.|+|+|
T Consensus         1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI   64 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARI   64 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEE
Confidence            47899999999999999999999999999999876543           357899999999986

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

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

Probab=98.34  E-value=7e-07  Score=86.86  Aligned_cols=58  Identities=26%  Similarity=0.499  Sum_probs=55.8

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVC  317 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~  317 (318)
                      .++..|-+++|+|+.+.+||+||+|. +..||+|.|+++..++.+|++.|.+||.+.++
T Consensus       664 ~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk  722 (760)
T KOG1067|consen  664 QDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVK  722 (760)
T ss_pred             cceEeeeEEEEEEeeecccceEEEecCCchhhccchhcccccccChHHHHhhcceeEEE
Confidence            47888999999999999999999999 99999999999999999999999999999986

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=98.32  E-value=3.4e-06  Score=59.69  Aligned_cols=61  Identities=18%  Similarity=0.196  Sum_probs=37.6

Q ss_pred             CCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034           99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus        99 ~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      +|++.+.+|.++.+.|+|++.+...+-+||.+|+...         +++|+.++|+|.  .+.++++.+|+|
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~---------~~~Gd~v~VFvY--~D~~~rl~AT~k   61 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEP---------LKVGDEVEVFVY--LDKEGRLVATTK   61 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG---------------TTSEEEEEEE--E-TTS-EEEE--
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCC---------CCCCCEEEEEEE--ECCCCCEEEecC
Confidence            4889999999999999999998879999999987422         789999999994  456789999875

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=98.32  E-value=1.7e-05  Score=75.16  Aligned_cols=116  Identities=19%  Similarity=0.200  Sum_probs=82.6

Q ss_pred             hccCCceeEEEEEEeccchhHHHHHHHHHHHH-HHHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEEC-C
Q 021034           36 NSRKNKTIVSAVAISNAETREREELNQLFEEA-YERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDN-R  113 (318)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e~-~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~-~  113 (318)
                      ....|..+.--+-..+-+   | .--.+.+.. .+++++.          +.+..+++|  .-+.|+++.|+|.++.. +
T Consensus        90 ~~~vGd~i~~~i~~~~fg---R-iaaq~akq~i~Qkir~~----------er~~i~~ey--~~~~Geiv~g~V~r~~~~~  153 (374)
T PRK12328         90 SVEIGDELTYELSLENMG---R-TAANTLFKELEYHIQRL----------LEESIFEKY--KKKVGKIVFGTVVRVDNEE  153 (374)
T ss_pred             CCCCCCEEEEecChhhCC---H-HHHHHHHHHHHHHHHHH----------HHHHHHHHH--HHhcCcEEEEEEEEEecCC
Confidence            456788887766555444   3 222333332 2333332          123566666  45689999999999997 5


Q ss_pred             eEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC---eEEEEeeehhhh
Q 021034          114 GALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD---SLVLSLRMIQYE  175 (318)
Q Consensus       114 G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~---~i~lS~k~~~~~  175 (318)
                      +++|+++ +.+|+||.+|..      |.+. |++|+.+.|.|.+++...+   ++.||+..+...
T Consensus       154 ~i~vdlg-~~ea~LP~~eqi------p~E~-~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p~~v  210 (374)
T PRK12328        154 NTFIEID-EIRAVLPMKNRI------KGEK-FKVGDVVKAVLKRVKIDKNNGILIELSRTSPKFL  210 (374)
T ss_pred             CEEEEcC-CeEEEeCHHHcC------CCCc-CCCCCEEEEEEEEEecCCCCCCEEEEEcCCHHHH
Confidence            6999997 699999998864      4555 9999999999999987654   799999888653

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=98.30  E-value=1e-06  Score=79.29  Aligned_cols=58  Identities=28%  Similarity=0.353  Sum_probs=54.1

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccc----cCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV----ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~----~~~~~~~~~Gq~V~v~V  318 (318)
                      ..++|++|.|.|.+++++|+||+++ ++.|++|.++++|.++    .++.+.|++||.|.|+|
T Consensus        60 ~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV  122 (235)
T PRK04163         60 IPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKV  122 (235)
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEE
Confidence            3468999999999999999999999 8999999999999887    78899999999999986

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

Probab=98.29  E-value=3.7e-06  Score=64.57  Aligned_cols=74  Identities=19%  Similarity=0.148  Sum_probs=62.4

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEe--------CCCeEEEEeCccccccccc--CccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034           97 SELGTKVKGTVFCTDNRGALVDI--------TAKSSAYLPTQEACIHKIK--HVEEAGIVPGLKEEFVIIGENEADDSLV  166 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i--------~~~~~g~lp~sEls~~~~~--~~~~~~~~~G~~v~v~Vl~vd~~~~~i~  166 (318)
                      .++|++|.|+|+++....+.|++        .....|+||.+++...+..  ++.+. |++||.+.++|+++++ ...+.
T Consensus         4 P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~-f~~GDiV~AkVis~~~-~~~~~   81 (92)
T cd05791           4 PKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKC-FRPGDIVRAKVISLGD-ASSYY   81 (92)
T ss_pred             CCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhh-cCCCCEEEEEEEEcCC-CCCcE
Confidence            57999999999999999999999        6678999999998766554  45555 9999999999999875 35688


Q ss_pred             EEeeeh
Q 021034          167 LSLRMI  172 (318)
Q Consensus       167 lS~k~~  172 (318)
                      ||.+..
T Consensus        82 Lst~~~   87 (92)
T cd05791          82 LSTAEN   87 (92)
T ss_pred             EEecCC
Confidence            998764

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

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

Probab=98.28  E-value=5.6e-06  Score=71.49  Aligned_cols=77  Identities=18%  Similarity=0.182  Sum_probs=63.4

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccccc-Cc----------cccCcCCCCEEEEEEEEEe-----
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-HV----------EEAGIVPGLKEEFVIIGEN-----  159 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~-~~----------~~~~~~~G~~v~v~Vl~vd-----  159 (318)
                      ....|+++.|+|++++++|++|+++ ..+|+++.+++..++.. ++          ... ++.|+.|+++|.+++     
T Consensus        78 ~p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~-~~~Gd~VrvrV~~v~~~~~~  155 (179)
T TIGR00448        78 KPELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKV-LDEGDKVRARIVALSLKDRR  155 (179)
T ss_pred             eccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeE-EcCCCEEEEEEEEEEccCCC
Confidence            4568999999999999999999996 59999999998754432 11          233 889999999999998     


Q ss_pred             CCCCeEEEEeeehhh
Q 021034          160 EADDSLVLSLRMIQY  174 (318)
Q Consensus       160 ~~~~~i~lS~k~~~~  174 (318)
                      ++..++.+|+|++-.
T Consensus       156 ~~~~~I~lt~k~~~L  170 (179)
T TIGR00448       156 PEGSKIGLTMRQPLL  170 (179)
T ss_pred             CCcceEEEEeccCcC
Confidence            556789999998754

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

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=98.22  E-value=5.1e-06  Score=61.40  Aligned_cols=70  Identities=7%  Similarity=0.098  Sum_probs=63.0

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEe-CCCeEEEEe-CcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034           97 SELGTKVKGTVFCTDNRGALVDI-TAKSSAYLP-TQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i-~~~~~g~lp-~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~  169 (318)
                      .++|+.+. .|+.+.+.|++|.+ +++.+|++. .+|++-.+++..++. + +|.++.+.|+.+|.++|.+-||.
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            47899999 89999999999998 456999888 999999888888876 6 99999999999999999999984

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

Probab=98.16  E-value=9.1e-06  Score=70.16  Aligned_cols=68  Identities=21%  Similarity=0.336  Sum_probs=58.0

Q ss_pred             CCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCcC---C----------c-chh-cCCeEeEEEEEEe-----cccCe
Q 021034          187 EDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS---T----------A-EEL-LGKDLPLKFVEVD-----EEQSR  246 (318)
Q Consensus       187 ~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~~---~----------~-~~~-vGq~v~~kVl~vd-----~~~~~  246 (318)
                      .|+++.|+|+++++.|+||+++.++|+++.+++.+..   +          . ..+ +|+.|+++|.++|     ++..+
T Consensus        81 ~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~~  160 (179)
T TIGR00448        81 LGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPEGSK  160 (179)
T ss_pred             CCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCCcce
Confidence            7899999999999999999999999999999988541   1          1 123 6999999999998     56778


Q ss_pred             Eeeehhhh
Q 021034          247 LVLSNRKA  254 (318)
Q Consensus       247 i~lS~K~~  254 (318)
                      +.+|+|+.
T Consensus       161 I~lt~k~~  168 (179)
T TIGR00448       161 IGLTMRQP  168 (179)
T ss_pred             EEEEeccC
Confidence            99999986

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

>TIGR02063 RNase_R ribonuclease R

Probab=98.16  E-value=1.4e-05  Score=83.06  Aligned_cols=73  Identities=8%  Similarity=0.156  Sum_probs=61.7

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccc-----------cCccccCcCCCCEEEEEEEEEeCCCC
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKI-----------KHVEEAGIVPGLKEEFVIIGENEADD  163 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~-----------~~~~~~~~~~G~~v~v~Vl~vd~~~~  163 (318)
                      .-.+|++++|+|+++.++|+||++.+ +.+|++|.+++++.+.           .+.... +++||.|+|+|.++|..++
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            44689999999999999999999975 6999999999986432           222233 8999999999999999999


Q ss_pred             eEEEEe
Q 021034          164 SLVLSL  169 (318)
Q Consensus       164 ~i~lS~  169 (318)
                      ++.+++
T Consensus       703 ~I~~~l  708 (709)
T TIGR02063       703 KIDFEL  708 (709)
T ss_pred             eEEEEE
Confidence            999875

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.

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

Probab=98.11  E-value=1.2e-05  Score=68.56  Aligned_cols=85  Identities=20%  Similarity=0.192  Sum_probs=66.0

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc----------cCccccCcCCCCEEEEEEEEEeCCC---
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI----------KHVEEAGIVPGLKEEFVIIGENEAD---  162 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~----------~~~~~~~~~~G~~v~v~Vl~vd~~~---  162 (318)
                      ....|+++.|+|+++.+.|+||.++. .+||+|.+++.+.++          ..-++..+..|+.|.++|++.+...   
T Consensus        78 kP~~gEVV~GeVv~~~~~G~fV~igp-~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~  156 (183)
T COG1095          78 KPFRGEVVEGEVVEVVEFGAFVRIGP-LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRP  156 (183)
T ss_pred             EeccccEEEEEEEEEeecceEEEecc-ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcc
Confidence            45679999999999999999999994 999999999988633          1111212778999999999887544   


Q ss_pred             --CeEEEEeeehhh-hHHHHHH
Q 021034          163 --DSLVLSLRMIQY-ELAWERC  181 (318)
Q Consensus       163 --~~i~lS~k~~~~-~~~~~~~  181 (318)
                        .++.+|+|++-. ...|-..
T Consensus       157 ~~~~I~lTmrq~~LGklew~~~  178 (183)
T COG1095         157 RESKIGLTMRQPGLGKLEWIEE  178 (183)
T ss_pred             ccceEEEEeccccCCcchhhhh
Confidence              578999998876 3356443

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

Probab=98.09  E-value=4.5e-06  Score=71.06  Aligned_cols=55  Identities=40%  Similarity=0.703  Sum_probs=47.8

Q ss_pred             cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccc----------cC-cccccCCCCEEEEEC
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV----------AD-IATVLQPGDTLKVCL  318 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~----------~~-~~~~~~~Gq~V~v~V  318 (318)
                      .|++|.|.|.++.++|+||.++-++||+|.+++.++..          .+ -...+++||.|++||
T Consensus        81 ~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RI  146 (183)
T COG1095          81 RGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARI  146 (183)
T ss_pred             cccEEEEEEEEEeecceEEEeccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEE
Confidence            48999999999999999999999999999999999832          22 233789999999986

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

Probab=98.05  E-value=8.2e-06  Score=62.64  Aligned_cols=56  Identities=25%  Similarity=0.487  Sum_probs=51.3

Q ss_pred             ccCeEEEEEEEEEEcceEEEEE--------C-CeEEEEecCCcCccccc--CcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDI--------G-GINGLLHVSQISHDRVA--DIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i--------~-gv~Glv~~s~ls~~~~~--~~~~~~~~Gq~V~v~V  318 (318)
                      ++|++|.|.|.+++...+.|++        . .+.|++|.+++......  ++.+.|++||-|+|+|
T Consensus         5 ~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkV   71 (92)
T cd05791           5 KVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKV   71 (92)
T ss_pred             CCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEE
Confidence            6899999999999999999999        6 68999999999877666  6889999999999986

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".

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=98.00  E-value=0.00019  Score=69.31  Aligned_cols=79  Identities=13%  Similarity=0.149  Sum_probs=64.4

Q ss_pred             HHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeC---C--CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCC
Q 021034           87 HSALEKYDFNSELGTKVKGTVFCTDNRGALVDIT---A--KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEA  161 (318)
Q Consensus        87 ~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~---~--~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~  161 (318)
                      ..++++|  .-..|+++.|+|.++..++++|+++   +  +.+|+||.+|..      |.+. |++|+.+.|.|.++...
T Consensus       142 ~~i~~ef--~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~-y~~Gdrika~i~~V~~~  212 (449)
T PRK12329        142 KMIQEEF--QDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDN-YRANATFKVFLKEVSEG  212 (449)
T ss_pred             HHHHHHH--HHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCc-CCCCCEEEEEEEEeecC
Confidence            3566666  4568999999999999999999983   3  389999998863      4555 99999999999999765


Q ss_pred             C---CeEEEEeeehhh
Q 021034          162 D---DSLVLSLRMIQY  174 (318)
Q Consensus       162 ~---~~i~lS~k~~~~  174 (318)
                      .   -++.||+..+..
T Consensus       213 ~~kGpqIilSRt~p~l  228 (449)
T PRK12329        213 PRRGPQLFVSRANAGL  228 (449)
T ss_pred             CCCCCEEEEEcCCHHH
Confidence            2   379999988765

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

Probab=97.97  E-value=9.1e-05  Score=64.33  Aligned_cols=77  Identities=19%  Similarity=0.176  Sum_probs=62.7

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccccc-----------CccccCcCCCCEEEEEEEEEeCCCC-
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADD-  163 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~-----------~~~~~~~~~G~~v~v~Vl~vd~~~~-  163 (318)
                      ....|+++.|+|+++.++|++|+++. .+|+++.+++...+..           +.... ++.|+.++++|.+++..++ 
T Consensus        78 ~P~~GEVv~g~V~~v~~~Gi~V~lg~-~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~-i~~Gd~VrvrV~~v~~~~~~  155 (187)
T PRK08563         78 KPELQEVVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYISYDPKNGRLIGKESKRV-LKVGDVVRARIVAVSLKERR  155 (187)
T ss_pred             eccCCCEEEEEEEEEEccEEEEEEeC-ceEEEEcHHcCCCceEEccccceEEEccCCeE-EcCCCEEEEEEEEEEcccCC
Confidence            45689999999999999999999984 9999999999765322           12233 7899999999999986543 


Q ss_pred             ----eEEEEeeehhh
Q 021034          164 ----SLVLSLRMIQY  174 (318)
Q Consensus       164 ----~i~lS~k~~~~  174 (318)
                          .+.+|++..-.
T Consensus       156 ~~~~~I~ls~~~~~L  170 (187)
T PRK08563        156 PRGSKIGLTMRQPGL  170 (187)
T ss_pred             CCCCEEEEEecCCCC
Confidence                78889998765

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=97.93  E-value=9.8e-05  Score=70.08  Aligned_cols=103  Identities=17%  Similarity=0.213  Sum_probs=71.4

Q ss_pred             cCCCCEEEEEEEEEeCCCCeEE-EEeeehhh--------hHHHHHHhhhcCCCcEEEEEEEEEEc-CeEEEEECCEEEEE
Q 021034          145 IVPGLKEEFVIIGENEADDSLV-LSLRMIQY--------ELAWERCRQLQSEDVVVKGKVVGANK-GGVVAEVEGLRGFV  214 (318)
Q Consensus       145 ~~~G~~v~v~Vl~vd~~~~~i~-lS~k~~~~--------~~~~~~~~~~~~~G~iv~g~V~~v~~-~G~~V~i~gl~gfi  214 (318)
                      +.+|+.+...+--.+  =+|+. -+.|+...        +..++.+.+  ..|++++|+|.++.. ++++|++++..|+|
T Consensus        91 ~~vGd~i~~~i~~~~--fgRiaaq~akq~i~Qkir~~er~~i~~ey~~--~~Geiv~g~V~r~~~~~~i~vdlg~~ea~L  166 (374)
T PRK12328         91 VEIGDELTYELSLEN--MGRTAANTLFKELEYHIQRLLEESIFEKYKK--KVGKIVFGTVVRVDNEENTFIEIDEIRAVL  166 (374)
T ss_pred             CCCCCEEEEecChhh--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hcCcEEEEEEEEEecCCCEEEEcCCeEEEe
Confidence            789999987663211  12221 12222221        111223333  489999999999986 56999999999999


Q ss_pred             eCcccCCcCCcchh-cCCeEeEEEEEEecccC---eEeeehhhh
Q 021034          215 PFSQISSKSTAEEL-LGKDLPLKFVEVDEEQS---RLVLSNRKA  254 (318)
Q Consensus       215 p~s~ls~~~~~~~~-vGq~v~~kVl~vd~~~~---~i~lS~K~~  254 (318)
                      |.++...+.   .| .|+.++|.|.+++...+   .+.||+...
T Consensus       167 P~~eqip~E---~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~p  207 (374)
T PRK12328        167 PMKNRIKGE---KFKVGDVVKAVLKRVKIDKNNGILIELSRTSP  207 (374)
T ss_pred             CHHHcCCCC---cCCCCCEEEEEEEEEecCCCCCCEEEEEcCCH
Confidence            999877542   24 79999999999998765   799998754

>TIGR02063 RNase_R ribonuclease R

Probab=97.93  E-value=1.9e-05  Score=82.10  Aligned_cols=58  Identities=28%  Similarity=0.555  Sum_probs=49.8

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEEC--CeEEEEecCCcCcccc-----------cCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~--gv~Glv~~s~ls~~~~-----------~~~~~~~~~Gq~V~v~V  318 (318)
                      .-+.|+++.|.|++|++||+||++.  |+.||+|.+++++++.           .+....|++||.|+|+|
T Consensus       624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv  694 (709)
T TIGR02063       624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRV  694 (709)
T ss_pred             hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEE
Confidence            3457999999999999999999997  6999999999996543           33456799999999986

This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.

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

Probab=97.92  E-value=9.4e-05  Score=55.87  Aligned_cols=74  Identities=19%  Similarity=-0.003  Sum_probs=61.3

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      ..++||.|-|+|+.+..+++.|||+....|+||..++... .++.... +++|+.|-++|..++.. ....|||..+
T Consensus         3 ~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~-L~~GDlV~ArV~~~~~~-~~~eLtc~~~   76 (86)
T cd05790           3 VPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPN-LNVGDLVYARVVKANRD-MEPELSCVDS   76 (86)
T ss_pred             cCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-ccccccc-CCCCCEEEEEEEecCCC-CCeEEEEeCC
Confidence            4678999999999999999999999889999999887543 2333334 89999999999998864 5689999875

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".

>PRK11642 exoribonuclease R; Provisional

Probab=97.87  E-value=9.1e-05  Score=77.70  Aligned_cols=73  Identities=14%  Similarity=0.121  Sum_probs=61.7

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCccccccccc-----------CccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034           98 ELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADDSL  165 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~-----------~~~~~~~~~G~~v~v~Vl~vd~~~~~i  165 (318)
                      .+|+.++|+|+++.++|+||++.. +++|++|.+++.+++..           +.... |++||.|+|+|.++|.+++++
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 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQT-YRLGDRVEVRVEAVNMDERKI  720 (813)
T ss_pred             cCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcE-ECCCCEEEEEEEEeecCCCeE
Confidence            689999999999999999999965 49999999999865321           11233 899999999999999999999


Q ss_pred             EEEeee
Q 021034          166 VLSLRM  171 (318)
Q Consensus       166 ~lS~k~  171 (318)
                      .+++-.
T Consensus       721 ~f~l~~  726 (813)
T PRK11642        721 DFSLIS  726 (813)
T ss_pred             EEEEec
Confidence            999853

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

Probab=97.86  E-value=5.3e-05  Score=57.67  Aligned_cols=55  Identities=22%  Similarity=0.318  Sum_probs=45.8

Q ss_pred             cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCc-----------ccccCCCCEEEEEC
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADI-----------ATVLQPGDTLKVCL  318 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~-----------~~~~~~Gq~V~v~V  318 (318)
                      .|+++.|.|++++++|+||.++.+.+|+|.+.++.+..-+|           ...+.+|+.|++||
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV   66 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKI   66 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEE
Confidence            48999999999999999999999999999998876543333           34478899999886

RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.

>PRK11642 exoribonuclease R; Provisional

Probab=97.86  E-value=7e-05  Score=78.56  Aligned_cols=67  Identities=16%  Similarity=0.276  Sum_probs=57.9

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCc---CC-----------cchh-cCCeEeEEEEEEecccCeEe
Q 021034          186 SEDVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSK---ST-----------AEEL-LGKDLPLKFVEVDEEQSRLV  248 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~---~~-----------~~~~-vGq~v~~kVl~vd~~~~~i~  248 (318)
                      ..|++++|+|++++++|+||+++  +++|++|.+++.+.   .+           .+.+ +||.|+++|.++|.++++|.
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            48999999999999999999996  59999999999854   11           1235 79999999999999999999


Q ss_pred             eehh
Q 021034          249 LSNR  252 (318)
Q Consensus       249 lS~K  252 (318)
                      +++-
T Consensus       722 f~l~  725 (813)
T PRK11642        722 FSLI  725 (813)
T ss_pred             EEEe
Confidence            9873

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

Probab=97.86  E-value=1.6e-05  Score=70.77  Aligned_cols=79  Identities=20%  Similarity=0.230  Sum_probs=73.4

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEe--CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i--~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      -.+++++|-+.|.+|.+-|+||.+  +++.+|++-.+|+|-.+++..+.+ .++|..--|.|+.+|.++|.+-||.++..
T Consensus        13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~kl-irVGr~E~vvVlrVDkekGYIDLSkrrVs   91 (304)
T KOG2916|consen   13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKL-IRVGRNEPVVVLRVDKEKGYIDLSKRRVS   91 (304)
T ss_pred             CCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHH-HhcCCcceEEEEEEcCCCCceechhccCC
Confidence            357899999999999999999998  678999999999999999999988 99999999999999999999999999987


Q ss_pred             hh
Q 021034          174 YE  175 (318)
Q Consensus       174 ~~  175 (318)
                      .+
T Consensus        92 ~e   93 (304)
T KOG2916|consen   92 PE   93 (304)
T ss_pred             HH
Confidence            63

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

Probab=97.86  E-value=3.7e-05  Score=66.80  Aligned_cols=55  Identities=38%  Similarity=0.698  Sum_probs=48.5

Q ss_pred             cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCccccc-----------CcccccCCCCEEEEEC
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVCL  318 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~-----------~~~~~~~~Gq~V~v~V  318 (318)
                      .|+++.|.|.+++++|+||+++.+.|++|.+++.+++..           +....|++||.|+++|
T Consensus        81 ~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV  146 (187)
T PRK08563         81 LQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARI  146 (187)
T ss_pred             CCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEE
Confidence            599999999999999999999999999999999876432           3456799999999986

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

Probab=97.81  E-value=0.00014  Score=74.92  Aligned_cols=72  Identities=14%  Similarity=0.174  Sum_probs=60.7

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEeC-CCeEEEEeCcccccccc-----------cCccccCcCCCCEEEEEEEEEeCCCCe
Q 021034           97 SELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEACIHKI-----------KHVEEAGIVPGLKEEFVIIGENEADDS  164 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i~-~~~~g~lp~sEls~~~~-----------~~~~~~~~~~G~~v~v~Vl~vd~~~~~  164 (318)
                      -.+|+.++|+|+++.++|+||++. .+.+|++|.+++.+.+.           ++.... |++||+|+|+|.++|.++++
T Consensus       570 ~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~-~~lGD~V~Vki~~vd~~~~~  648 (654)
T TIGR00358       570 DKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKV-YRIGDRVTVKLTEVNMETRS  648 (654)
T ss_pred             hCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcE-ECCCCEEEEEEEEEecccCe
Confidence            357999999999999999999996 67999999999986531           112233 88999999999999999999


Q ss_pred             EEEEe
Q 021034          165 LVLSL  169 (318)
Q Consensus       165 i~lS~  169 (318)
                      +.+++
T Consensus       649 I~f~l  653 (654)
T TIGR00358       649 IIFEL  653 (654)
T ss_pred             EEEEE
Confidence            98874

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.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.73  E-value=4.7e-05  Score=73.93  Aligned_cols=59  Identities=34%  Similarity=0.581  Sum_probs=50.2

Q ss_pred             hhcccCeEEEEEEEEEEcc--eEEEEEC-CeEEEEecCCcCcc------------cccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPY--GAFIDIG-GINGLLHVSQISHD------------RVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~--G~fV~i~-gv~Glv~~s~ls~~------------~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ....+|+++.|.|.++.|+  |+||+++ +-.||+|.+++.+.            +..++.+.+++||.|.|.|
T Consensus        21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV   94 (414)
T TIGR00757        21 SRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQV   94 (414)
T ss_pred             CcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEE
Confidence            3456899999999999998  9999999 89999999999763            2335567899999999976

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.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=97.66  E-value=0.00014  Score=70.58  Aligned_cols=61  Identities=20%  Similarity=0.218  Sum_probs=50.6

Q ss_pred             CCCCCCEEEEEEEEEECC--eEEEEeCCCeEEEEeCcccccc------------cccCccccCcCCCCEEEEEEEE
Q 021034           96 NSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACIH------------KIKHVEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~--G~~V~i~~~~~g~lp~sEls~~------------~~~~~~~~~~~~G~~v~v~Vl~  157 (318)
                      ...+|+++.|+|.++.++  ||||++|.+..||||.+|+...            ..++..+. +++||.+-|.|.+
T Consensus        22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~-l~~G~~IlVQV~K   96 (414)
T TIGR00757        22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISEL-LRPGQSVLVQVVK   96 (414)
T ss_pred             cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHh-CcCCCEEEEEEee
Confidence            345899999999999998  9999999989999999998642            12234445 8899999999977

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.

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

Probab=97.63  E-value=0.0002  Score=73.76  Aligned_cols=66  Identities=15%  Similarity=0.391  Sum_probs=56.8

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcC---C-----------cchh-cCCeEeEEEEEEecccCeEe
Q 021034          186 SEDVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKS---T-----------AEEL-LGKDLPLKFVEVDEEQSRLV  248 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~---~-----------~~~~-vGq~v~~kVl~vd~~~~~i~  248 (318)
                      ..|+.++|+|++++++|+||+++  ++.|++|.+++.+..   +           ...+ +||+|+++|.++|.++++|.
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            47999999999999999999996  799999999998641   0           1234 79999999999999999998


Q ss_pred             eeh
Q 021034          249 LSN  251 (318)
Q Consensus       249 lS~  251 (318)
                      +++
T Consensus       651 f~l  653 (654)
T TIGR00358       651 FEL  653 (654)
T ss_pred             EEE
Confidence            874

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.

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

Probab=97.63  E-value=0.00018  Score=75.51  Aligned_cols=95  Identities=18%  Similarity=0.114  Sum_probs=76.6

Q ss_pred             CCCCHHHHHHHHhhhc-cCCCCCCEEEEEEEEEECCe---EEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEE
Q 021034           79 VSFTLEEFHSALEKYD-FNSELGTKVKGTVFCTDNRG---ALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFV  154 (318)
Q Consensus        79 ~~~s~~~~~~~~~~~~-~~~~~G~iv~G~V~~i~~~G---~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~  154 (318)
                      -.++.++.=.++..-. ..+..|.+|.++|.+++.+-   +-|.+..+..||||..++|+..+.+|.+. +++||++.|+
T Consensus       964 ~~l~~eeiF~mLTget~et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~-v~vgq~v~~k 1042 (1299)
T KOG1856|consen  964 HELTGEEIFDMLTGETPETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENR-VKVGQTVYCK 1042 (1299)
T ss_pred             CCCCHHHHHHHHhCCChhHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHh-hccCceEEEE
Confidence            3455555444554332 35889999999999998754   34577788999999999999999999887 9999999999


Q ss_pred             EEEEeCCCCeEEEEeeehhh
Q 021034          155 IIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus       155 Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      |+++|.++=.+.|||+.+..
T Consensus      1043 vi~id~e~f~v~Ls~r~sdl 1062 (1299)
T KOG1856|consen 1043 VIKIDKERFSVELSCRTSDL 1062 (1299)
T ss_pred             eeeeeHhhhhhhhhhhhHHh
Confidence            99999877778899998765

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=97.60  E-value=0.00022  Score=52.79  Aligned_cols=65  Identities=12%  Similarity=0.300  Sum_probs=55.4

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEE-C-CEEEEEe-CcccCCc--CCcchh-cCCeEeEEEEEEecccCeEeeeh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEV-E-GLRGFVP-FSQISSK--STAEEL-LGKDLPLKFVEVDEEQSRLVLSN  251 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i-~-gl~gfip-~s~ls~~--~~~~~~-vGq~v~~kVl~vd~~~~~i~lS~  251 (318)
                      +.|+++. .|+.+.+.|++|.+ + |++|+|. .++++.+  ...++. +|....+.|+.+|++++-|-||.
T Consensus        15 ~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kllVGk~e~v~ViRVDk~KGYIDLs~   85 (86)
T PHA02858         15 NINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKLVGKTINVQVIRTDKLKGYIDVRH   85 (86)
T ss_pred             CCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhhcCCeeEEEEEEECCCCCEEEeEc
Confidence            5788888 88899999999998 4 7999998 9999965  344444 89999999999999999998884

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

Probab=97.57  E-value=0.00065  Score=51.65  Aligned_cols=64  Identities=14%  Similarity=0.137  Sum_probs=47.6

Q ss_pred             CCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCcc----------ccCcCCCCEEEEEEEEEeCCCC
Q 021034           99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE----------EAGIVPGLKEEFVIIGENEADD  163 (318)
Q Consensus        99 ~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~----------~~~~~~G~~v~v~Vl~vd~~~~  163 (318)
                      .|+++.|+|.++++.|+++++|. +++|++...+..+...++.          +..+..|+.|+++|+++..+.+
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gp-l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~   74 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGP-LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDAT   74 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcC-ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccC
Confidence            48999999999999999999985 8888888777544333321          1226678889988877765433

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.

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

Probab=97.54  E-value=0.00064  Score=60.44  Aligned_cols=75  Identities=21%  Similarity=0.190  Sum_probs=62.9

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccc----ccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK----IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~----~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~  171 (318)
                      ..++||+|-|.|+.+...++.||+++...|+||.+++-...    ..+.... +.+||.+.++|..+|. ++.+.|++|.
T Consensus        61 iP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~-l~vGD~v~AkV~~vd~-~~~~~L~~k~  138 (239)
T COG1097          61 IPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPF-LNVGDLVYAKVVDVDR-DGEVELTLKD  138 (239)
T ss_pred             cCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccc-cccCCEEEEEEEEccC-CCceEEEeec
Confidence            67899999999999999999999999999999999993322    2344455 8999999999999985 6778888855


Q ss_pred             h
Q 021034          172 I  172 (318)
Q Consensus       172 ~  172 (318)
                      .
T Consensus       139 ~  139 (239)
T COG1097         139 E  139 (239)
T ss_pred             C
Confidence            3

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=97.35  E-value=0.00078  Score=65.15  Aligned_cols=66  Identities=20%  Similarity=0.273  Sum_probs=54.7

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEE----C--CEEEEEeCcccCCcCCcchh-cCCeEeEEEEEEeccc---CeEeeehhhh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEV----E--GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVEVDEEQ---SRLVLSNRKA  254 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i----~--gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~vd~~~---~~i~lS~K~~  254 (318)
                      ..|++++|+|.++.+++++|++    +  ++.|+||.++...+..   | .|+.++|.|.+++...   -.|.||+-..
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            3899999999999999999998    4  2899999998775433   3 7999999999998653   3699998654

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

Probab=97.30  E-value=0.0015  Score=56.26  Aligned_cols=77  Identities=8%  Similarity=0.006  Sum_probs=57.1

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccccc-----------CccccCcCCCCEEEEEEEEEeCC--C
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEA--D  162 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~-----------~~~~~~~~~G~~v~v~Vl~vd~~--~  162 (318)
                      ..-.|+++.|.|+++++.|+++++|. .++|+|.+.|.+...-           +.++..+..|+.|+++|+++..+  +
T Consensus        78 rPf~gEVv~g~V~~v~~~G~~v~~Gp-~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~  156 (176)
T PTZ00162         78 KPFKDEVLDAIVTDVNKLGFFAQAGP-LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASN  156 (176)
T ss_pred             ecCCCCEEEEEEEEEecceEEEEeeC-eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCC
Confidence            45689999999999999999999985 7799999999743111           11112277899999999776543  3


Q ss_pred             CeEEEEeeehh
Q 021034          163 DSLVLSLRMIQ  173 (318)
Q Consensus       163 ~~i~lS~k~~~  173 (318)
                      .....|+|.+-
T Consensus       157 ~~~i~T~~~~~  167 (176)
T PTZ00162        157 LFAIATINSDY  167 (176)
T ss_pred             cEEEEEecCCC
Confidence            45777887753

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

Probab=97.22  E-value=0.00075  Score=58.04  Aligned_cols=55  Identities=22%  Similarity=0.342  Sum_probs=45.5

Q ss_pred             cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccc------------cCcccccCCCCEEEEEC
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV------------ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~------------~~~~~~~~~Gq~V~v~V  318 (318)
                      .|+++.|.|++++++|+||++|-+++++|.++|.++..            .+-...+..|+.|++||
T Consensus        81 ~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV  147 (176)
T PTZ00162         81 KDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRL  147 (176)
T ss_pred             CCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEE
Confidence            59999999999999999999997889999999975321            11235689999999986

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=97.13  E-value=0.0012  Score=46.65  Aligned_cols=47  Identities=32%  Similarity=0.504  Sum_probs=29.1

Q ss_pred             cCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .|++.+..|..++++|+|++-+ +-+-|+|.+++...        +++||+|.|.|
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~--------~~~Gd~v~VFv   48 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEP--------LKVGDEVEVFV   48 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG--------------TTSEEEEEE
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCC--------CCCCCEEEEEE
Confidence            4889999999999999999998 69999999987633        89999999875

>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=97.05  E-value=0.00084  Score=50.23  Aligned_cols=56  Identities=20%  Similarity=0.445  Sum_probs=38.6

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC-------------------CeEEEEecCCcCccccc--CcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG-------------------GINGLLHVSQISHDRVA--DIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~-------------------gv~Glv~~s~ls~~~~~--~~~~~~~~Gq~V~v~V  318 (318)
                      ++|++|.|.|+++++.-++++|-                   .+.|+++++++......  ++.+.|++||-|.|+|
T Consensus         3 ~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~V   79 (82)
T PF10447_consen    3 KVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARV   79 (82)
T ss_dssp             -TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEE
T ss_pred             CCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEE
Confidence            47999999999999888877763                   36899999998776544  4689999999999986

The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.

>PRK05054 exoribonuclease II; Provisional

Probab=96.94  E-value=0.0045  Score=63.73  Aligned_cols=63  Identities=19%  Similarity=0.366  Sum_probs=52.9

Q ss_pred             CcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCc---C----C--------cchh-cCCeEeEEEEEEecccCeEee
Q 021034          188 DVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSK---S----T--------AEEL-LGKDLPLKFVEVDEEQSRLVL  249 (318)
Q Consensus       188 G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~---~----~--------~~~~-vGq~v~~kVl~vd~~~~~i~l  249 (318)
                      |+.++|.|++++++|+||++.  |+.||+|.+.|.+.   +    +        -+.| +||.|+++|.++|..+++|.+
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            459999999999999999995  89999999998642   1    1        1234 799999999999999999877


Q ss_pred             e
Q 021034          250 S  250 (318)
Q Consensus       250 S  250 (318)
                      +
T Consensus       642 ~  642 (644)
T PRK05054        642 R  642 (644)
T ss_pred             E
Confidence            5

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

Probab=96.91  E-value=0.0028  Score=54.28  Aligned_cols=73  Identities=22%  Similarity=0.323  Sum_probs=59.8

Q ss_pred             CeEeeehhhhhhhhHhhcccCeEEEEEEEEEEcceEEEEECC-----------eEEEEecCCcCcccccCcccccCCCCE
Q 021034          245 SRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGG-----------INGLLHVSQISHDRVADIATVLQPGDT  313 (318)
Q Consensus       245 ~~i~lS~K~~l~~~~~~l~~G~~v~G~V~~i~~~G~fV~i~g-----------v~Glv~~s~ls~~~~~~~~~~~~~Gq~  313 (318)
                      ++...|.++... .+.-++.|++|-|.|+.+....+.|++.+           ..|-+|.|+++.....+.++.|++||.
T Consensus        46 ~n~~~~V~p~~~-~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDi  124 (188)
T COG1096          46 KNRVISVKPGKK-TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDI  124 (188)
T ss_pred             cceEEEeccCCC-CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccE
Confidence            444555554332 34568889999999999999999999853           456789999999999999999999999


Q ss_pred             EEEEC
Q 021034          314 LKVCL  318 (318)
Q Consensus       314 V~v~V  318 (318)
                      |+|+|
T Consensus       125 vrA~V  129 (188)
T COG1096         125 VRARV  129 (188)
T ss_pred             EEEEE
Confidence            99986

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

Probab=96.86  E-value=0.0057  Score=52.36  Aligned_cols=74  Identities=20%  Similarity=0.157  Sum_probs=62.7

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCC----------CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITA----------KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL  165 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~----------~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i  165 (318)
                      -++.|++|-|.|+++....+.|.+.+          ...|-+|+++.++.+.++.++. |++||.+.++|++.-   ..+
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            56789999999999999999988732          1468999999999999998887 999999999998864   568


Q ss_pred             EEEeeehh
Q 021034          166 VLSLRMIQ  173 (318)
Q Consensus       166 ~lS~k~~~  173 (318)
                      .||.+...
T Consensus       137 ~Lst~~~d  144 (188)
T COG1096         137 QLSTKGND  144 (188)
T ss_pred             EEEecCCc
Confidence            88887653

>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=96.74  E-value=0.0057  Score=45.75  Aligned_cols=61  Identities=18%  Similarity=0.175  Sum_probs=38.7

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEeC------------------CCeEEEEeCcccccccccC--ccccCcCCCCEEEEEEE
Q 021034           97 SELGTKVKGTVFCTDNRGALVDIT------------------AKSSAYLPTQEACIHKIKH--VEEAGIVPGLKEEFVII  156 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i~------------------~~~~g~lp~sEls~~~~~~--~~~~~~~~G~~v~v~Vl  156 (318)
                      .++|++|.|+|+++.+.-++++|-                  ....|.|+.+++......+  +.+- |++||.|.++|+
T Consensus         2 P~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~-FrpGDIVrA~Vi   80 (82)
T PF10447_consen    2 PKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDC-FRPGDIVRARVI   80 (82)
T ss_dssp             --TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT---SSSEEEEEEE
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhc-cCCCCEEEEEEe
Confidence            368999999999999999988771                  1356888888876543332  3444 999999999998


Q ss_pred             EE
Q 021034          157 GE  158 (318)
Q Consensus       157 ~v  158 (318)
                      +.
T Consensus        81 Sl   82 (82)
T PF10447_consen   81 SL   82 (82)
T ss_dssp             EE
T ss_pred             eC
Confidence            73

The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.

>PRK10811 rne ribonuclease E; Reviewed

Probab=96.65  E-value=0.0053  Score=64.37  Aligned_cols=59  Identities=19%  Similarity=0.253  Sum_probs=47.7

Q ss_pred             CCCCEEEEEEEEEEC--CeEEEEeCCCeEEEEeCcccccccccC---------ccccCcCCCCEEEEEEEE
Q 021034           98 ELGTKVKGTVFCTDN--RGALVDITAKSSAYLPTQEACIHKIKH---------VEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~--~G~~V~i~~~~~g~lp~sEls~~~~~~---------~~~~~~~~G~~v~v~Vl~  157 (318)
                      .+|.|+.|+|.++.+  +++||+||.+..||||+++.......+         ..+. +++||.|-|-|.+
T Consensus        37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~-Lk~GqeILVQV~K  106 (1068)
T PRK10811         37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDV-LREGQEVIVQIDK  106 (1068)
T ss_pred             CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccc-cCCCCEEEEEEee
Confidence            489999999999998  699999999999999999996432211         1233 7889999999966

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

Probab=96.50  E-value=0.021  Score=56.77  Aligned_cols=145  Identities=14%  Similarity=0.160  Sum_probs=98.2

Q ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      ++++.|....|+|.++.+.|+||+++..+.|+++.++++..    +   .+.+|+.+-+.+..+.+.++.+.+.-..+..
T Consensus       118 ~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~----~---~~~vgdeiiV~v~~vr~~~geidf~~~~~~~  190 (715)
T COG1107         118 EDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD----P---DYAVGDEIIVQVSDVRPEKGEIDFEPVGLDR  190 (715)
T ss_pred             hhcccceeeeccccchhhhcceeecChhhhccccccccCCC----C---CCCCCCeEEEEeeccCCCCCccceeecCCcc
Confidence            38899999999999999999999999999999999998752    1   2789999999999998877776655544431


Q ss_pred             -----------hHHHHHHhhhcCCC--cEEEEEEEEEE-cCe-EEEEECCEEEEEeCcccCCc--CCcchh-cCCeEeEE
Q 021034          175 -----------ELAWERCRQLQSED--VVVKGKVVGAN-KGG-VVAEVEGLRGFVPFSQISSK--STAEEL-LGKDLPLK  236 (318)
Q Consensus       175 -----------~~~~~~~~~~~~~G--~iv~g~V~~v~-~~G-~~V~i~gl~gfip~s~ls~~--~~~~~~-vGq~v~~k  236 (318)
                                 ......+.+.  .|  ..++|.|+.+. ..| -+..+..=.|+++..-....  ...-++ +|+.|.+.
T Consensus       191 Y~~~~~~ke~~r~~i~~id~~--ig~tV~I~GeV~qikqT~GPTVFtltDetg~i~aAAFe~aGvRAyP~IevGdiV~Vi  268 (715)
T COG1107         191 YREVQVEKELPRTLIDDLDEM--IGKTVRIEGEVTQIKQTSGPTVFTLTDETGAIWAAAFEEAGVRAYPEIEVGDIVEVI  268 (715)
T ss_pred             chhhhhhhhcccccHHHHHhh--cCceEEEEEEEEEEEEcCCCEEEEEecCCCceehhhhccCCcccCCCCCCCceEEEE
Confidence                       0112334442  45  35789999983 333 34455444677776655532  221223 78887754


Q ss_pred             EEEEecccCeEee
Q 021034          237 FVEVDEEQSRLVL  249 (318)
Q Consensus       237 Vl~vd~~~~~i~l  249 (318)
                       =+++...+++.+
T Consensus       269 -G~V~~r~g~lQi  280 (715)
T COG1107         269 -GEVTRRDGRLQI  280 (715)
T ss_pred             -EEEeecCCcEEE
Confidence             234445566544

>PRK11712 ribonuclease G; Provisional

Probab=96.44  E-value=0.0088  Score=59.34  Aligned_cols=61  Identities=21%  Similarity=0.312  Sum_probs=47.6

Q ss_pred             CCCCCCEEEEEEEEEEC--CeEEEEeCCCeEEEEeCcccccc------------cccCccccCcCCCCEEEEEEEE
Q 021034           96 NSELGTKVKGTVFCTDN--RGALVDITAKSSAYLPTQEACIH------------KIKHVEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~--~G~~V~i~~~~~g~lp~sEls~~------------~~~~~~~~~~~~G~~v~v~Vl~  157 (318)
                      ...+|.++.|+|.++.+  ++|||++|.+-.||||.+++...            ......+. +++||.+-|.|.+
T Consensus        35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~-l~~Gq~iLVQV~K  109 (489)
T PRK11712         35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISEL-VRQGQDIMVQVVK  109 (489)
T ss_pred             ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHh-ccCCCEEEEEEEe
Confidence            34589999999999998  69999999999999999987310            01112334 7889999998866

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

Probab=96.41  E-value=0.027  Score=43.52  Aligned_cols=67  Identities=19%  Similarity=0.202  Sum_probs=51.0

Q ss_pred             HHHHHHHhhhc---cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEE
Q 021034           84 EEFHSALEKYD---FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE  158 (318)
Q Consensus        84 ~~~~~~~~~~~---~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~v  158 (318)
                      +.|++++..+-   ..-..|.+|.|+|..+.++-+|+|+|++..++++..+...       +. +..|..|.+++.+.
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            46777774432   1124799999999999999999999999999999765432       22 77899999888543

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 [].

>PRK05054 exoribonuclease II; Provisional

Probab=96.38  E-value=0.022  Score=58.67  Aligned_cols=72  Identities=13%  Similarity=0.117  Sum_probs=55.9

Q ss_pred             CCC--CEEEEEEEEEECCeEEEEe-CCCeEEEEeCcccccc---ccc--C------ccccCcCCCCEEEEEEEEEeCCCC
Q 021034           98 ELG--TKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACIH---KIK--H------VEEAGIVPGLKEEFVIIGENEADD  163 (318)
Q Consensus        98 ~~G--~iv~G~V~~i~~~G~~V~i-~~~~~g~lp~sEls~~---~~~--~------~~~~~~~~G~~v~v~Vl~vd~~~~  163 (318)
                      .+|  +...|.|+.++++|+||.+ ..+++|++|.+.+.+.   +.-  +      .....|++||.|+|+|.++|..++
T Consensus       558 ~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~  637 (644)
T PRK05054        558 KAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR  637 (644)
T ss_pred             ccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence            365  4999999999999999999 4569999999998652   110  1      011128899999999999999998


Q ss_pred             eEEEEe
Q 021034          164 SLVLSL  169 (318)
Q Consensus       164 ~i~lS~  169 (318)
                      ++.++.
T Consensus       638 ~i~~~~  643 (644)
T PRK05054        638 SIIARP  643 (644)
T ss_pred             eEEEEE
Confidence            887653

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

Probab=96.28  E-value=0.0026  Score=62.98  Aligned_cols=54  Identities=24%  Similarity=0.503  Sum_probs=47.2

Q ss_pred             HhhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          259 QAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       259 ~~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +.++..|..++|+|.++..||+||+++ .+.||+|.++++..      ..|.+|+.+-|.+
T Consensus       117 ~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------~~~~vgdeiiV~v  171 (715)
T COG1107         117 MEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------PDYAVGDEIIVQV  171 (715)
T ss_pred             hhhcccceeeeccccchhhhcceeecChhhhccccccccCCC------CCCCCCCeEEEEe
Confidence            467899999999999999999999999 89999999999863      2378899887764

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

Probab=96.19  E-value=0.01  Score=52.82  Aligned_cols=57  Identities=30%  Similarity=0.462  Sum_probs=50.6

Q ss_pred             cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCccc----ccCcccccCCCCEEEEEC
Q 021034          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR----VADIATVLQPGDTLKVCL  318 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~----~~~~~~~~~~Gq~V~v~V  318 (318)
                      -+.||.|-|.|..+.+.+..|+++ -..+++|.|++.+..    ..+....|++||.|.|+|
T Consensus        62 P~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV  123 (239)
T COG1097          62 PEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKV  123 (239)
T ss_pred             CCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEE
Confidence            446999999999999999999999 699999999996655    356788899999999986

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

Probab=96.18  E-value=0.0079  Score=63.65  Aligned_cols=59  Identities=17%  Similarity=0.251  Sum_probs=53.4

Q ss_pred             hhcccCeEEEEEEEEEEcce---EEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYG---AFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G---~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +.+.+|.+|.++|++++..-   +-|.+. |++|+|+.+++|+..+.+|...+++||+|.|+|
T Consensus       981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kv 1043 (1299)
T KOG1856|consen  981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKV 1043 (1299)
T ss_pred             hHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEe
Confidence            56889999999999999644   567777 999999999999999999999999999999986

>TIGR02062 RNase_B exoribonuclease II

Probab=96.12  E-value=0.027  Score=58.04  Aligned_cols=63  Identities=17%  Similarity=0.364  Sum_probs=51.5

Q ss_pred             CcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCC--c-C--C-------c--c-hh-cCCeEeEEEEEEecccCeEee
Q 021034          188 DVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISS--K-S--T-------A--E-EL-LGKDLPLKFVEVDEEQSRLVL  249 (318)
Q Consensus       188 G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~--~-~--~-------~--~-~~-vGq~v~~kVl~vd~~~~~i~l  249 (318)
                      |....|.|++++++|+||++.  |+.||+|.+.+.+  . .  +       +  . .| +||.|+++|.++|.++++|.+
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            458999999999999999994  8999999999865  1 1  1       1  1 24 799999999999999888875


Q ss_pred             e
Q 021034          250 S  250 (318)
Q Consensus       250 S  250 (318)
                      .
T Consensus       638 ~  638 (639)
T TIGR02062       638 R  638 (639)
T ss_pred             e
Confidence            3

This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.

>PRK11712 ribonuclease G; Provisional

Probab=96.09  E-value=0.0087  Score=59.38  Aligned_cols=58  Identities=31%  Similarity=0.516  Sum_probs=46.1

Q ss_pred             hcccCeEEEEEEEEEEc--ceEEEEEC-CeEEEEecCCcCcc------------cccCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISHD------------RVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~--~G~fV~i~-gv~Glv~~s~ls~~------------~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ...+|.++.|.|.+|.|  .++||++| +-.||+|.+++...            ...+..+.+++||.|-|.|
T Consensus        35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV  107 (489)
T PRK11712         35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQV  107 (489)
T ss_pred             ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEE
Confidence            44579999999999998  78999999 99999999987321            0112355699999998875

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

Probab=96.09  E-value=0.02  Score=43.30  Aligned_cols=55  Identities=22%  Similarity=0.134  Sum_probs=45.9

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ++||.|-|.|..++..+.+|+++ -..|++|.+.+.-. ..+....|++||-|-|||
T Consensus         5 ~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV   60 (86)
T cd05790           5 AKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA-TKRNRPNLNVGDLVYARV   60 (86)
T ss_pred             CCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-cccccccCCCCCEEEEEE
Confidence            57999999999999999999998 78999999776432 333456699999999986

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".

>PRK10811 rne ribonuclease E; Reviewed

Probab=96.09  E-value=0.0097  Score=62.47  Aligned_cols=56  Identities=25%  Similarity=0.509  Sum_probs=46.1

Q ss_pred             ccCeEEEEEEEEEEc--ceEEEEEC-CeEEEEecCCcCccccc---------CcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISHDRVA---------DIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~--~G~fV~i~-gv~Glv~~s~ls~~~~~---------~~~~~~~~Gq~V~v~V  318 (318)
                      .+|.++.|+|.+|.+  .++||+|| |-.||+|.+++......         +....+++||.|-|.|
T Consensus        37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV  104 (1068)
T PRK10811         37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQI  104 (1068)
T ss_pred             CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEE
Confidence            479999999999987  78999999 99999999998643221         2345689999999875

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

Probab=96.08  E-value=0.0067  Score=54.46  Aligned_cols=71  Identities=21%  Similarity=0.423  Sum_probs=61.2

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEE---CCEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhhhhh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEV---EGLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRKAMA  256 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i---~gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~~l~  256 (318)
                      +.+++|-+.|.++..-|++|.+   +++.|++-.|+||.+  ....++  ||..=.|.|+.+|++++-|-||.+..-.
T Consensus        15 ev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~   92 (304)
T KOG2916|consen   15 EVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP   92 (304)
T ss_pred             CcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCCCceechhccCCH
Confidence            4789999999999999999987   599999999999976  344444  7988889999999999999999887543

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=95.87  E-value=0.015  Score=60.71  Aligned_cols=58  Identities=28%  Similarity=0.569  Sum_probs=48.3

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEEC--CeEEEEecCCcCcccc-----------cCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~--gv~Glv~~s~ls~~~~-----------~~~~~~~~~Gq~V~v~V  318 (318)
                      .-.+|+...|+|.+++.+|+||.+.  +++|++|.+.+..++.           ......|+.||.|++++
T Consensus       619 ~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v  689 (706)
T COG0557         619 KKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKV  689 (706)
T ss_pred             HHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEE
Confidence            4557999999999999999999997  6999999999996322           23344699999999985

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=95.78  E-value=0.027  Score=58.74  Aligned_cols=74  Identities=11%  Similarity=0.086  Sum_probs=58.9

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCC-eEEEEeCcccccccccCcc----------ccCcCCCCEEEEEEEEEeCCCCe
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAK-SSAYLPTQEACIHKIKHVE----------EAGIVPGLKEEFVIIGENEADDS  164 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~-~~g~lp~sEls~~~~~~~~----------~~~~~~G~~v~v~Vl~vd~~~~~  164 (318)
                      .-.+|+...|+|.++..+|++|.+... .+|++|.+.+...+.....          ...++.|+.|++++.+++...+.
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            446899999999999999999999654 8999999999853321111          11278999999999999988888


Q ss_pred             EEEEe
Q 021034          165 LVLSL  169 (318)
Q Consensus       165 i~lS~  169 (318)
                      +.++.
T Consensus       699 i~~~~  703 (706)
T COG0557         699 IDFEL  703 (706)
T ss_pred             eEEEe
Confidence            87764

>TIGR02062 RNase_B exoribonuclease II

Probab=95.71  E-value=0.1  Score=53.73  Aligned_cols=69  Identities=13%  Similarity=0.138  Sum_probs=53.5

Q ss_pred             CCEEEEEEEEEECCeEEEEe-CCCeEEEEeCccccc--c-cc--cCc------cccCcCCCCEEEEEEEEEeCCCCeEEE
Q 021034          100 GTKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACI--H-KI--KHV------EEAGIVPGLKEEFVIIGENEADDSLVL  167 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i-~~~~~g~lp~sEls~--~-~~--~~~------~~~~~~~G~~v~v~Vl~vd~~~~~i~l  167 (318)
                      |+...|.|+.+.++|+||.+ ..+.+|++|.+.+.+  + +.  .+.      .+..|++||.|+|+|.++|.+++++.+
T Consensus       558 ~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~  637 (639)
T TIGR02062       558 NTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIA  637 (639)
T ss_pred             CcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEee
Confidence            45899999999999999999 567999999999864  2 11  100      111288999999999999988888765


Q ss_pred             E
Q 021034          168 S  168 (318)
Q Consensus       168 S  168 (318)
                      .
T Consensus       638 ~  638 (639)
T TIGR02062       638 R  638 (639)
T ss_pred             e
Confidence            3

This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.

>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=94.74  E-value=0.25  Score=39.84  Aligned_cols=62  Identities=15%  Similarity=0.109  Sum_probs=44.4

Q ss_pred             CCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc---------ccc---CccccCcCCCCEEEEEEEEEeC
Q 021034           99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH---------KIK---HVEEAGIVPGLKEEFVIIGENE  160 (318)
Q Consensus        99 ~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~---------~~~---~~~~~~~~~G~~v~v~Vl~vd~  160 (318)
                      +|+++.|+|.+-++.|+.|.++---+-|+|.+.|-..         ++-   .-.++-+..|+.|+++|.++.-
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            6999999999999999999998777899999888631         111   1122225789999999987654

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

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

Probab=94.11  E-value=0.19  Score=42.10  Aligned_cols=55  Identities=22%  Similarity=0.315  Sum_probs=38.5

Q ss_pred             cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCc----ccccC-c------ccccCCCCEEEEEC
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISH----DRVAD-I------ATVLQPGDTLKVCL  318 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~----~~~~~-~------~~~~~~Gq~V~v~V  318 (318)
                      .|++|+|+|+.+...|+|++.|-++-++..-.+..    .+-++ |      ....++|..|+++|
T Consensus        81 KGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~ki  146 (170)
T KOG3298|consen   81 KGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKI  146 (170)
T ss_pred             CCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEE
Confidence            49999999999999999999997777665544432    22222 2      12467777777664

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

Probab=93.90  E-value=0.29  Score=37.91  Aligned_cols=49  Identities=18%  Similarity=0.331  Sum_probs=42.0

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .+|.+|.|.|..+.+.-+||+|| .+.+.|+......       +.|+.|..|.+++
T Consensus        22 ~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~~-------~~y~~G~rV~lrL   71 (104)
T PF10246_consen   22 PEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVNG-------EKYVRGSRVRLRL   71 (104)
T ss_pred             ccCCEEEEEEEEEecCceEEEeCCceeEEEecccccc-------cccccCCEEEEEE
Confidence            36999999999999999999999 7999999765432       4589999999874

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 [].

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

Probab=93.61  E-value=0.53  Score=39.47  Aligned_cols=66  Identities=17%  Similarity=0.196  Sum_probs=42.0

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccc----ccccCc------cccCcCCCCEEEEEEEEEeCCCC
Q 021034           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACI----HKIKHV------EEAGIVPGLKEEFVIIGENEADD  163 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~----~~~~~~------~~~~~~~G~~v~v~Vl~vd~~~~  163 (318)
                      .-.|+++.|+|.++.+.|+|++.|. .+.|+...-+-.    ..-.++      .+.....|.+|+++|++...+..
T Consensus        79 pfKGEVvdgvV~~Vnk~G~F~~~GP-l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~  154 (170)
T KOG3298|consen   79 PFKGEVVDGVVTKVNKMGVFARSGP-LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDET  154 (170)
T ss_pred             ecCCcEEEEEEEEEeeeeEEEeccc-eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEeee
Confidence            3479999999999999999999986 555544322211    111110      11125678888888887654333

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

Probab=93.47  E-value=0.44  Score=40.38  Aligned_cols=72  Identities=19%  Similarity=0.142  Sum_probs=51.8

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEe---CC-----CeEEEEeCccccccc--ccCccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034           97 SELGTKVKGTVFCTDNRGALVDI---TA-----KSSAYLPTQEACIHK--IKHVEEAGIVPGLKEEFVIIGENEADDSLV  166 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i---~~-----~~~g~lp~sEls~~~--~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~  166 (318)
                      ...|++|+++|..+...-+-|+|   +.     ..+|+||..++-...  .-++-+. |++||.|.++|++... +....
T Consensus        66 P~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ks-FrPgDiVlAkVis~~~-~~~y~  143 (193)
T KOG3409|consen   66 PFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKS-FRPGDIVLAKVISLGD-GSNYL  143 (193)
T ss_pred             CccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhc-cCCCcEEEEEEeecCC-CCcEE
Confidence            35799999999999998887766   32     358999998885321  1123333 8999999999999654 44566


Q ss_pred             EEee
Q 021034          167 LSLR  170 (318)
Q Consensus       167 lS~k  170 (318)
                      ||.-
T Consensus       144 LTtA  147 (193)
T KOG3409|consen  144 LTTA  147 (193)
T ss_pred             EEEe
Confidence            6653

>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=93.01  E-value=0.55  Score=37.88  Aligned_cols=56  Identities=18%  Similarity=0.251  Sum_probs=42.1

Q ss_pred             CCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc------CC-----c---chh---cCCeEeEEEEEEec
Q 021034          187 EDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK------ST-----A---EEL---LGKDLPLKFVEVDE  242 (318)
Q Consensus       187 ~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~------~~-----~---~~~---vGq~v~~kVl~vd~  242 (318)
                      .|+++.|+|.+.++.|+.|.++ --+-|||.+.|...      ..     .   .++   .|+.|++||.++.-
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            6899999999999999999998 46789999998843      10     1   122   59999999988754

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

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

Probab=91.98  E-value=0.26  Score=49.13  Aligned_cols=63  Identities=22%  Similarity=0.230  Sum_probs=49.6

Q ss_pred             CCCCCCEEEEEEEEEECC--eEEEEeCCCeEEEEeCcccccccccCccc----cCcCCCCEEEEEEEEEe
Q 021034           96 NSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACIHKIKHVEE----AGIVPGLKEEFVIIGEN  159 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~--G~~V~i~~~~~g~lp~sEls~~~~~~~~~----~~~~~G~~v~v~Vl~vd  159 (318)
                      ...+|.++.|.|.++.++  .+|||+|..-.||||.+|+.. +.+.+.+    ..++.||.+-+.|+...
T Consensus        34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~  102 (487)
T COG1530          34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEP  102 (487)
T ss_pred             EeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEEEeec
Confidence            345899999999999995  799999999999999999988 3333322    12788998888886643

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

Probab=91.64  E-value=0.38  Score=40.72  Aligned_cols=55  Identities=20%  Similarity=0.353  Sum_probs=42.2

Q ss_pred             cCeEEEEEEEEEEcceEEEEEC---------CeEEEEecCCcCccc--ccCcccccCCCCEEEEEC
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIG---------GINGLLHVSQISHDR--VADIATVLQPGDTLKVCL  318 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~---------gv~Glv~~s~ls~~~--~~~~~~~~~~Gq~V~v~V  318 (318)
                      +|++|.+.|.+++.-=+-|+|-         .+.|++|+.++....  -.++-+.|++||.|.|+|
T Consensus        68 ~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkV  133 (193)
T KOG3409|consen   68 VGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKV  133 (193)
T ss_pred             cCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEE
Confidence            5888888888887766666653         289999998886642  345777899999999986

>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]

Probab=91.51  E-value=2  Score=35.10  Aligned_cols=69  Identities=19%  Similarity=0.202  Sum_probs=53.1

Q ss_pred             HHHHHHHHhhhc---cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEe
Q 021034           83 LEEFHSALEKYD---FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGEN  159 (318)
Q Consensus        83 ~~~~~~~~~~~~---~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd  159 (318)
                      .+.|++++....   ..-..|..|.|+|..+..+-+|+|||++..+.+..-++..      + . +..|..|..++++.+
T Consensus        63 nqsFASlLRnSkl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n~------e-~-Y~~GaRVrlRl~DlE  134 (173)
T KOG4078|consen   63 NQSFASLLRNSKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALNG------E-A-YQKGARVRLRLIDLE  134 (173)
T ss_pred             hhhHHHHHhcCccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcCH------H-H-hhcCceEEEEEcChh
Confidence            568999885432   2335799999999999999999999999999888766532      2 2 678988888886543

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

Probab=90.94  E-value=0.21  Score=49.75  Aligned_cols=58  Identities=33%  Similarity=0.492  Sum_probs=47.6

Q ss_pred             hhcccCeEEEEEEEEEEc--ceEEEEEC-CeEEEEecCCcCcccccC-----cccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISHDRVAD-----IATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~--~G~fV~i~-gv~Glv~~s~ls~~~~~~-----~~~~~~~Gq~V~v~V  318 (318)
                      ....+|.++.|.|++|.|  -.+||+++ +-.||+|.+++.+ +...     .+..++.||.+-|.|
T Consensus        33 ~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv   98 (487)
T COG1530          33 KEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQV   98 (487)
T ss_pred             cEeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccccceeeecCCceEEEEE
Confidence            455679999999999998  56999999 8999999999998 3333     245789999987754

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

Probab=86.92  E-value=3.4  Score=36.31  Aligned_cols=63  Identities=17%  Similarity=0.037  Sum_probs=50.0

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeC
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENE  160 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~  160 (318)
                      -..+|+.|-|.|+....+..-||+++...|.||.--+....-++-.+  +.+|+-+-++|...++
T Consensus        62 iP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe~AtkrNrPn--l~vGdliyakv~~a~~  124 (230)
T KOG1004|consen   62 IPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFEGATKRNRPN--LQVGDLIYAKVVDANK  124 (230)
T ss_pred             cCCCCCEEEEEEEeccCceEEEecCCCCeeeeeeccccCccccCCCc--cccccEEEEEEEecCC
Confidence            56789999999999999999999998788988876665443232222  8899999999977553

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=86.84  E-value=3.2  Score=31.21  Aligned_cols=65  Identities=17%  Similarity=0.163  Sum_probs=44.7

Q ss_pred             cEEEEEEEEEEcCeEE-EEEC-CEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeeehhh
Q 021034          189 VVVKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRK  253 (318)
Q Consensus       189 ~iv~g~V~~v~~~G~~-V~i~-gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K~  253 (318)
                      -.++|+|++...++.| |.++ |..-+.+.+-=......+-+.||.|.+.+...|..+++|+.-.|+
T Consensus         7 ie~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~   73 (87)
T PRK12442          7 IELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHKD   73 (87)
T ss_pred             EEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence            3689999999888877 6886 654444322211111223336999999999999999999877663

>TIGR00008 infA translation initiation factor IF-1

Probab=86.60  E-value=4.8  Score=28.96  Aligned_cols=60  Identities=15%  Similarity=0.166  Sum_probs=40.9

Q ss_pred             EEEEEEEEEECCeEE-EEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034          102 KVKGTVFCTDNRGAL-VDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLV  166 (318)
Q Consensus       102 iv~G~V~~i~~~G~~-V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~  166 (318)
                      .+.|+|++..+++.| |.+.++..-..+++-    .++.- .....+||.|.+.+-.+|.++++++
T Consensus         6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~G----Kmr~~-rI~I~~GD~V~Ve~spyd~tkgrIi   66 (68)
T TIGR00008         6 EMEGKVTESLPNAMFRVELENGHEVLAHISG----KIRMH-YIRILPGDKVKVELSPYDLTRGRIT   66 (68)
T ss_pred             EEEEEEEEECCCCEEEEEECCCCEEEEEecC----cchhc-cEEECCCCEEEEEECcccCCcEeEE
Confidence            568999999999877 687665544444321    11110 1126789999999998988888875

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).

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=86.33  E-value=5.7  Score=29.94  Aligned_cols=64  Identities=9%  Similarity=0.036  Sum_probs=45.2

Q ss_pred             EEEEEEEEEECCeEE-EEeCCCeEEEEeCcc-cccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034          102 KVKGTVFCTDNRGAL-VDITAKSSAYLPTQE-ACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (318)
Q Consensus       102 iv~G~V~~i~~~G~~-V~i~~~~~g~lp~sE-ls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~  171 (318)
                      .++|+|+...+++.| |.+.++..-+.+++- |.-.+      ....+||.|.|.+-.+|..+++|+.-.+.
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            568999999998877 688665544444321 11111      12678999999999999999999877664

>TIGR00008 infA translation initiation factor IF-1

Probab=85.32  E-value=5.1  Score=28.81  Aligned_cols=59  Identities=19%  Similarity=0.233  Sum_probs=39.8

Q ss_pred             EEEEEEEEEEcCeEE-EEEC-CEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEe
Q 021034          190 VVKGKVVGANKGGVV-AEVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLV  248 (318)
Q Consensus       190 iv~g~V~~v~~~G~~-V~i~-gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~  248 (318)
                      .+.|+|++...++.| |.++ |..-..+.+-=......+-..|+.|.+.+-..|.++++|+
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 EMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRIT   66 (68)
T ss_pred             EEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECcccCCcEeEE
Confidence            589999999888876 6875 6554444322111111222369999999999998888876

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).

>PRK15464 cold shock-like protein CspH; Provisional

Probab=84.96  E-value=8.6  Score=27.73  Aligned_cols=50  Identities=18%  Similarity=0.319  Sum_probs=35.8

Q ss_pred             EEEEEEEEEC-CeE-EEEe-CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034          103 VKGTVFCTDN-RGA-LVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus       103 v~G~V~~i~~-~G~-~V~i-~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~  157 (318)
                      .+|+|...++ .|. |+.- .++-+.|+|++.+.....+.     +.+||.|++.+..
T Consensus         5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~-----l~~G~~V~f~v~~   57 (70)
T PRK15464          5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEV-----LIPGLRVEFCRVN   57 (70)
T ss_pred             ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCC-----CCCCCEEEEEEEE
Confidence            4799999976 333 4544 45679999999996442222     6789999998854

>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=84.06  E-value=12  Score=26.13  Aligned_cols=50  Identities=16%  Similarity=0.236  Sum_probs=35.3

Q ss_pred             EEEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034          103 VKGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus       103 v~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~  157 (318)
                      .+|+|....+   +|.+..-++..+-|+|.+++......     .+..|+.|++.+..
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            3699999986   35544445556999999999765411     17889999999966

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 ....

>PRK10943 cold shock-like protein CspC; Provisional

Probab=83.36  E-value=13  Score=26.55  Aligned_cols=51  Identities=20%  Similarity=0.244  Sum_probs=36.6

Q ss_pred             EEEEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034          102 KVKGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus       102 iv~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~  157 (318)
                      .++|+|...++   +|.+-.-.++-+-|+|++.+.....+.     +..|+.|++.+..
T Consensus         3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~~~-----l~~G~~V~f~~~~   56 (69)
T PRK10943          3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKT-----LAEGQNVEFEIQD   56 (69)
T ss_pred             ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCCCC-----CCCCCEEEEEEEE
Confidence            56899999876   344444455679999999986542222     6789999998854

>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional

Probab=82.89  E-value=12  Score=27.37  Aligned_cols=60  Identities=13%  Similarity=0.127  Sum_probs=40.0

Q ss_pred             EEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034          104 KGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus       104 ~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      +|+|...+.   +|.+..-.++-+.|+|++.+.....+.     +..||.|++.+..  ..++.-.....
T Consensus         3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~~~-----l~~G~~V~f~~~~--~~~G~~A~~V~   65 (74)
T PRK09937          3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRT-----LKAGQSVQFDVHQ--GPKGNHASVIV   65 (74)
T ss_pred             CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCCCC-----CCCCCEEEEEEEE--CCCCceeeEEE
Confidence            488988875   344444456689999999986442222     6789999999854  44555444333

>PRK09507 cspE cold shock protein CspE; Reviewed

Probab=81.25  E-value=9.3  Score=27.38  Aligned_cols=51  Identities=20%  Similarity=0.283  Sum_probs=36.1

Q ss_pred             EEEEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034          102 KVKGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus       102 iv~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~  157 (318)
                      .++|+|...++   +|.+-.-.++-+-|+|.+.+.....+.     +.+|+.|.+.+..
T Consensus         3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~-----l~~G~~V~f~~~~   56 (69)
T PRK09507          3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKT-----LAEGQRVEFEITN   56 (69)
T ss_pred             ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCC-----CCCCCEEEEEEEE
Confidence            46799999875   344443355679999999986432222     6789999998854

>COG4044 Uncharacterized protein conserved in archaea [Function unknown]

Probab=80.70  E-value=5.5  Score=34.95  Aligned_cols=73  Identities=22%  Similarity=0.151  Sum_probs=51.9

Q ss_pred             cCCCCCCEEEEEEEEEECC--eEEEEeCC----CeEEEEeCcccccccccCc-cc----cCcCCCCEEEEEEEEEeCCCC
Q 021034           95 FNSELGTKVKGTVFCTDNR--GALVDITA----KSSAYLPTQEACIHKIKHV-EE----AGIVPGLKEEFVIIGENEADD  163 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~--G~~V~i~~----~~~g~lp~sEls~~~~~~~-~~----~~~~~G~~v~v~Vl~vd~~~~  163 (318)
                      .+++.|+++-|+.....+.  |++|+++-    -.++++|..++...+-.+| .+    .++-....++|.|..+|...+
T Consensus        71 ~~~~~Gdv~vGrl~~l~~vgyg~yvdigV~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~evnk~~~  150 (247)
T COG4044          71 SKVEEGDVYVGRLIDLGKVGYGAYVDIGVLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEVNKLAQ  150 (247)
T ss_pred             ccCCCCcEEEEEEeeeccceeEEEccccccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEeccchhh
Confidence            4788999999999999775  56677643    2579999999876554444 22    234456789999988887555


Q ss_pred             eEEE
Q 021034          164 SLVL  167 (318)
Q Consensus       164 ~i~l  167 (318)
                      .+-+
T Consensus       151 EIea  154 (247)
T COG4044         151 EIEA  154 (247)
T ss_pred             hhhh
Confidence            5443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	318
2k4k_A	130	Solution Structure Of Gsp13 From Bacillus Subtilis		3e-05
4aim_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		4e-05
4aid_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		6e-05
4am3_A	717	Crystal Structure Of C. Crescentus Pnpase Bound To		6e-05
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		2e-04
1sro_A	76	S1 Rna Binding Domain, Nmr, 20 Structures Length =		4e-04
3bzc_A	785	Crystal Structure Of The Tex Protein From Pseudomon		4e-04
2oce_A	780	Crystal Structure Of Tex Family Protein Pa5201 From		4e-04

>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis Length = 130

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKV 316
           A+  +GSV  G V  L+ YGAF+ +     GL+H+S+++H  V DI   L  GD ++V
Sbjct: 3   AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318
           IG +  G V  +  +GAF++  G  +GL+HVSQIS++RVA  + VL+ G  +KV L
Sbjct: 637 IGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKL 692

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318
           +G +  G V  +  +GAF++  G  +GL+HVSQIS++RVA  + VL+ G  +KV L
Sbjct: 637 VGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKL 692

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318
           +G +  G V  +  +GAF++  G  +GL+HVSQIS++RVA  + VL+ G  +KV L
Sbjct: 628 VGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKL 683

>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase Length = 723

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 46/86 (53%), Gaps = 4/86 (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 LHVSQISHDRVADIATVLQPGDTLKV 316
           +H+SQI+  RV  +   LQ G  + V
Sbjct: 655 VHISQIADKRVEKVTDYLQMGQEVPV 680

>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures Length = 76

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKV 316
           A++ +G V  G V  +  +GAF+ IGG   GL+H+SQI+  RV  +   LQ G  + V
Sbjct: 1   AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPV 58

>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas Aeruginosa, Crystal Form I Length = 785

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
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 V 316
           V
Sbjct: 707 V 707

>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From Pseudomonas Aeruginosa Length = 780

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
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 V 316
           V
Sbjct: 708 V 708

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	318
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	1e-15
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	5e-10
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	2e-14
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	3e-14
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	3e-12
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	5e-12
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	3e-06
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	7e-12
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	1e-11
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	3e-11
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	4e-11
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	5e-11
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	6e-11
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	3e-05
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	7e-11
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	7e-11
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	1e-08
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	6e-08
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	7e-08
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	9e-08
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	3e-06
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	3e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	1e-04
2bh8_A	101	1B11; transcription, molecular evolution, unique a	2e-04
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	9e-04

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

 Score = 71.3 bits (175), Expect = 1e-15
 Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           A+  +GSV  G V  L+ YGAF+ +     GL+H+S+++H  V DI   L  GD ++V
Sbjct: 3   AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60

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

 Score = 55.5 bits (134), Expect = 5e-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

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 109

 Score = 67.6 bits (166), Expect = 2e-14
 Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 5/83 (6%)

Query: 239 EVDEEQSRLVLSNRKAMAD----SQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHV 293
                            +       A    G++V G V ++   GA +++  G+ G L  
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRA 61

Query: 294 SQISHDRVADIATVLQPGDTLKV 316
           S+ S DRV D   VL  GD ++ 
Sbjct: 62  SEASRDRVEDATLVLSVGDEVEA 84

>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 = 67.1 bits (164), Expect = 3e-14
 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGIN--GLLHVSQISHDRVADIATVLQPGDTLKV 316
           + ++  G V  +  YGAFI I G    GL+H + +S  RV   + ++  GD + V
Sbjct: 22  LYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWV 76

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Length = 80

 Score = 60.4 bits (147), Expect = 3e-12
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 5/54 (9%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
            G    G V  ++ YGAFI++   + GLL    +   R+ +    L  GD + V
Sbjct: 5   PGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRLEN----LNVGDEIIV 54

>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 = 62.9 bits (153), Expect = 5e-12
 Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 3/56 (5%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +  VV+  V+S+   GA++ +     I G++ +S++S  R+  I  +++ G    V
Sbjct: 15  VEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECV 70

>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 = 46.0 bits (109), Expect = 3e-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 = 62.1 bits (151), Expect = 7e-12
 Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 3/56 (5%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           I  +V+  VQ +   GA++ +     I G++ +S++S  R+  I  +++ G     
Sbjct: 15  IDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVA 70

>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 = 63.1 bits (153), Expect = 1e-11
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 3/56 (5%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
            G ++I TV+ +  YG+++ +   GG+   L  S++S   V +I  VL+    + V
Sbjct: 11  EGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIV 66

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 62.9 bits (154), Expect = 3e-11
 Identities = 23/54 (42%), Positives = 36/54 (66%), Gaps = 1/54 (1%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +G +  G V  +  +GAF++  G  +GL+HVSQIS++RVA  + VL+ G  +KV
Sbjct: 637 VGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKV 690

>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 = 61.6 bits (149), Expect = 4e-11
 Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 3/56 (5%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
            G  V+ TV+ +  YGAF+++    G    +H+S+++   V +I   L+ G  +  
Sbjct: 11  EGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVA 66

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Length = 115

 Score = 58.0 bits (141), Expect = 5e-11
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 7/85 (8%)

Query: 238 VEVDEEQSRLVLSNRKAMAD----SQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLH 292
           +                          +   G+ + G V +L  YG F++I  G+ GL+H
Sbjct: 1   MGSSHHHHHHSSG-LVPRGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVH 59

Query: 293 VSQISHD-RVADIATVLQPGDTLKV 316
           VS++    +    + V+  GD ++V
Sbjct: 60  VSEMDWTNKNIHPSKVVNVGDVVEV 84

>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 = 61.5 bits (149), Expect = 6e-11
 Identities = 15/56 (26%), Positives = 32/56 (57%), Gaps = 3/56 (5%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +  VV+  V+S++  GA++ +     I G++H+S++S  R+  I  +++ G    V
Sbjct: 13  VEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECV 68

>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 = 44.2 bits (104), Expect = 3e-05
 Identities = 20/125 (16%), Positives = 47/125 (37%), Gaps = 11/125 (8%)

Query: 187 EDVVVKGKVVGANKGGV---VAEVEGLRGFVPFSQISS---KSTAEEL-LGKDLPLKFVE 239
            + VV   V    + G    + E   + G +  S++S    +S  + + +G++  +K + 
Sbjct: 13  VEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIR 72

Query: 240 VDEEQSRLVLSNRKAMADSQAQLG----IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQ 295
           VD+E+  + LS R+   +   +          V   ++ +     +     +  L   + 
Sbjct: 73  VDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTA 132

Query: 296 ISHDR 300
              D 
Sbjct: 133 WVFDD 137

>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 = 57.3 bits (139), Expect = 7e-11
 Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 5/58 (8%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGIN----GLLHVSQISHD-RVADIATVLQPGDTLKV 316
           IG +  G V S+  +G F+ + G+     GL+H+S++  + RVA++A V+  G  +KV
Sbjct: 12  IGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKV 69

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

 Score = 62.1 bits (152), Expect = 7e-11
 Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +G V  G V  +  +GAF+ I GG  GL+H+SQI+  RV  +   LQ G  + V
Sbjct: 627 VGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPV 680

>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 = 54.9 bits (133), Expect = 1e-08
 Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 5/58 (8%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQIS----HDRVADIATVLQPGDTLKV 316
           +G  ++G+V     +GAF+ +  G +GLLH+SQI       RV ++  VL  G  ++V
Sbjct: 667 VGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQV 724

>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 = 53.0 bits (128), Expect = 6e-08
 Identities = 23/56 (41%), Positives = 35/56 (62%), Gaps = 1/56 (1%)

Query: 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           L  G V+ G V ++  +GAF+DIG   +GL+H+S +S   V D   V++ GD +KV
Sbjct: 652 LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKV 707

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

 Score = 53.0 bits (127), Expect = 7e-08
 Identities = 5/57 (8%), Positives = 18/57 (31%), Gaps = 2/57 (3%)

Query: 262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVAD-IATVLQPGDTLKV 316
              GS++   V+              +  +++  + +  ++      + + G T   
Sbjct: 903 FFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPA 959

>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 = 51.5 bits (123), Expect = 9e-08
 Identities = 36/231 (15%), Positives = 64/231 (27%), Gaps = 45/231 (19%)

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--GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
               V  LK  G F+ +    + G +H S+   +         + G  L  
Sbjct: 156 WPAIVYRLKLSGTFVYLPENNMLGFIHPSERYAE--------PRLGQVLDA 198

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Length = 285

 Score = 46.9 bits (111), Expect = 3e-06
 Identities = 21/132 (15%), Positives = 44/132 (33%), Gaps = 21/132 (15%)

Query: 190 VVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVL 249
            + G ++  N      + +G    +       K   +  +G  +   F   D +Q +L L
Sbjct: 9   FIVGLIIDENDRFYFVQKDGQTYALA------KEEGQHTVGDTVKG-FAYTDMKQ-KLRL 60

Query: 250 SNRKAMADSQAQLGIGSVVIGTVQSLKP-YGAFIDIG--GINGLLHVSQISHDRVADIAT 306
           +  +  A             G V  ++   G F+D G      ++ +  +   +      
Sbjct: 61  TTLEVTAT------QDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKELWP-- 112

Query: 307 VLQPGDTLKVCL 318
             + GD L + L
Sbjct: 113 --KKGDQLYIRL 122

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

 Score = 51.0 bits (122), Expect = 3e-07
 Identities = 6/61 (9%), Positives = 20/61 (32%), Gaps = 2/61 (3%)

Query: 258 SQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVAD-IATVLQPGDTLK 315
           S+     GS++   V+              +  +++  + +  ++      + + G T  
Sbjct: 896 SEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYP 955

Query: 316 V 316
            
Sbjct: 956 A 956

>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 = 49.1 bits (116), Expect = 1e-06
 Identities = 39/300 (13%), Positives = 91/300 (30%), Gaps = 89/300 (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-QSEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGK---- 231
               C+ L  +    V    + A     ++               +    + LL K    
Sbjct: 262 FNLSCKILLTTRFKQVT-DFLSAATTTHISLDHHSMTL-------TPDEVKSLLLKYLDC 313

Query: 232 ---DLPLKFVEVDEEQSRLVLS-------NRKAMADSQAQLG---IGSVVIGTVQSLKPY 278
              DLP + +      +   LS       +  A  D+   +    + +++  ++  L+P 
Sbjct: 314 RPQDLPREVLTT----NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA 369

>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 = 41.0 bits (95), Expect = 4e-04
 Identities = 55/347 (15%), Positives = 113/347 (32%), Gaps = 72/347 (20%)

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-DIGG-----INGLLH-VSQISHDRV-ADIATVLQ 309
           T+Q LK Y  +I D        +N +L  + +I  + + +    +L+
Sbjct: 523 TLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLR 569

>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 = 41.0 bits (96), Expect = 1e-04
 Identities = 22/99 (22%), Positives = 41/99 (41%), Gaps = 17/99 (17%)

Query: 235 LKFVEVDEEQSRLVLSNRKAMADSQA------QLGIGSVVIGTVQSLKPYGAFIDIGGIN 288
           L  + V   +  +++    A               +  VV G V  +  YG F+++G ++
Sbjct: 46  LAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQEVVEGEVLQVDNYGVFVNLGPMD 105

Query: 289 GLLHVSQISHDRVADIAT-----------VLQPGDTLKV 316
           GL+H+SQI+ D +                V+Q GD ++ 
Sbjct: 106 GLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRA 144

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} Length = 101

 Score = 39.0 bits (91), Expect = 2e-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

>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 = 37.7 bits (87), Expect = 9e-04
 Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 3/63 (4%)

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 KVC 317
              
Sbjct: 75  NCI 77

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	318
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	100.0
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.9
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.72
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.68
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.61
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.52
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.52
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.5
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.47
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.46
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.46
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.45
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.43
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	99.39
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	99.38
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.38
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.37
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.36
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	99.32
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	99.31
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	99.27
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	99.27
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	99.25
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	99.25
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	99.24
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	99.24
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	99.13
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	99.13
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	99.12
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.11
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	99.03
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.01
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.99
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.97
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.96
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.96
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.94
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.94
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.9
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	98.89
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.89
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.84
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.83
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.82
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	98.82
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.82
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.8
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.8
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	98.79
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.79
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.79
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.77
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.76
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	98.75
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.75
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.74
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.71
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.71
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.69
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.68
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	98.63
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	98.61
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.59
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.5
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.48
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.39
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.37
2bh8_A	101	1B11; transcription, molecular evolution, unique a	98.25
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.21
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.2
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	98.19
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	98.03
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	97.97
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.89
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.88
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	97.87
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	97.77
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.75
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.74
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.69
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	97.41
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	97.38
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.34
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.27
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	97.22
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	97.19
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	97.19
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	95.85
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	94.64
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	92.9
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	92.06
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	89.44
3h8z_A	128	FragIle X mental retardation syndrome-related Pro;	86.61
3h8z_A	128	FragIle X mental retardation syndrome-related Pro;	85.3
2r7d_A	469	Ribonuclease II family protein; structural genomic	84.68
4b9x_A	226	TDRD1, tudor domain-containing protein 1; replicat	84.65
3cam_A	67	Cold-shock domain family protein; cold shock prote	82.78
1wfq_A	89	UNR protein; beta-barrel, translational regulation	81.09
1jjg_A	102	M156R; beta barrel, S1 motif, OB fold, MYXV156R, N	81.02
4b9w_A	201	TDRD1, tudor domain-containing protein 1; replicat	80.87
3i2z_B	71	RNA chaperone, negative regulator of CSPA transcri	80.7

>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-31  Score=243.03  Aligned_cols=186  Identities=17%  Similarity=0.114  Sum_probs=160.8

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHH
Q 021034           98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELA  177 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~  177 (318)
                      .+|++++|+|+++.++|+||+++ +.+||||.+|+..           ++||+++|+|+.  +.++++++|.+.+.    
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            47999999999999999999997 7999999999832           589999999973  45778889987653    


Q ss_pred             HHHHhhhcCCCcEEEEEEEEEE-cCeEEEEECC--EEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeeehhhh
Q 021034          178 WERCRQLQSEDVVVKGKVVGAN-KGGVVAEVEG--LRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKA  254 (318)
Q Consensus       178 ~~~~~~~~~~G~iv~g~V~~v~-~~G~~V~i~g--l~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K~~  254 (318)
                             ++.|+++.|+|++++ ++|+||+++.  .+||+|.|++++..+....+||++.+. +++|+ ++||.+|+|+.
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                   369999999999999 7999999973  899999999998654333489999765 68998 78999999865


Q ss_pred             -hhhh----HhhcccCeEEEEEEEEEEcceEEE-EEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          255 -MADS----QAQLGIGSVVIGTVQSLKPYGAFI-DIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       255 -l~~~----~~~l~~G~~v~G~V~~i~~~G~fV-~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                       ..++    .+.+++|++|+|+|++++++|+|| .++ |+.||||+||+++        .+++||.|+|+|
T Consensus       138 ~~~~~~~~~~~~~~~G~~V~g~V~~i~~~G~fV~~i~~g~~Glih~SEl~~--------~l~~Gd~v~~~V  200 (285)
T 3go5_A          138 EDFQRLARPAYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERYA--------EPRLGQVLDARV  200 (285)
T ss_dssp             HHHHHHCCCCCSCCTTCEEEEEEEEEETTEEEEEETTTTEEEEECGGGCSS--------CCCTTCEEEEEE
T ss_pred             hhcchhhhhhhhCCCCCEEEEEEEEEeCCcEEEEEeCCCeEEEEEHHHccc--------cCCCCCEEEEEE
Confidence             2333    367899999999999999999999 997 8999999999984        499999999986

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

Probab=99.90  E-value=1.2e-22  Score=185.58  Aligned_cols=148  Identities=16%  Similarity=0.039  Sum_probs=130.1

Q ss_pred             CCCCCCEEEEEEEEEE-CCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           96 NSELGTKVKGTVFCTD-NRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~-~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      .+++|+++.|+|++++ +.||||++|. +.+||+|.+|+++....    . +++||.+.|+ +.+|+ ++|+.+|+|...
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----W-PKKGDQLYIR-LEVDK-KDRIWGLLAYQE  138 (285)
T ss_dssp             CSCSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGGSCSSGGG----S-CCTTCEEEEE-EEECT-TSCEEEEECCHH
T ss_pred             cccCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHHCCccccc----c-cCCCCEEEEE-EEECC-CCcEEEEehhhh
Confidence            4679999999999999 7999999987 68999999999875321    2 6899999766 68887 789999999876


Q ss_pred             hhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEE-EEC-CEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeeeh
Q 021034          174 YELAWERCRQLQSEDVVVKGKVVGANKGGVVA-EVE-GLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSN  251 (318)
Q Consensus       174 ~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V-~i~-gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS~  251 (318)
                      ...+|+...+.++.|+.|+|+|.+++++|+|| .++ |+.||||.|+++....    +||+|+++|+++|++++||.||+
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            56789877777889999999999999999999 996 8999999999985422    89999999999999899999999


Q ss_pred             hhh
Q 021034          252 RKA  254 (318)
Q Consensus       252 K~~  254 (318)
                      |+.
T Consensus       215 k~~  217 (285)
T 3go5_A          215 KPR  217 (285)
T ss_dssp             SCC
T ss_pred             Chh
Confidence            985

>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=99.72  E-value=5.5e-20  Score=157.35  Aligned_cols=122  Identities=16%  Similarity=0.122  Sum_probs=101.0

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEe--CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034           97 SELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i--~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      +++|+++.|+|+++.++|+||++  +++.+|++|+||+++.++.++.+. +++||.|.|+|+++|.+++++.||+|+...
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            47999999999999999999999  567999999999999999999998 999999999999999999999999999875


Q ss_pred             hHHHHHHhhhcCCCcEEEEEEEEEEc-CeEEEEEC-CEEEEEeCcccCCc
Q 021034          175 ELAWERCRQLQSEDVVVKGKVVGANK-GGVVAEVE-GLRGFVPFSQISSK  222 (318)
Q Consensus       175 ~~~~~~~~~~~~~G~iv~g~V~~v~~-~G~~V~i~-gl~gfip~s~ls~~  222 (318)
                       .+|..+.+.++.|+.++|+|..+.+ +|  ++++ |++|++|.+++++.
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             5899999889999999999999987 99  6775 99999999987653

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5

Probab=99.68  E-value=2.9e-19  Score=152.81  Aligned_cols=116  Identities=16%  Similarity=0.273  Sum_probs=97.3

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEE---CCEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhhhhhhh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEV---EGLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRKAMADS  258 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i---~gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~  258 (318)
                      +.|+++.|+|++++++|+||++   +|++||||.|++++.  .++.++  +||.|+|+|+++|+++++|.||+|+...++
T Consensus        14 ~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~~~~~p   93 (182)
T 1kl9_A           14 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEE   93 (182)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTTCCHHH
T ss_pred             CCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeecCcCh
Confidence            6899999999999999999999   589999999999976  445554  799999999999999999999999987665


Q ss_pred             H----hhcccCeEEEEEEEEEEc-ceEEEEEC-CeEEEEecCCcCccc-ccC
Q 021034          259 Q----AQLGIGSVVIGTVQSLKP-YGAFIDIG-GINGLLHVSQISHDR-VAD  303 (318)
Q Consensus       259 ~----~~l~~G~~v~G~V~~i~~-~G~fV~i~-gv~Glv~~s~ls~~~-~~~  303 (318)
                      +    +.++.|+.++|.|+++++ ||  |++. |+.||+|.++++|.+ ..+
T Consensus        94 ~~~~~~~~~~g~~v~g~v~~i~~~~g--v~l~~giegl~h~s~~~~~~~~~~  143 (182)
T 1kl9_A           94 AIKCEDKFTKSKTVYSILRHVAEVLE--YTKDEQLESLFQRTAWVFDDKYKR  143 (182)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTT--CCSHHHHHHHHHHTHHHHHHHHTC
T ss_pred             HHHHHHhccCCCEEEEEEEEchhhcC--CcccCChhheEEeeecchhhhcCC
Confidence            4    678899999999999998 99  7887 999999999888753 344

>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=99.61  E-value=1.1e-16  Score=136.22  Aligned_cols=104  Identities=16%  Similarity=0.168  Sum_probs=88.8

Q ss_pred             CCCCEEEEEEEEEECCeEEEEe--CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhh
Q 021034           98 ELGTKVKGTVFCTDNRGALVDI--TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE  175 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i--~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~  175 (318)
                      ++|+++.|+|+++.++|+||++  +++.+|++|++|+++.++.++.+. +++||.+.|+|+++|.+++++.||+|.... 
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            5899999999999999999999  367999999999999999999998 999999999999999999999999999876 


Q ss_pred             HHHHHHhhhcCCCcEEEEEEEEEE-cCeE
Q 021034          176 LAWERCRQLQSEDVVVKGKVVGAN-KGGV  203 (318)
Q Consensus       176 ~~~~~~~~~~~~G~iv~g~V~~v~-~~G~  203 (318)
                      .+|..+.+.++.|+.++|+|.+++ ++|+
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            699999998999999999999987 6776

>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=99.52  E-value=1.2e-15  Score=140.43  Aligned_cols=109  Identities=16%  Similarity=0.132  Sum_probs=100.0

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC--CCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~--~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      .+++|+++.|+|.++.++|+||+++  ++.+||+|++++++.++.++.+. +++||.+.|+|+++|++++++.||+|...
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            4569999999999999999999997  68999999999999999999988 99999999999999999999999999987


Q ss_pred             hhHHHHHHhhhcCCCcEEEEEEEEEEc-CeEEEE
Q 021034          174 YELAWERCRQLQSEDVVVKGKVVGANK-GGVVAE  206 (318)
Q Consensus       174 ~~~~~~~~~~~~~~G~iv~g~V~~v~~-~G~~V~  206 (318)
                      . .+|..+.+.++.|+++.|+|+++.+ +|+|++
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 6999988888899999999999987 598653

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

Probab=99.52  E-value=2.9e-14  Score=112.10  Aligned_cols=86  Identities=21%  Similarity=0.314  Sum_probs=78.2

Q ss_pred             HHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEE
Q 021034           88 SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVL  167 (318)
Q Consensus        88 ~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~l  167 (318)
                      ++|+.+..++++|+++.|+|.++.++|+||+++++.+||||.+|+++.+..++.+. +++||.+.|+|+++|.+++++.|
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            46777777889999999999999999999999888999999999999888888887 99999999999999998889999


Q ss_pred             Eeeehhh
Q 021034          168 SLRMIQY  174 (318)
Q Consensus       168 S~k~~~~  174 (318)
                      |++....
T Consensus        99 S~k~~~~  105 (109)
T 2khj_A           99 SVRAKDE  105 (109)
T ss_dssp             ETTSSSS
T ss_pred             EEeecCh
Confidence            9998654

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

Probab=99.50  E-value=3.1e-14  Score=113.00  Aligned_cols=93  Identities=19%  Similarity=0.230  Sum_probs=79.7

Q ss_pred             HHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc-cccCccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034           88 SALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH-KIKHVEEAGIVPGLKEEFVIIGENEADDSLV  166 (318)
Q Consensus        88 ~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~-~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~  166 (318)
                      ..|+....++++|+++.|+|.++.++|+||+++++.+||+|.+|+++. +..++.+. +++||.+.|+|+++|.+++++.
T Consensus        19 ~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~-~~vGd~V~vkV~~vd~~~~rI~   97 (115)
T 2khi_A           19 SHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKV-VNVGDVVEVMVLDIDEERRRIS   97 (115)
T ss_dssp             --CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTT-CCTTCEEEEEEEEEETTTTEEE
T ss_pred             CCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccE-ECCCCEEEEEEEEEECCCCEEE
Confidence            356665568899999999999999999999998889999999999873 66777776 9999999999999999899999


Q ss_pred             EEeeehhhhHHHHHHh
Q 021034          167 LSLRMIQYELAWERCR  182 (318)
Q Consensus       167 lS~k~~~~~~~~~~~~  182 (318)
                      ||+|.... .+|+.+.
T Consensus        98 lslk~~~~-~p~~~~~  112 (115)
T 2khi_A           98 LGLKQCKA-NPWQQFA  112 (115)
T ss_dssp             ECCCCCCS-SCCCCCC
T ss_pred             EEEEecCc-CHHHHHH
Confidence            99999765 4776553

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

Probab=99.47  E-value=4.9e-13  Score=99.15  Aligned_cols=74  Identities=15%  Similarity=0.194  Sum_probs=66.8

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      ++++|+++.|+|.++.++|+||+++++.+|++|.+|+++.+.    +. +++||.+.|+|+++|.+++++.||+++...
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            578999999999999999999999888999999999987654    34 899999999999999988999999998753

>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=99.46  E-value=8.9e-15  Score=124.35  Aligned_cols=94  Identities=18%  Similarity=0.292  Sum_probs=79.4

Q ss_pred             CCcEEEEEEEEEEcCeEEEEE---CCEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhhhhhhhH
Q 021034          187 EDVVVKGKVVGANKGGVVAEV---EGLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRKAMADSQ  259 (318)
Q Consensus       187 ~G~iv~g~V~~v~~~G~~V~i---~gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~~  259 (318)
                      .|+++.|+|+++.++|+||++   +|++||||.|++++.  .++.++  +||.|.|+|+++|++++++.||+|+...+++
T Consensus        15 ~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~~~~~~~   94 (175)
T 2a19_A           15 IDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSSEDI   94 (175)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTTCCHHHH
T ss_pred             CCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEecCcChH
Confidence            899999999999999999999   589999999999976  345554  7999999999999999999999999876654


Q ss_pred             ----hhcccCeEEEEEEEEEE-cceE
Q 021034          260 ----AQLGIGSVVIGTVQSLK-PYGA  280 (318)
Q Consensus       260 ----~~l~~G~~v~G~V~~i~-~~G~  280 (318)
                          +.++.|+.+.|+|++++ ++|+
T Consensus        95 ~~~~~~~~~g~~v~g~V~~i~~~~G~  120 (175)
T 2a19_A           95 IKCEEKYQKSKTVHSILRYCAEKFQI  120 (175)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHhccCCCcceEEEEEchhhcCC
Confidence                67889999999999998 6886

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

Probab=99.46  E-value=4e-13  Score=108.83  Aligned_cols=78  Identities=21%  Similarity=0.302  Sum_probs=73.4

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      ++++|+++.|+|.++.++|+||++.++.+||||++|+++.++.++.+. +++||.|.|+|+++|.+++++.||++....
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            678999999999999999999999878999999999999988888887 999999999999999989999999998765

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

Probab=99.45  E-value=1.6e-13  Score=103.65  Aligned_cols=76  Identities=11%  Similarity=0.183  Sum_probs=69.8

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC--CCeEEEEeCc-ccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQ-EACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~--~~~~g~lp~s-Els~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      ..++|+++.|+|+ +.++|+||++.  ++.+|++|+| |+++.+..++++. + +||+++|+|+++|.+++++.||+|..
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            5689999999999 99999999995  3699999999 9999888888887 8 99999999999999999999999986


Q ss_pred             hh
Q 021034          173 QY  174 (318)
Q Consensus       173 ~~  174 (318)
                      ..
T Consensus        85 ~~   86 (88)
T 1luz_A           85 CR   86 (88)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

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

Probab=99.43  E-value=2.7e-14  Score=129.55  Aligned_cols=109  Identities=20%  Similarity=0.157  Sum_probs=98.0

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC--CCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~--~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      .+++|+++.|+|.++.++|+||+++  ++.+||||++|+++.++.++.+. +++||.+.|+|+++|.+++++.||+|...
T Consensus         8 ~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~-~kvGd~V~vkVi~vD~~~~~I~LSlk~~~   86 (275)
T 3aev_A            8 YPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDY-LKEGQKVVAKVIRVDPRKGHIDLSLRRVT   86 (275)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGT-CCTTCEEEEEEEEEETTTTEEEEESTTCC
T ss_pred             CCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhc-cCCCCEEEEEEEEEECCCCEEEEEEeecC
Confidence            3468999999999999999999997  57999999999999999999888 99999999999999999999999999986


Q ss_pred             hhHHHHHHhhhcCCCcEEEEEEEEEE-cCeEEEE
Q 021034          174 YELAWERCRQLQSEDVVVKGKVVGAN-KGGVVAE  206 (318)
Q Consensus       174 ~~~~~~~~~~~~~~G~iv~g~V~~v~-~~G~~V~  206 (318)
                      . .+|....+.+..|+.+.|+|..+. ++|+.++
T Consensus        87 ~-~~~~~~~~~~~~g~~v~g~v~~v~~~~G~~~e  119 (275)
T 3aev_A           87 Q-QQRKAKLQEFKRAQKAENLLRLAAEKLGKDFE  119 (275)
T ss_dssp             H-HHHHHHHHHHHHHHHHHHHHHHHHHHHTCCHH
T ss_pred             c-chhHHHHHhccCCCeEEEEEEEchhhcCCCHH
Confidence            5 588888888889999999999987 7787443

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

Probab=99.39  E-value=5.1e-13  Score=104.93  Aligned_cols=88  Identities=25%  Similarity=0.368  Sum_probs=71.0

Q ss_pred             EEeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcch-h-cCCeEeEEEEEEe
Q 021034          167 LSLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEE-L-LGKDLPLKFVEVD  241 (318)
Q Consensus       167 lS~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~-~-vGq~v~~kVl~vd  241 (318)
                      -|+|+... .+|+.+...++.|++++|+|+++.++|+||+++ ++.||||.+++++.  .++.+ + +||.|.|+|+++|
T Consensus        12 ~~iKq~~~-~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd   90 (109)
T 2khj_A           12 SGLVPRGS-HMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVD   90 (109)
T ss_dssp             ----------CHHHHTTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEE
T ss_pred             cchhhccc-CHHHHHhhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEE
Confidence            36666665 589998888889999999999999999999997 99999999999875  34444 4 7999999999999


Q ss_pred             cccCeEeeehhhhh
Q 021034          242 EEQSRLVLSNRKAM  255 (318)
Q Consensus       242 ~~~~~i~lS~K~~l  255 (318)
                      ++++++.||+|+..
T Consensus        91 ~~~~ki~LS~k~~~  104 (109)
T 2khj_A           91 RKNRAISLSVRAKD  104 (109)
T ss_dssp             TTTTEEEEETTSSS
T ss_pred             CCCCEEEEEEeecC
Confidence            99899999999764

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

Probab=99.38  E-value=5.4e-13  Score=105.80  Aligned_cols=94  Identities=21%  Similarity=0.351  Sum_probs=73.3

Q ss_pred             EeeehhhhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc---CCcch-h-cCCeEeEEEEEEe
Q 021034          168 SLRMIQYELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK---STAEE-L-LGKDLPLKFVEVD  241 (318)
Q Consensus       168 S~k~~~~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~---~~~~~-~-vGq~v~~kVl~vd  241 (318)
                      |+|+... .+|+.+...++.|+++.|+|+++.++|+||+++ |+.||+|.+++++.   .++.+ + +||.|+|+|+++|
T Consensus        12 ~~k~~~~-~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd   90 (115)
T 2khi_A           12 SGLVPRG-SHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDID   90 (115)
T ss_dssp             ----------CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEE
T ss_pred             chhhccc-CCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEE
Confidence            5565554 488877666789999999999999999999997 89999999999873   23443 3 7999999999999


Q ss_pred             cccCeEeeehhhhhhhhHhhc
Q 021034          242 EEQSRLVLSNRKAMADSQAQL  262 (318)
Q Consensus       242 ~~~~~i~lS~K~~l~~~~~~l  262 (318)
                      .+++++.||+|+...++++.+
T Consensus        91 ~~~~rI~lslk~~~~~p~~~~  111 (115)
T 2khi_A           91 EERRRISLGLKQCKANPWQQF  111 (115)
T ss_dssp             TTTTEEEECCCCCCSSCCCCC
T ss_pred             CCCCEEEEEEEecCcCHHHHH
Confidence            999999999999877766543

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

Probab=99.38  E-value=6.8e-13  Score=105.80  Aligned_cols=90  Identities=17%  Similarity=0.188  Sum_probs=77.3

Q ss_pred             HhhhccCCCCCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCC--CeEE
Q 021034           90 LEKYDFNSELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD--DSLV  166 (318)
Q Consensus        90 ~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~--~~i~  166 (318)
                      |+.+...+++|+++.|+|.++.++|+||++.+ +.+||||++++++.++.++.+. +++||.|.|+|+++|.++  +++.
T Consensus        13 ~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~-~~~Gd~V~VkV~~vd~~~~~~~i~   91 (119)
T 2cqo_A           13 PETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEI-VDVGDKVWVKLIGREMKNDRIKVS   91 (119)
T ss_dssp             CCCSCCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHHH-CCTTCEEEEEEEEEEECSSCEEEE
T ss_pred             hhhhhcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhhc-CCCCCEEEEEEEEEeccccCceEE
Confidence            44445578899999999999999999999965 4799999999999888888887 999999999999999764  6999


Q ss_pred             EEeeehhhhHHHHHH
Q 021034          167 LSLRMIQYELAWERC  181 (318)
Q Consensus       167 lS~k~~~~~~~~~~~  181 (318)
                      ||+|.... ..|+.+
T Consensus        92 LSlk~~~~-~~~~~~  105 (119)
T 2cqo_A           92 LSMKVVNQ-GTGKDL  105 (119)
T ss_dssp             EESTTBCS-SSCCBS
T ss_pred             EEEeeccc-CCcccc
Confidence            99999865 356544

>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=99.37  E-value=4.5e-14  Score=129.85  Aligned_cols=98  Identities=18%  Similarity=0.306  Sum_probs=87.0

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEEC---CEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhhhhhhh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEVE---GLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRKAMADS  258 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i~---gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~  258 (318)
                      +.|+++.|+|+++.++|+||+++   |++||+|.|++++.  .++.++  +||.|.|+|+++|++++++.||+|+...++
T Consensus        12 ~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~~~~p   91 (308)
T 1q8k_A           12 EVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRVSPEE   91 (308)
T ss_dssp             SSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSSCCHHH
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEecccCh
Confidence            48999999999999999999994   89999999999976  345554  799999999999999999999999887665


Q ss_pred             H----hhcccCeEEEEEEEEEEc-ceEEEE
Q 021034          259 Q----AQLGIGSVVIGTVQSLKP-YGAFID  283 (318)
Q Consensus       259 ~----~~l~~G~~v~G~V~~i~~-~G~fV~  283 (318)
                      +    +.++.|+++.|+|.++.+ ||+|++
T Consensus        92 ~~~~~~~~~~G~~v~G~V~~v~~~~G~fi~  121 (308)
T 1q8k_A           92 AIKCEDKFTKSKTVYSILRHVAEVLEYTKD  121 (308)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCCSS
T ss_pred             HHHHHHHccCCCeeEEEEEEcccccCCccC
Confidence            4    578899999999999999 699864

>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=99.36  E-value=2.7e-12  Score=99.79  Aligned_cols=76  Identities=13%  Similarity=0.238  Sum_probs=69.2

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCC---CeEEEEeCccc-ccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITA---KSSAYLPTQEA-CIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~---~~~g~lp~sEl-s~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~  171 (318)
                      ++++|+++.|+|.++.++|+||++++   +.+||||++|+ ++.++.++.+. +++||.+.|+|+++|.  +++.||+|.
T Consensus         9 ~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~-~~~Gd~V~VkV~~vd~--~~i~LSlk~   85 (103)
T 2eqs_A            9 EPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADV-VSKGQRVKVKVLSFTG--TKTSLSMKD   85 (103)
T ss_dssp             SCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHH-CCTTCEEEEEEEEEET--TEEEEESTT
T ss_pred             cCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccE-eCCCCEEEEEEEEEEC--CeeEEEEee
Confidence            67899999999999999999999985   79999999999 66677788887 9999999999999996  699999998


Q ss_pred             hhh
Q 021034          172 IQY  174 (318)
Q Consensus       172 ~~~  174 (318)
                      ...
T Consensus        86 ~~~   88 (103)
T 2eqs_A           86 VDQ   88 (103)
T ss_dssp             BCT
T ss_pred             ccc
Confidence            765

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

Probab=99.32  E-value=2.5e-12  Score=104.13  Aligned_cols=59  Identities=39%  Similarity=0.708  Sum_probs=56.2

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .++++|+++.|+|++|++||+||+|. |+.||||+|+++|.++.++.+.|++||.|+|+|
T Consensus         3 ~~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV   62 (130)
T 2k4k_A            3 AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKV   62 (130)
T ss_dssp             CCCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEE
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEE
Confidence            36789999999999999999999997 999999999999999999999999999999986

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

Probab=99.31  E-value=9.1e-12  Score=92.22  Aligned_cols=71  Identities=18%  Similarity=0.259  Sum_probs=62.7

Q ss_pred             cCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCcCCcchh-cCCeEeEEEEEEecccCeEeeehhhhhh
Q 021034          185 QSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVEVDEEQSRLVLSNRKAMA  256 (318)
Q Consensus       185 ~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~vd~~~~~i~lS~K~~l~  256 (318)
                      ++.|+++.|+|+++.++|+||+++ ++.||+|.|++++... +.+ +||.|+|+|+++|++++++.||+|+...
T Consensus         3 ~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel~~~~~-~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~~~~   75 (80)
T 2k52_A            3 VEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRL-ENLNVGDEIIVQAIDVRPEKREIDFKYIPLEH   75 (80)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSCCG-GGCCTTCEEEEEEEEEETTTTEEEEEECSCC-
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCcccc-eeeCCCCEEEEEEEEEECCCCEEEEEEeeccc
Confidence            368999999999999999999997 9999999999987532 344 7999999999999999999999998653

>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=99.27  E-value=4.9e-12  Score=98.26  Aligned_cols=59  Identities=32%  Similarity=0.631  Sum_probs=54.7

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC----CeEEEEecCCc-CcccccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG----GINGLLHVSQI-SHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~----gv~Glv~~s~l-s~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .++++|+++.|+|++|++||+||+++    ++.||||+|++ ++.++.++.+.|++||.|+|+|
T Consensus         8 ~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV   71 (103)
T 2eqs_A            8 EEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKV   71 (103)
T ss_dssp             SSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEE
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEE
Confidence            46789999999999999999999998    69999999999 6778889999999999999986

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

Probab=99.27  E-value=6.9e-13  Score=120.35  Aligned_cols=98  Identities=17%  Similarity=0.264  Sum_probs=86.0

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEEC---CEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhhhhhhh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEVE---GLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRKAMADS  258 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i~---gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~  258 (318)
                      +.|+++.|+|+++.++|+||+++   |+.||||.|++++.  .++.+.  +||.|.|+|+++|++++++.||+|+...++
T Consensus        10 ~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~~~~~   89 (275)
T 3aev_A           10 EEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQQQ   89 (275)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESTTCCHHH
T ss_pred             CCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEEeecCcch
Confidence            48999999999999999999995   89999999999976  345554  799999999999999999999999876554


Q ss_pred             H----hhcccCeEEEEEEEEEE-cceEEEE
Q 021034          259 Q----AQLGIGSVVIGTVQSLK-PYGAFID  283 (318)
Q Consensus       259 ~----~~l~~G~~v~G~V~~i~-~~G~fV~  283 (318)
                      +    +.++.|+.+.|.|+++. ++|++++
T Consensus        90 ~~~~~~~~~~g~~v~g~v~~v~~~~G~~~e  119 (275)
T 3aev_A           90 RKAKLQEFKRAQKAENLLRLAAEKLGKDFE  119 (275)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTCCHH
T ss_pred             hHHHHHhccCCCeEEEEEEEchhhcCCCHH
Confidence            3    67889999999999999 8998654

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

Probab=99.25  E-value=7.7e-12  Score=94.32  Aligned_cols=70  Identities=14%  Similarity=0.226  Sum_probs=61.2

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEEC---CEEEEEeCc-ccCCc--CCcchh-cCCeEeEEEEEEecccCeEeeehhhhhh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEVE---GLRGFVPFS-QISSK--STAEEL-LGKDLPLKFVEVDEEQSRLVLSNRKAMA  256 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i~---gl~gfip~s-~ls~~--~~~~~~-vGq~v~~kVl~vd~~~~~i~lS~K~~l~  256 (318)
                      +.|++++|+|+ ++++|+||+++   |++|++|.| ++++.  .+++++ +||+|+++|+++|++++++.||+|+...
T Consensus        10 ~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~kI~lslk~~~~   86 (88)
T 1luz_A           10 NAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKLVGKTVKVKVIRVDYTKGYIDVNYKRMCR   86 (88)
T ss_dssp             CTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEEEECS
T ss_pred             CCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHEeCCCEEEEEEEEEECCCCEEEEEEeecCC
Confidence            68999999999 99999999994   799999999 99965  233333 8999999999999999999999997643

>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=99.25  E-value=2e-12  Score=116.91  Aligned_cols=102  Identities=14%  Similarity=0.092  Sum_probs=89.4

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC--CCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~--~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      .+++|+++.|+|.++.++|+||+++  ++.+||||.+|+++.++.++.+. +++||.+.|+|+++|.+++++.||+|...
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            6789999999999999999999996  78999999999999999999888 99999999999999988999999999987


Q ss_pred             hhHHHHHHhhhcCCCcEEEEEEEEEE
Q 021034          174 YELAWERCRQLQSEDVVVKGKVVGAN  199 (318)
Q Consensus       174 ~~~~~~~~~~~~~~G~iv~g~V~~v~  199 (318)
                      . .+|..+.+.++.|+.+.+.|..+.
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            5 588887777777765666555543

>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=99.24  E-value=3.9e-12  Score=101.40  Aligned_cols=88  Identities=18%  Similarity=0.259  Sum_probs=72.4

Q ss_pred             HHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECC--EEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEeccc--CeEe
Q 021034          177 AWERCRQLQSEDVVVKGKVVGANKGGVVAEVEG--LRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQ--SRLV  248 (318)
Q Consensus       177 ~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~g--l~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~--~~i~  248 (318)
                      .|+.+....+.|+++.|+|+++.++|+||++++  .+||||.+++++.  .++.+.  +||.|.|+|+++|+++  +++.
T Consensus        12 ~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~~~~i~   91 (119)
T 2cqo_A           12 RPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS   91 (119)
T ss_dssp             CCCCSCCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECSSCEEEE
T ss_pred             chhhhhcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEeccccCceEE
Confidence            455565667799999999999999999999975  5999999999976  344443  7999999999999864  6999


Q ss_pred             eehhhhhhhhHhhccc
Q 021034          249 LSNRKAMADSQAQLGI  264 (318)
Q Consensus       249 lS~K~~l~~~~~~l~~  264 (318)
                      ||+|+...+.++++.+
T Consensus        92 LSlk~~~~~~~~~~~~  107 (119)
T 2cqo_A           92 LSMKVVNQGTGKDLDP  107 (119)
T ss_dssp             EESTTBCSSSCCBSCT
T ss_pred             EEEeecccCCccccCc
Confidence            9999987766655544

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

Probab=99.24  E-value=3.7e-11  Score=127.53  Aligned_cols=117  Identities=12%  Similarity=-0.004  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCCCHHHHHHHHh-hhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc
Q 021034           57 REELNQLFEEAYERCRTAPMEGVSFTLEEFHSALE-KYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH  135 (318)
Q Consensus        57 ~~~~~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~-~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~  135 (318)
                      +..|+.|++|.....++.......++.++.-.++. ....++++|++++|+|.++.++|+||+++.+.+|++|++++++.
T Consensus       859 ~~TL~dI~~EL~~P~rD~R~~f~~~~~~e~~~mltget~~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~  938 (1219)
T 3psi_A          859 LNNLNTIVLELLDGFEELRNDFHPLQGDEIFQSLTGESEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGA  938 (1219)
T ss_dssp             HHHHHHHHHHHHSSSCCCSBCCCCBCHHHHHHHHTCCCTTTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSST
T ss_pred             cchHHHHHHHHhccCCCCCcccCCCCHHHHHHhhccCcHhhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCC
Confidence            45677788887777777777777777776555553 23358999999999999999999999998889999999999998


Q ss_pred             c-ccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034          136 K-IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus       136 ~-~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      + +.+|.+. +++||.|+|+|+++|.+++++.||+|....
T Consensus       939 ~~v~~p~~v-~kvGd~V~vkVl~VD~~~~rI~LSlk~~dl  977 (1219)
T 3psi_A          939 QLRRPANEI-YEIGKTYPAKVIYIDYANITAEVSLLDHDV  977 (1219)
T ss_dssp             TSCSCSTTT-SCTTCEEEEEEEEEEGGGTEEEEECCHHHH
T ss_pred             cccCCHHHc-CCCCCEEEEEEEEEECCCCEEEEEecHHHh
Confidence            8 7889888 999999999999999999999999997765

>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=99.13  E-value=9.8e-11  Score=93.25  Aligned_cols=78  Identities=22%  Similarity=0.244  Sum_probs=66.6

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC-CCeEEEEeCcccc-cccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEAC-IHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~-~~~~g~lp~sEls-~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      ++++|+++.|+|.++.++|+||+++ ++..|++|.+++. +....++.+. +++||.++|+|+++|.+++++.||+++..
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            7899999999999999999999998 5688888887753 2233456666 99999999999999998899999999875


Q ss_pred             h
Q 021034          174 Y  174 (318)
Q Consensus       174 ~  174 (318)
                      .
T Consensus        97 l   97 (119)
T 1wi5_A           97 V   97 (119)
T ss_dssp             S
T ss_pred             c
Confidence            4

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

Probab=99.13  E-value=1.8e-11  Score=128.13  Aligned_cols=121  Identities=12%  Similarity=-0.001  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCCCHHHHHHHHhh-hccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc
Q 021034           57 REELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEK-YDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH  135 (318)
Q Consensus        57 ~~~~~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~~-~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~  135 (318)
                      +..|+.|++|.....++.......++.++.-.++.- ...++++|++++|+|.++.++|+||+++.+.+|++|++++++.
T Consensus       862 ~~TL~dI~~EL~~P~~D~R~~f~~~~~~e~~~~LTget~~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~  941 (1030)
T 3psf_A          862 LNNLNTIVLELLDGFEELRNDFHPLQGDEIFQSLTGESEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGA  941 (1030)
T ss_dssp             HHHHHHHHHHHHSTTCCCSCCCCCCCHHHHHHHHHCCC------------------------------------------
T ss_pred             cchHHHHHHHHhccCCCCCcccCccchhhhhhhhccccHHHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCC
Confidence            457888888888888887777777777766556542 3358899999999999999999999998889999999999998


Q ss_pred             c-ccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHH
Q 021034          136 K-IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAW  178 (318)
Q Consensus       136 ~-~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~  178 (318)
                      + +.+|.+. +++||.|+|+|+++|.+++++.||+|.......|
T Consensus       942 ~~v~~~~~v-~kvGd~V~vkVl~VD~~~~rI~LSlk~~dl~~~~  984 (1030)
T 3psf_A          942 QLRRPANEI-YEIGKTYPAKVIYIDYANITAEVSLLDHDVKQQY  984 (1030)
T ss_dssp             --------------------------------------------
T ss_pred             cccCCHHHc-CCCCCEEEEEEEEEECCCCEEEEEechHHhcccc
Confidence            7 7889888 9999999999999999999999999987765444

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=99.12  E-value=1.5e-10  Score=107.54  Aligned_cols=123  Identities=20%  Similarity=0.187  Sum_probs=91.8

Q ss_pred             hccCCceeEEEEEEeccchhHHHHHHHHHHH-HHHHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCe
Q 021034           36 NSRKNKTIVSAVAISNAETREREELNQLFEE-AYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRG  114 (318)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~e-~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G  114 (318)
                      .+..|..+...+...+.+   |.- -.+.+. .++.+++.+          ++.++++|  ..+.|++++|+|.++.++|
T Consensus        86 ~~~vGd~ie~~I~~~dfg---R~a-a~~aKqvi~qkireae----------re~i~~e~--~~~~GeIV~G~V~ri~~~~  149 (344)
T 1hh2_P           86 LAEVGSIVKKELNVKNFG---RIA-AQTAKQVLIQRIRELE----------KEKQFEKY--SELKGTVTTAEVIRVMGEW  149 (344)
T ss_dssp             TCCTTCEEEEECCCCCSS---SCS-GGGHHHHHHHHHHHHT----------TCCSSCCT--TCCTTCEEEEEEEEECSSE
T ss_pred             cccCCCEEEEEEccccCc---cHH-HHHHHHHHHHHHHHHH----------HHHHHHHH--hhcCCCEEEEEEEEEecCc
Confidence            578999999988776654   321 122222 223444421          12455555  3568999999999999999


Q ss_pred             EEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCC--CeEEEEeeehhhhHHHHHHh
Q 021034          115 ALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD--DSLVLSLRMIQYELAWERCR  182 (318)
Q Consensus       115 ~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~--~~i~lS~k~~~~~~~~~~~~  182 (318)
                      +||++| +.+|+||.+|++      |.+. +++||+++|+|++++.++  .++.||++.+.....|.+++
T Consensus       150 v~VDlG-k~EgiLp~sE~i------p~E~-~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p~~lk~LfelE  211 (344)
T 1hh2_P          150 ADIRIG-KLETRLPKKEWI------PGEE-IKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVIGLMKLE  211 (344)
T ss_dssp             EEEEET-TEEEEEEGGGSC------TTCC-CCTTCEEEEEEEEEEEETTEEEEEEESSSHHHHHHHHHHH
T ss_pred             EEEEeC-CeEEEEeHHHcC------CCcC-CCCCCEEEEEEEEEEcCCCCcEEEEEeeccHHHHHHHHhh
Confidence            999998 799999999996      4455 999999999999998654  48999999998887887764

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

Probab=99.11  E-value=6e-12  Score=127.34  Aligned_cols=133  Identities=11%  Similarity=0.152  Sum_probs=2.8

Q ss_pred             eEEEEEEeccchhHHHHHHHHHHHHHHHhhcCCCCCCCCC---HHHHHH---HHhhhccCCCCCCEEEEEEEEEECCeEE
Q 021034           43 IVSAVAISNAETREREELNQLFEEAYERCRTAPMEGVSFT---LEEFHS---ALEKYDFNSELGTKVKGTVFCTDNRGAL  116 (318)
Q Consensus        43 ~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~~~~~~~~~s---~~~~~~---~~~~~~~~~~~G~iv~G~V~~i~~~G~~  116 (318)
                      -|-|-++...+    +.|+.+++++=..++-.+.+.+...   .+..+.   .++.+..++++|+++.|+|+++.++|+|
T Consensus       579 ~ki~~vig~gg----~~i~~i~~~tg~~idi~ddG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V~~I~~fGaF  654 (726)
T 4aid_A          579 DKIREVIGSGG----KVIREIVATTGAKVDINDDGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAF  654 (726)
T ss_dssp             ---------------------------------------CCSCHHHHHHHHHC---------------------------
T ss_pred             HHHHhhcCCCc----hhHHHHHHHHCCceeEECCceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEEEEEEEEeccEEE
Confidence            34455666444    6899999997666665555554333   333333   3455556789999999999999999999


Q ss_pred             EEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHHHh
Q 021034          117 VDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERCR  182 (318)
Q Consensus       117 V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~~~  182 (318)
                      |++.++.+|++|+||+++.++.++++. +++||.|+|+|+++|+ ++++.||+|....+ .++.+.
T Consensus       655 Vel~~g~eGLvHiSels~~rv~~~~d~-~kvGD~V~VkVi~iD~-~grI~LS~K~~~~~-~G~~~~  717 (726)
T 4aid_A          655 VNFFGAKDGLVHVSQISNERVAKPSDV-LKEGQMVKVKLLGFDD-RGKTKLSMKVVDQE-TGEDLS  717 (726)
T ss_dssp             ------------------------------------------------------------------
T ss_pred             EEECCCcEEEEEHHHcCcccccCcccc-CCCCCEEEEEEEEECC-CCcEEEEEeecccC-cchhhh
Confidence            999888999999999999999999998 9999999999999997 78999999998763 555553

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=99.03  E-value=1.4e-09  Score=93.34  Aligned_cols=78  Identities=12%  Similarity=0.138  Sum_probs=68.1

Q ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccccc-----------CccccCcCCCCEEEEEEEEEeCCCC
Q 021034           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK-----------HVEEAGIVPGLKEEFVIIGENEADD  163 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~-----------~~~~~~~~~G~~v~v~Vl~vd~~~~  163 (318)
                      ....+|+++.|+|+++.++|+||++++ .+|++|.+++++.+..           ++.+. +++||.|.|+|+++|..++
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            467899999999999999999999975 9999999999876654           56666 9999999999999998654


Q ss_pred             -----eEEEEeeehhh
Q 021034          164 -----SLVLSLRMIQY  174 (318)
Q Consensus       164 -----~i~lS~k~~~~  174 (318)
                           ++.||++.+..
T Consensus       155 ~p~~~~I~lS~k~~~L  170 (187)
T 1go3_E          155 RKRGSKIALTMRQPYL  170 (187)
T ss_dssp             ----CEEEEECCSTTC
T ss_pred             CCCccEEEEEEcCCCC
Confidence                 99999998754

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

Probab=99.01  E-value=3.2e-11  Score=122.47  Aligned_cols=121  Identities=14%  Similarity=0.148  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCCCHHHHHH------HHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcc
Q 021034           58 EELNQLFEEAYERCRTAPMEGVSFTLEEFHS------ALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQE  131 (318)
Q Consensus        58 ~~~~~~i~e~~~~~~~~~~~~~~~s~~~~~~------~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sE  131 (318)
                      +.++.++++.=..++-.+.+.+..+..+...      .++.+..++++|++++|+|.++.++|+||++.++.+||+|+||
T Consensus       580 k~I~~I~~~~G~~IdI~~dg~v~I~~~~~~~~~~a~~~i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSe  659 (723)
T 3cdi_A          580 SVIRALTEETGTTIEIEDDGTVKIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQ  659 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             eeeeeeehhhCceEEecCCccEEEecCCHHHHHHHHHHHHHHhhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHH
Confidence            5778888874333443334445444443332      3455556789999999999999999999999888999999999


Q ss_pred             cccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHHH
Q 021034          132 ACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWERC  181 (318)
Q Consensus       132 ls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~~  181 (318)
                      +++.++.++++. +++||.|+|+|+++|. ++++.||+|.... ..|..+
T Consensus       660 l~~~~v~~~~~~-~~vGd~V~VkVi~vd~-~grI~LS~k~~~~-~~g~~~  706 (723)
T 3cdi_A          660 IADKRVEKVTDY-LQMGQEVPVKVLEVDR-QGRIRLSIKEATE-QSQPAA  706 (723)
T ss_dssp             --------------------------------------------------
T ss_pred             cCCccccCcccc-cCCCCEEEEEEEEECC-CCcEEEEEEeccC-CCCccc
Confidence            999999999988 9999999999999997 8999999998764 355544

>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=98.99  E-value=1.4e-10  Score=118.51  Aligned_cols=111  Identities=21%  Similarity=0.268  Sum_probs=85.6

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCCCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc
Q 021034           58 EELNQLFEEAYERCRTAPMEGVSFTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI  137 (318)
Q Consensus        58 ~~~~~~i~e~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~  137 (318)
                      ..+..++++.....++...+   |....+.+-.+.. .++++|++++|+|.++.++|+||+++.+.+|++|++++++.++
T Consensus       617 ~tl~rIi~eL~kpg~d~R~~---~~~~~~~~~ve~~-~~l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v  692 (785)
T 3bzc_A          617 PTVTDILKELDKPGRDPRPE---FKTAEFQEGVESL-KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFV  692 (785)
T ss_dssp             HHHHHHHHHHHSTTCCCSCC---CCTTTTCCCCCSS-TTCCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCC
T ss_pred             HHHHHHHHHHhccCCChhhh---cccchhhhcccch-hhcCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCcccc
Confidence            35666666665444443222   1111111111222 3688999999999999999999999988999999999999999


Q ss_pred             cCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034          138 KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus       138 ~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      .++.+. +++||.|+|+|+++|.+++++.||+|...
T Consensus       693 ~d~~~~-~~vGd~V~VkVi~VD~~~~rI~LSlk~~~  727 (785)
T 3bzc_A          693 KDPYEV-VKAGDIVKVKVMEVDIPRNRVGLSMRMSD  727 (785)
T ss_dssp             SCHHHH-CCTTCCCCCBEEEEETTTTEEEECCSSCC
T ss_pred             CChhhe-eCCCCEEEEEEEEEECCCCEEEEEEecCC
Confidence            999888 99999999999999999999999998654

>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=98.97  E-value=1.4e-09  Score=94.84  Aligned_cols=77  Identities=16%  Similarity=0.143  Sum_probs=69.2

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC--------CCeEEEEeCccccccccc--CccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDIT--------AKSSAYLPTQEACIHKIK--HVEEAGIVPGLKEEFVIIGENEADDSL  165 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~--------~~~~g~lp~sEls~~~~~--~~~~~~~~~G~~v~v~Vl~vd~~~~~i  165 (318)
                      .+++|++|.|+|+++.++|++|+|+        .+.+|+||++|+++.+..  ++.+. |++||.|.++|+++++.++++
T Consensus        78 ~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~-l~~GD~V~akVisi~~~~~~i  156 (209)
T 2nn6_I           78 LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKS-FRPGDIVLAKVISLGDAQSNY  156 (209)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGT-CCSSSEEEEEEEEEETTTTEE
T ss_pred             CCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhh-cCCCCEEEEEEEEEeCCCCeE
Confidence            6789999999999999999999984        357899999999987776  78887 999999999999999877799


Q ss_pred             EEEeeehh
Q 021034          166 VLSLRMIQ  173 (318)
Q Consensus       166 ~lS~k~~~  173 (318)
                      .||.|...
T Consensus       157 ~LS~k~~~  164 (209)
T 2nn6_I          157 LLTTAENE  164 (209)
T ss_dssp             EEECCSSS
T ss_pred             EEEEecCC
Confidence            99998864

>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=98.96  E-value=2.3e-10  Score=91.07  Aligned_cols=70  Identities=24%  Similarity=0.339  Sum_probs=55.6

Q ss_pred             eehhhhhhhh---HhhcccCeEEEEEEEEEEcceEEEEEC--CeEEEEecCCc-CcccccCcccccCCCCEEEEEC
Q 021034          249 LSNRKAMADS---QAQLGIGSVVIGTVQSLKPYGAFIDIG--GINGLLHVSQI-SHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       249 lS~K~~l~~~---~~~l~~G~~v~G~V~~i~~~G~fV~i~--gv~Glv~~s~l-s~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +|+++...+.   ..++++|+++.|+|++|++||+||+|+  +..||+|.++. +|.+..++.+.|++||.|+|+|
T Consensus         3 ~sl~P~~vn~~~~~~~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV   78 (119)
T 1wi5_A            3 SGSSGKNVNRVLSAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIV   78 (119)
T ss_dssp             CCCCCSCSSCCCCTTTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEE
T ss_pred             cccCHHHhhccccHhcCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccccccccCccCEeCCCCEEEEEE
Confidence            4566655442   468999999999999999999999998  56666665553 3555668899999999999986

>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=98.96  E-value=9.7e-11  Score=108.88  Aligned_cols=124  Identities=15%  Similarity=0.085  Sum_probs=86.0

Q ss_pred             cCCCCEEEEEEEEEeCCCCeEEEEeeehhhhHHHHH----HhhhcC--CCcEEEEEEEEEEcCeEEEEECCEEEEEeCcc
Q 021034          145 IVPGLKEEFVIIGENEADDSLVLSLRMIQYELAWER----CRQLQS--EDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQ  218 (318)
Q Consensus       145 ~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~~~~~~----~~~~~~--~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~  218 (318)
                      +.+|+.+++.|...+. ++....+.|+.......+.    +.+.+.  .|++|+|+|.+++++|++|++|+.+|+||.++
T Consensus        87 ~~vGd~ie~~I~~~df-gR~aa~~aKqvi~qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~v~VDlGk~EgiLp~sE  165 (344)
T 1hh2_P           87 AEVGSIVKKELNVKNF-GRIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIGKLETRLPKKE  165 (344)
T ss_dssp             CCTTCEEEEECCCCCS-SSCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEETTEEEEEEGGG
T ss_pred             ccCCCEEEEEEccccC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCcEEEEeCCeEEEEeHHH
Confidence            7899999999976553 2333344455443222222    112233  79999999999999999999999999999999


Q ss_pred             cCCcCCcchh-cCCeEeEEEEEEecccC--eEeeehhhh-hhhhHhhcccCeEEEEEE
Q 021034          219 ISSKSTAEEL-LGKDLPLKFVEVDEEQS--RLVLSNRKA-MADSQAQLGIGSVVIGTV  272 (318)
Q Consensus       219 ls~~~~~~~~-vGq~v~~kVl~vd~~~~--~i~lS~K~~-l~~~~~~l~~G~~v~G~V  272 (318)
                      ++.+.   .+ +|+++++.|++++.+++  .+.||++.. +.+.+..+.+.++..|.|
T Consensus       166 ~ip~E---~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p~~lk~LfelEVPEI~dG~V  220 (344)
T 1hh2_P          166 WIPGE---EIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVIGLMKLEIPEVENGIV  220 (344)
T ss_dssp             SCTTC---CCCTTCEEEEEEEEEEEETTEEEEEEESSSHHHHHHHHHHHCHHHHHSSE
T ss_pred             cCCCc---CCCCCCEEEEEEEEEEcCCCCcEEEEEeeccHHHHHHHHhhcccceeeeE
Confidence            98432   34 79999999999997654  799999865 233343444444444444

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

Probab=98.94  E-value=1.2e-09  Score=84.34  Aligned_cols=81  Identities=31%  Similarity=0.407  Sum_probs=64.9

Q ss_pred             CCcEEEEEEEEEE---cCeEEEEE--CCEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeeehhhhhhhhHhh
Q 021034          187 EDVVVKGKVVGAN---KGGVVAEV--EGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQ  261 (318)
Q Consensus       187 ~G~iv~g~V~~v~---~~G~~V~i--~gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~~~~  261 (318)
                      .++.++|+|+..+   .+| |+.-  ++.+.|+|.+.+.+..-                                 ....
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            5667899999984   457 5554  36999999999986420                                 1145


Q ss_pred             cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccc
Q 021034          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV  301 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~  301 (318)
                      +++|+.|.+.|.++++||+||++. +++||+|+|+++|.++
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            789999999999999999999997 9999999999999875

>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=98.94  E-value=3.4e-10  Score=102.30  Aligned_cols=58  Identities=28%  Similarity=0.513  Sum_probs=55.1

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEE---CCeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i---~gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .+++|+++.|+|+++++||+||++   +|+.||+|.|+++|+++.++.+.|++||.|.|+|
T Consensus         8 ~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~~~~~~~~vGd~V~VkV   68 (266)
T 3cw2_C            8 LPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKV   68 (266)
T ss_dssp             SCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEE
T ss_pred             cCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccccCHHHhCcCCCEEEEEE
Confidence            567899999999999999999999   4899999999999999999999999999999986

>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=98.90  E-value=1.9e-09  Score=92.52  Aligned_cols=58  Identities=31%  Similarity=0.585  Sum_probs=53.5

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCccccc-----------CcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA-----------DIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~-----------~~~~~~~~Gq~V~v~V  318 (318)
                      ...+|+++.|+|++++++|+||++++++||+|+|++++++..           ++.+.|++||.|+|+|
T Consensus        78 ~~~~Gev~~G~V~~v~~~G~fV~l~~~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV  146 (187)
T 1go3_E           78 IPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARI  146 (187)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEE
T ss_pred             ccCCCCEEEEEEEEEeCcEEEEEEcCccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEE
Confidence            356799999999999999999999999999999999998775           7889999999999986

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

Probab=98.89  E-value=1.5e-09  Score=115.35  Aligned_cols=59  Identities=8%  Similarity=0.089  Sum_probs=56.9

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCccc-ccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR-VADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~-~~~~~~~~~~Gq~V~v~V  318 (318)
                      +++++|++|.|+|++|++||+||+|+ |++||||+|+++|.+ +.+|.+.|++||.|+|+|
T Consensus       898 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~p~~v~kvGd~V~vkV  958 (1219)
T 3psi_A          898 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKV  958 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEE
T ss_pred             hhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEE
Confidence            68899999999999999999999999 999999999999998 899999999999999987

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

Probab=98.89  E-value=4.3e-09  Score=89.62  Aligned_cols=71  Identities=24%  Similarity=0.207  Sum_probs=65.0

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCC----------CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITA----------KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSL  165 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~----------~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i  165 (318)
                      ..+ |++|.|+|+++.++|++|++..          +.+|+||++|+++.+..++.+. |++||.|.++|++     +++
T Consensus        55 ~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~-~~~GD~V~akVi~-----~~i  127 (179)
T 3m7n_A           55 IVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEA-VGYLDILKARVIG-----DNL  127 (179)
T ss_dssp             CCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGT-CCTTCEEEEEEEE-----TTT
T ss_pred             cCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhc-CCCCCEEEEEEEC-----CeE
Confidence            567 9999999999999999999976          7999999999999888888888 9999999999987     789


Q ss_pred             EEEeeehh
Q 021034          166 VLSLRMIQ  173 (318)
Q Consensus       166 ~lS~k~~~  173 (318)
                      .||+|...
T Consensus       128 ~LS~k~~~  135 (179)
T 3m7n_A          128 RLSTKEEE  135 (179)
T ss_dssp             EEECCSTT
T ss_pred             EEEEecCC
Confidence            99998753

>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=98.84  E-value=7.2e-09  Score=92.76  Aligned_cols=75  Identities=24%  Similarity=0.161  Sum_probs=67.0

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc---cCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI---KHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~---~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      .+++|++|.|+|+++.++|++|++++..+|+||.+|++..+.   .++.+. +++||.|.|+|+++++ ++++.||+|..
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 YPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRY-LDVGDYVIARIENFDR-SIDPVLSVKGK  148 (251)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSS-CCTTCEEEEEEEEEET-TEEEEEECCST
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCccccccchhhc-CCCCCEEEEEEEEECC-CCcEEEEEccc
Confidence            678999999999999999999999988999999999987665   666666 9999999999999986 46899999764

>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=98.83  E-value=1.9e-08  Score=85.63  Aligned_cols=78  Identities=17%  Similarity=0.234  Sum_probs=65.6

Q ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc-----------cCccccCcCCCCEEEEEEEEEeCC--
Q 021034           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI-----------KHVEEAGIVPGLKEEFVIIGENEA--  161 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~-----------~~~~~~~~~~G~~v~v~Vl~vd~~--  161 (318)
                      ..+.+|++++|+|++++++|+||+++. .+|++|.+++.+++.           ++..+. +++||.|+|+|+++|.+  
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            467899999999999999999999975 899999999998765           345555 89999999999999864  


Q ss_pred             --CCeEEEEeeehhh
Q 021034          162 --DDSLVLSLRMIQY  174 (318)
Q Consensus       162 --~~~i~lS~k~~~~  174 (318)
                        ..++.+|+|++-.
T Consensus       155 ~~~~rI~ls~k~~gL  169 (180)
T 4ayb_E          155 GRLPRIALTMRQPYL  169 (180)
T ss_dssp             ----CEEEECCSTTC
T ss_pred             cccCcEEEEcCCCCC
Confidence              3589999998654

>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=98.82  E-value=1.5e-08  Score=89.53  Aligned_cols=75  Identities=20%  Similarity=0.187  Sum_probs=66.7

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc-cccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH-KIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~-~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      .+++|++|.|+|+++.++|++|++++..+|+||.+|++.. +..+..+. +++||.|.|+|+++++ ++.+.||+|..
T Consensus        54 ~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~~~~~~~~~~-l~~GD~V~arVi~v~~-~~~i~LS~r~~  129 (229)
T 2ba0_A           54 TPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEV-LDIGDAIIAKVLNIDP-KMKVTLTMKDR  129 (229)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGT-CCTTCEEEEEEEEECT-TCCEEEECCSS
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHccccccccchhcc-cCCCCEEEEEEEEECC-CCcEEEEEccc
Confidence            5789999999999999999999999889999999999963 55667777 9999999999999986 47899999763

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=98.82  E-value=1.3e-10  Score=118.44  Aligned_cols=87  Identities=20%  Similarity=0.199  Sum_probs=38.1

Q ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccc----ccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEee
Q 021034           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEA----CIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLR  170 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEl----s~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k  170 (318)
                      .++++|++++|+|.++.++|+||++.++.+||||+||+    ++.++.++++. +++||.|+|+|+++|+ ++++.||+|
T Consensus       663 ~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s~~rv~~~~~~-~~vGd~V~VkVi~vd~-~grI~LS~k  740 (757)
T 1e3p_A          663 TSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDV-LGVGQKVQVEIAEIDS-RGKLSLIPV  740 (757)
T ss_dssp             ----------CBEEECC-CSCEECCC---CCCCC--------------------CCSSCBCCCCCCCCCS-SCC------
T ss_pred             hhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccCCCcccCcccc-cCCCCEEEEEEEEECC-CCCEEEEEe
Confidence            46789999999999999999999998889999999999    99999999988 9999999999999998 899999999


Q ss_pred             ehhhhHHHHHHhhh
Q 021034          171 MIQYELAWERCRQL  184 (318)
Q Consensus       171 ~~~~~~~~~~~~~~  184 (318)
                      .... .+|...+..
T Consensus       741 ~~~~-~pw~~~~~~  753 (757)
T 1e3p_A          741 IEGE-EAASDEKKD  753 (757)
T ss_dssp             --------------
T ss_pred             cCCC-Cchhhhhhc
Confidence            9875 588776543

>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=98.82  E-value=6.5e-09  Score=88.58  Aligned_cols=58  Identities=33%  Similarity=0.629  Sum_probs=53.4

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccc-----------cCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV-----------ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~-----------~~~~~~~~~Gq~V~v~V  318 (318)
                      +..+|+++.|+|++++++|+||+++.++||+|+|++++++.           .+..+.|++||.|++||
T Consensus        78 ~p~~Gev~~G~V~~v~~~G~fv~l~~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV  146 (180)
T 4ayb_E           78 VPVVQEVVEGEVLQVDNYGVFVNLGPMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARV  146 (180)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEE
T ss_pred             eccCCCEEEEEEeeeccceEEEEECCccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEE
Confidence            45679999999999999999999999999999999999876           57888999999999986

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

Probab=98.80  E-value=8.3e-09  Score=87.86  Aligned_cols=56  Identities=32%  Similarity=0.447  Sum_probs=53.1

Q ss_pred             cccCeEEEEEEEEEEcceEEEEEC-----------CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          262 LGIGSVVIGTVQSLKPYGAFIDIG-----------GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~~G~fV~i~-----------gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .+ |++|.|+|++++++|+||+|.           ++.|++|+|++++.+..++.+.|++||.|.|+|
T Consensus        56 p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akV  122 (179)
T 3m7n_A           56 VK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARV  122 (179)
T ss_dssp             CT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEE
T ss_pred             CC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEE
Confidence            46 999999999999999999995           589999999999999999999999999999986

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

Probab=98.80  E-value=5.7e-10  Score=112.96  Aligned_cols=59  Identities=39%  Similarity=0.619  Sum_probs=0.0

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .++++|+++.|+|++|++||+||+|. |++||||+|+++|+++.++.+.|++||.|+|+|
T Consensus       633 ~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~~rv~~~~d~~kvGD~V~VkV  692 (726)
T 4aid_A          633 DEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKL  692 (726)
T ss_dssp             ------------------------------------------------------------
T ss_pred             hhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCcccccCccccCCCCCEEEEEE
Confidence            67899999999999999999999998 999999999999999999999999999999986

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=98.79  E-value=1.2e-10  Score=118.72  Aligned_cols=130  Identities=17%  Similarity=0.238  Sum_probs=50.5

Q ss_pred             CCCEE--EEEEEE--EECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhh
Q 021034           99 LGTKV--KGTVFC--TDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQY  174 (318)
Q Consensus        99 ~G~iv--~G~V~~--i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~  174 (318)
                      .|+++  .|++++  +.+.|++|+++.  +|.++++..++.......+.       ++.           +  .  .   
T Consensus       609 i~~vIG~gGk~Ik~I~~~~G~~IdI~~--dG~v~Is~~~~~~~~~a~~~-------i~~-----------i--~--~---  661 (757)
T 1e3p_A          609 IGEVIGPKRQMINQIQEDTGAEITIED--DGTIYIGAADGPAAEAARAT-------ING-----------I--A--N---  661 (757)
T ss_dssp             ------------CTTCCCCCSCC----------CCCBSSHHHHCC-----------------------------------
T ss_pred             eehcccccceeeehhhHhhCCEEEecC--CceEEEecCCHHHHHHHHHH-------HHH-----------h--c--c---
Confidence            46655  266776  567899999984  79999988775433221110       000           0  0  0   


Q ss_pred             hHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCccc----CCc--CCcchh--cCCeEeEEEEEEecccC
Q 021034          175 ELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQI----SSK--STAEEL--LGKDLPLKFVEVDEEQS  245 (318)
Q Consensus       175 ~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~l----s~~--~~~~~~--vGq~v~~kVl~vd~~~~  245 (318)
                        +     ..++.|++++|+|+++.++|+||++. |++||+|.|++    ++.  .++.+.  +||+|+++|+++|+ ++
T Consensus       662 --p-----~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s~~rv~~~~~~~~vGd~V~VkVi~vd~-~g  733 (757)
T 1e3p_A          662 --P-----TSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDS-RG  733 (757)
T ss_dssp             ------------------CBEEECC-CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCS-SC
T ss_pred             --h-----hhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccCCCcccCcccccCCCCEEEEEEEEECC-CC
Confidence              0     12468999999999999999999995 89999999999    765  344443  79999999999998 89


Q ss_pred             eEeeehhhhhhhhHhhcc
Q 021034          246 RLVLSNRKAMADSQAQLG  263 (318)
Q Consensus       246 ~i~lS~K~~l~~~~~~l~  263 (318)
                      ++.||+|+...++|.+.+
T Consensus       734 rI~LS~k~~~~~pw~~~~  751 (757)
T 1e3p_A          734 KLSLIPVIEGEEAASDEK  751 (757)
T ss_dssp             C-----------------
T ss_pred             CEEEEEecCCCCchhhhh
Confidence            999999998888775544

>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=98.79  E-value=1.1e-08  Score=86.49  Aligned_cols=56  Identities=21%  Similarity=0.250  Sum_probs=48.1

Q ss_pred             ccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCc----------ccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADI----------ATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~----------~~~~~~Gq~V~v~V  318 (318)
                      .+|+++.|+|+++++||+||+++..+||+|+|++++.+.-++          ++.|++||.|+|+|
T Consensus        82 ~~Gev~~G~V~~v~~fG~FV~l~~~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV  147 (171)
T 1y14_B           82 FKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKI  147 (171)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEecCEEEEEecCeEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEE
Confidence            489999999999999999999988999999999986533222          26799999999986

>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=98.79  E-value=1.1e-09  Score=112.00  Aligned_cols=59  Identities=39%  Similarity=0.638  Sum_probs=56.4

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .++++|+++.|+|++|++||+||+++ +++||||+|+++|.++.+|.+.|++||.|+|+|
T Consensus       650 ~~l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkV  709 (785)
T 3bzc_A          650 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKV  709 (785)
T ss_dssp             TTCCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCCSCHHHHCCTTCCCCCBE
T ss_pred             hhcCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCccccCChhheeCCCCEEEEEE
Confidence            56889999999999999999999999 899999999999999999999999999999876

>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=98.77  E-value=1.4e-08  Score=90.22  Aligned_cols=74  Identities=16%  Similarity=0.146  Sum_probs=65.2

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc----cccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH----KIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~----~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~  171 (318)
                      .+++|++|.|+|+++.++|++|+++++.+|+||.+|++..    +..++.+. |++||.|.++|+++++ ++++.||+|.
T Consensus        63 ~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~~~~~~~~~~~~~-l~~GD~V~a~Vi~v~~-~~~i~LS~k~  140 (235)
T 2z0s_A           63 VPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSL-LKVGDYIKAKVVAFDK-TRSPLLTVQG  140 (235)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTS-SCTTCEEEEEEEEECT-TSCEEEECCS
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCccccchhhHhhc-CCCCCEEEEEEEEECC-CCcEEEEEec
Confidence            6899999999999999999999999889999999999862    34566666 9999999999999986 4689999874

>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=98.76  E-value=4.3e-08  Score=82.78  Aligned_cols=75  Identities=19%  Similarity=0.161  Sum_probs=60.0

Q ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCc----------cccCcCCCCEEEEEEEEEeCCCCe
Q 021034           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV----------EEAGIVPGLKEEFVIIGENEADDS  164 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~----------~~~~~~~G~~v~v~Vl~vd~~~~~  164 (318)
                      ....+|++++|+|++++++|+||+++. .+||+|.+++++.+.-++          ++. +++||.|+|+|+++|.+.+.
T Consensus        79 ~~~~~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~-~~~Gd~V~vkV~~vd~~~~~  156 (171)
T 1y14_B           79 FKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDV-ITIKSRIRVKIEGCISQVSS  156 (171)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCE-ECTTCEEEEEEEEEEEETTE
T ss_pred             ccCCCCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceE-ECCCCEEEEEEEEEEcCCCC
Confidence            467899999999999999999999998 999999999976533222          245 89999999999999976642


Q ss_pred             --EEEEeee
Q 021034          165 --LVLSLRM  171 (318)
Q Consensus       165 --i~lS~k~  171 (318)
                        .+-|+++
T Consensus       157 ~~~igsm~~  165 (171)
T 1y14_B          157 IHAIGSIKE  165 (171)
T ss_dssp             EEEEEECCS
T ss_pred             cEEEEEcCC
Confidence              2335554

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

Probab=98.75  E-value=9.1e-10  Score=115.32  Aligned_cols=59  Identities=8%  Similarity=0.089  Sum_probs=0.0

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCccc-ccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR-VADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~-~~~~~~~~~~Gq~V~v~V  318 (318)
                      +++++|++|.|+|++|++||+||+++ |+.||||+|+++|.+ +.+|.+.|++||.|+|+|
T Consensus       901 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~~~~v~kvGd~V~vkV  961 (1030)
T 3psf_A          901 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKV  961 (1030)
T ss_dssp             -------------------------------------------------------------
T ss_pred             HHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEE
Confidence            67899999999999999999999999 999999999999998 899999999999999987

>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=98.75  E-value=1.4e-08  Score=85.96  Aligned_cols=56  Identities=21%  Similarity=0.351  Sum_probs=47.9

Q ss_pred             ccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccc----cC--------cccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV----AD--------IATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~----~~--------~~~~~~~Gq~V~v~V  318 (318)
                      .+|+++.|+|+++++||+||+++.+.||+|+|++++...    .+        ....|++||.|+|+|
T Consensus        80 ~~Gev~~G~V~~v~~fG~fV~l~~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV  147 (172)
T 2c35_B           80 FKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKI  147 (172)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEE
T ss_pred             CCCCEEEEEEEEEeCCEEEEEECCEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEE
Confidence            489999999999999999999997889999999986532    21        155799999999986

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

Probab=98.74  E-value=1.1e-09  Score=111.16  Aligned_cols=60  Identities=38%  Similarity=0.702  Sum_probs=0.0

Q ss_pred             HhhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          259 QAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       259 ~~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ..++++|+++.|+|+++++||+||++. |+.||+|+|+++|+++.++++.|++||.|+|+|
T Consensus       622 ~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~~~~v~~~~~~~~vGd~V~VkV  682 (723)
T 3cdi_A          622 TAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKV  682 (723)
T ss_dssp             -------------------------------------------------------------
T ss_pred             hhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCccccCcccccCCCCEEEEEE
Confidence            367889999999999999999999998 999999999999999999999999999999986

>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=98.71  E-value=1.9e-08  Score=87.88  Aligned_cols=56  Identities=21%  Similarity=0.250  Sum_probs=48.6

Q ss_pred             ccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCc----------ccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADI----------ATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~----------~~~~~~Gq~V~v~V  318 (318)
                      .+|+++.|+|+++++||+||+++..+||+|+|+|++.+.-++          ++.|++||.|+|+|
T Consensus        82 ~vGev~~G~V~~vt~fG~FVelg~~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV  147 (215)
T 2b8k_G           82 FKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKI  147 (215)
T ss_dssp             CTTEEEEEEEEEEETTEEEEECTTSEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEE
T ss_pred             CCCCEEEEEEEEEecceEEEEecCcEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEE
Confidence            689999999999999999999987999999999986543222          26799999999986

>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=98.71  E-value=4.4e-08  Score=85.59  Aligned_cols=77  Identities=16%  Similarity=0.118  Sum_probs=62.9

Q ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCcc----------ccCcCCCCEEEEEEEEEeCCCC-
Q 021034           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVE----------EAGIVPGLKEEFVIIGENEADD-  163 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~----------~~~~~~G~~v~v~Vl~vd~~~~-  163 (318)
                      ...++|++++|+|++++++|+||+++. .+||+|+++|++.+.-++.          +. +++||.|+|+|+++|.+.+ 
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            456899999999999999999999987 9999999999865443332          44 8899999999999998765 


Q ss_pred             --eEEEEeeehhh
Q 021034          164 --SLVLSLRMIQY  174 (318)
Q Consensus       164 --~i~lS~k~~~~  174 (318)
                        ++- |++..-.
T Consensus       157 i~~Ig-Smk~~~L  168 (215)
T 2b8k_G          157 IHAIG-SIKEDYL  168 (215)
T ss_dssp             EEEEE-ECCSTTC
T ss_pred             cEEEE-EcCCCCC
Confidence              444 8877543

>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=98.69  E-value=9.6e-09  Score=89.51  Aligned_cols=58  Identities=19%  Similarity=0.292  Sum_probs=54.2

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEEC---------CeEEEEecCCcCccccc--CcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIG---------GINGLLHVSQISHDRVA--DIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~---------gv~Glv~~s~ls~~~~~--~~~~~~~~Gq~V~v~V  318 (318)
                      .+++|++|.|+|++++++|+||+|+         ++.|++|++++++.+..  ++.+.|++||.|+|+|
T Consensus        78 ~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akV  146 (209)
T 2nn6_I           78 LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKV  146 (209)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEE
T ss_pred             CCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEE
Confidence            5788999999999999999999984         67999999999999888  8999999999999986

>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=98.68  E-value=7.4e-08  Score=81.38  Aligned_cols=76  Identities=16%  Similarity=0.123  Sum_probs=59.6

Q ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCc------------cccCcCCCCEEEEEEEEEeCCC
Q 021034           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV------------EEAGIVPGLKEEFVIIGENEAD  162 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~------------~~~~~~~G~~v~v~Vl~vd~~~  162 (318)
                      ....+|++++|+|++++++|+||+++ ..+|++|.+++++.+.-++            .+. +++||.|+|+|+++|.+.
T Consensus        77 ~~~~~Gev~~G~V~~v~~fG~fV~l~-~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~-~~~Gd~V~vkV~~vd~~~  154 (172)
T 2c35_B           77 FRPFKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIV-IQQDDEIRLKIVGTRVDK  154 (172)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSE-EETTCEEEEEEEEEEEET
T ss_pred             eeCCCCCEEEEEEEEEeCCEEEEEEC-CEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEE-ECCCCEEEEEEEEEEcCC
Confidence            35679999999999999999999997 4779999999976533222            224 889999999999999765


Q ss_pred             Ce--EEEEeeeh
Q 021034          163 DS--LVLSLRMI  172 (318)
Q Consensus       163 ~~--i~lS~k~~  172 (318)
                      +.  .+.|+++.
T Consensus       155 ~~~~~igsm~~~  166 (172)
T 2c35_B          155 NDIFAIGSLMDD  166 (172)
T ss_dssp             TEEEEEEECCST
T ss_pred             CCcEEEEEecCC
Confidence            52  33377653

>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=98.63  E-value=2e-07  Score=86.85  Aligned_cols=79  Identities=16%  Similarity=0.206  Sum_probs=63.1

Q ss_pred             HHHhhhccCCCCCCEEEEEEEE----EECCeEEEEeCC---CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeC
Q 021034           88 SALEKYDFNSELGTKVKGTVFC----TDNRGALVDITA---KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENE  160 (318)
Q Consensus        88 ~~~~~~~~~~~~G~iv~G~V~~----i~~~G~~V~i~~---~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~  160 (318)
                      .++++|  .-..|++++|+|.+    +.+++++|++|+   +.+|+||.+|+.      |.+. |++||+++|+|++++.
T Consensus       121 ~i~~ef--~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi------P~E~-~~~GDrVkvyV~~V~~  191 (366)
T 1k0r_A          121 RTYGEF--STREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV------PGES-YEHGNRLRCYVVGVTR  191 (366)
T ss_dssp             --------CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC------TTCC-CCTTCEEEEEEEEEEC
T ss_pred             HHHHHH--HhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC------CCcc-CCCCCEEEEEEEEEec
Confidence            455655  35699999999999    999999999986   599999999986      3455 9999999999999987


Q ss_pred             CC--CeEEEEeeehhhh
Q 021034          161 AD--DSLVLSLRMIQYE  175 (318)
Q Consensus       161 ~~--~~i~lS~k~~~~~  175 (318)
                      +.  .++.||+..+...
T Consensus       192 ~~kgpqI~LSRT~p~lv  208 (366)
T 1k0r_A          192 GAREPLITLSRTHPNLV  208 (366)
T ss_dssp             CSSSCEEEEESSCHHHH
T ss_pred             CCCccEEEEEeCChHHH
Confidence            63  4799999888663

>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=98.61  E-value=1.5e-07  Score=83.25  Aligned_cols=79  Identities=16%  Similarity=0.144  Sum_probs=67.4

Q ss_pred             CCCCCCEEEEEEEE----EECCeEEEEeCC---CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCC--CeEE
Q 021034           96 NSELGTKVKGTVFC----TDNRGALVDITA---KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEAD--DSLV  166 (318)
Q Consensus        96 ~~~~G~iv~G~V~~----i~~~G~~V~i~~---~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~--~~i~  166 (318)
                      .-..|++++|+|.+    +.++.++|++|.   +.+|+||.+|+.      |.+. |++||+++|+|++++...  .++.
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            34689999999999    899999999986   699999999985      4555 999999999999998764  6899


Q ss_pred             EEeeehhhhHHHHHH
Q 021034          167 LSLRMIQYELAWERC  181 (318)
Q Consensus       167 lS~k~~~~~~~~~~~  181 (318)
                      ||+..+.....|-++
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            999999876666444

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

Probab=98.59  E-value=1.4e-08  Score=85.98  Aligned_cols=57  Identities=23%  Similarity=0.333  Sum_probs=49.6

Q ss_pred             cccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccccCc----------ccccCCCCEEEEEC
Q 021034          262 LGIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVADI----------ATVLQPGDTLKVCL  318 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~~~~----------~~~~~~Gq~V~v~V  318 (318)
                      ..+|+++.|+|++++++|+||+++.++||+|.|+|++.+.-++          .+.|++||.|++||
T Consensus        82 p~~Gev~~G~V~~v~~fG~FV~l~~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV  148 (172)
T 3h0g_G           82 PFRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKI  148 (172)
T ss_dssp             CCTTCEEECCCCEEETTEEECCBTTBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEE
T ss_pred             cCCCCEEEEEEEEEEcceEEEEeCCeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEE
Confidence            3479999999999999999999998889999999987644333          57899999999986

>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=98.50  E-value=7e-08  Score=86.34  Aligned_cols=58  Identities=26%  Similarity=0.395  Sum_probs=54.1

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccc---cCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV---ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~---~~~~~~~~~Gq~V~v~V  318 (318)
                      ..++|++|.|+|++++++|+||+++ +..|++|++++++.+.   .++.+.|++||.|.|+|
T Consensus        71 ~p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arV  132 (251)
T 2je6_I           71 YPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARI  132 (251)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEE
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEE
Confidence            4578999999999999999999999 8999999999998777   78899999999999986

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

Probab=98.48  E-value=1.1e-07  Score=80.30  Aligned_cols=75  Identities=12%  Similarity=0.209  Sum_probs=59.9

Q ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCc----------cccCcCCCCEEEEEEEEEeCCCCe
Q 021034           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHV----------EEAGIVPGLKEEFVIIGENEADDS  164 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~----------~~~~~~~G~~v~v~Vl~vd~~~~~  164 (318)
                      .....|++++|+|++++++|+||+++. .+||+|.++|++.+.-++          .+. +++||.|+|+|+++|.+.+.
T Consensus        80 f~p~~Gev~~G~V~~v~~fG~FV~l~~-~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~-~~~Gd~VrvkV~~vd~~~~~  157 (172)
T 3h0g_G           80 WRPFRGEVVDAIVTTVNKMGFFANIGP-LNVFVSSHLVPPDMKFDPTANPPNYSGEDQV-IEKGSNVRLKIVGTRTDATE  157 (172)
T ss_dssp             ECCCTTCEEECCCCEEETTEEECCBTT-BCCEEEGGGSCTTCCCBSSSSSCBEESSSCE-ECSSCCEEEEEEEEEESSSC
T ss_pred             eccCCCCEEEEEEEEEEcceEEEEeCC-eEEEEEHHHCCCccccCcccccceEecCCcE-ECCCCEEEEEEEEEECCCCC
Confidence            467899999999999999999999975 779999999976544333          334 89999999999999987643


Q ss_pred             E--EEEeee
Q 021034          165 L--VLSLRM  171 (318)
Q Consensus       165 i--~lS~k~  171 (318)
                      +  +-|+|+
T Consensus       158 ~~~Igtm~~  166 (172)
T 3h0g_G          158 IFAIATMKE  166 (172)
T ss_dssp             EEEEEECCS
T ss_pred             ceEEEEcCC
Confidence            2  226554

>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=98.39  E-value=3.8e-07  Score=80.48  Aligned_cols=58  Identities=26%  Similarity=0.324  Sum_probs=53.3

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcc-cccCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHD-RVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~-~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ..++|++|.|+|+.++++|+||+++ ...|++|.+++++. ...+..+.|++||.|.|+|
T Consensus        54 ~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arV  113 (229)
T 2ba0_A           54 TPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKV  113 (229)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEE
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHccccccccchhcccCCCCEEEEEE
Confidence            3578999999999999999999999 79999999999974 5678899999999999986

>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=98.37  E-value=1.8e-07  Score=82.91  Aligned_cols=58  Identities=31%  Similarity=0.425  Sum_probs=52.6

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcc----cccCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHD----RVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~----~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ..++|++|.|+|++++++|+||+++ +..|++|++++++.    ...++.+.|++||.|.|+|
T Consensus        63 ~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~V  125 (235)
T 2z0s_A           63 VPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKV  125 (235)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEE
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEE
Confidence            5688999999999999999999999 89999999999863    3567888999999999986

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

Probab=98.25  E-value=1.5e-06  Score=66.80  Aligned_cols=81  Identities=19%  Similarity=0.255  Sum_probs=61.5

Q ss_pred             CCCCEEEEEEEEEE---CCeEEEEe-CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           98 ELGTKVKGTVFCTD---NRGALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        98 ~~G~iv~G~V~~i~---~~G~~V~i-~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      +.++..+|+|...+   .+| |+.- .++.+.|+|.+++....        +                            
T Consensus        12 ~~~~~~~G~Vk~fn~~kGfG-FI~~~~gg~dvfvH~s~l~~~~--------~----------------------------   54 (101)
T 2bh8_A           12 LQSGKMTGIVKWFNADKGFG-FITPDDGSKDVFVHFSAGSSGA--------A----------------------------   54 (101)
T ss_dssp             ----CEEEEEEEEEGGGTEE-EEEESSSSCEEEEECCCSCSSS--------C----------------------------
T ss_pred             cccccceeEEEEEECCCCCE-EEEeCCCCcEEEEEEEEEecCC--------c----------------------------
Confidence            46788999999985   357 5554 45689999999986431        2                            


Q ss_pred             hhHHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc
Q 021034          174 YELAWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK  222 (318)
Q Consensus       174 ~~~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~  222 (318)
                             ....++.|+.|++.|..+.++|+||+++ +++|++|.|++++.
T Consensus        55 -------~~~~l~~Ge~V~g~V~~i~~fG~fv~l~~~~eGlvhis~i~~~   97 (101)
T 2bh8_A           55 -------VRGNPQQGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISWA   97 (101)
T ss_dssp             -------CCCCCCTTCEEEEEEEECCSEEEEECTTSCEEEEEEEEEEEEC
T ss_pred             -------cccCCCCCCEEEEEEEEeCCcEEEEEcCCCceEEEEHHHCccC
Confidence                   0112368999999999999999999995 99999999999875

>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=98.21  E-value=1.4e-06  Score=84.95  Aligned_cols=59  Identities=24%  Similarity=0.484  Sum_probs=52.3

Q ss_pred             hhcccCeEEEEEEEEEEcc--eEEEEEC-CeEEEEecCCcCcccc---------cCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPY--GAFIDIG-GINGLLHVSQISHDRV---------ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~--G~fV~i~-gv~Glv~~s~ls~~~~---------~~~~~~~~~Gq~V~v~V  318 (318)
                      ....+|.++.|+|+++.|+  |+||+++ |-.||+|.++++|.+.         .++++.+++||.|.|+|
T Consensus        41 ~~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV  111 (517)
T 2bx2_L           41 HEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQI  111 (517)
T ss_dssp             SCCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEE
T ss_pred             CcCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEE
Confidence            3456899999999999999  9999999 9999999999998763         34678899999999986

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

Probab=98.20  E-value=1.4e-06  Score=75.56  Aligned_cols=56  Identities=13%  Similarity=0.217  Sum_probs=49.2

Q ss_pred             ccCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccc-------------------cCcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV-------------------ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~-------------------~~~~~~~~~Gq~V~v~V  318 (318)
                      .+|+++.|+|++++++|+||+++.++|++|.+++.+++.                   .+....|++||.|++||
T Consensus        80 ~~GEv~~G~Vs~vt~~GifV~lg~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV  154 (203)
T 3ayh_B           80 FRGEVMLGKIKSCSEEGIRVTISFFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQI  154 (203)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEeccEEEEEEeCceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEE
Confidence            469999999999999999999988899999999977653                   44566799999999986

>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=98.19  E-value=4.6e-06  Score=81.44  Aligned_cols=73  Identities=18%  Similarity=0.269  Sum_probs=58.5

Q ss_pred             CCCCCCEEEEEEEEEECC--eEEEEeCCCeEEEEeCcccccccc---------cCccccCcCCCCEEEEEEEEEeCCCCe
Q 021034           96 NSELGTKVKGTVFCTDNR--GALVDITAKSSAYLPTQEACIHKI---------KHVEEAGIVPGLKEEFVIIGENEADDS  164 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~--G~~V~i~~~~~g~lp~sEls~~~~---------~~~~~~~~~~G~~v~v~Vl~vd~~~~~  164 (318)
                      ...+|+++.|+|.++.++  ||||+++.+..||||++|+++.+.         .++++. +++||.+.|.|++....++.
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  999999999999999999986653         234565 89999999999886544443


Q ss_pred             EEEEe
Q 021034          165 LVLSL  169 (318)
Q Consensus       165 i~lS~  169 (318)
                      ..||.
T Consensus       121 a~lTt  125 (517)
T 2bx2_L          121 AALTT  125 (517)
T ss_dssp             CEEES
T ss_pred             ceEEe
Confidence            33333

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

Probab=98.03  E-value=5.4e-06  Score=72.50  Aligned_cols=56  Identities=7%  Similarity=0.179  Sum_probs=46.9

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccc--------------cCcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV--------------ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~--------------~~~~~~~~~Gq~V~v~V  318 (318)
                      ..|+++.|+|++++++|+||++. .++|++|.+++..+..              .+-...|++||.|++||
T Consensus        80 ~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV  150 (218)
T 2ckz_B           80 FLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRI  150 (218)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEE
Confidence            36999999999999999999994 6899999999976542              23356699999999986

>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=97.97  E-value=3e-05  Score=78.21  Aligned_cols=73  Identities=12%  Similarity=0.119  Sum_probs=60.6

Q ss_pred             CCCCCC--EEEEEEEEEECCeEEEEe-CCCeEEEEeCccccc--ccc-c---------CccccCcCCCCEEEEEEEEEeC
Q 021034           96 NSELGT--KVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACI--HKI-K---------HVEEAGIVPGLKEEFVIIGENE  160 (318)
Q Consensus        96 ~~~~G~--iv~G~V~~i~~~G~~V~i-~~~~~g~lp~sEls~--~~~-~---------~~~~~~~~~G~~v~v~Vl~vd~  160 (318)
                      .-++|+  ..+|+|+++.++|+||.+ ..+.+|++|.+++++  ++. -         +.... +++||.|+|+|.++|.
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            346899  999999999999999999 567999999999963  221 0         22344 8999999999999999


Q ss_pred             CCCeEEEEe
Q 021034          161 ADDSLVLSL  169 (318)
Q Consensus       161 ~~~~i~lS~  169 (318)
                      +++++.+++
T Consensus       634 ~~~~I~~~l  642 (644)
T 2id0_A          634 ETRSIIARP  642 (644)
T ss_dssp             TTTEEEEEE
T ss_pred             CCCEEEEEE
Confidence            999999886

>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=97.89  E-value=5.2e-05  Score=63.91  Aligned_cols=74  Identities=12%  Similarity=-0.057  Sum_probs=62.2

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      ..++||+|.|+|+.+..++++|+++. ...|+||.+.+... .++.... +++||.|.++|.+++. ++.+.|||-.+
T Consensus         4 ~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~g~-~k~~r~~-l~~GDlV~ArV~~~~~-~~~~~Ltc~~~   78 (175)
T 2ja9_A            4 IPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNA-SKKNRPT-LQVGDLVYARVCTAEK-ELEAEIECFDS   78 (175)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTC-CSSSCCC-CCTTCEEEEEEEECCT-TSCCEEESSCT
T ss_pred             cCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCCch-hhhhhcc-CCCCCEEEEEEEEecC-CCceEEEeccc
Confidence            57899999999999999999999998 79999999988632 3444444 8999999999999875 46789998654

>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=97.88  E-value=1.9e-05  Score=72.31  Aligned_cols=75  Identities=13%  Similarity=0.084  Sum_probs=60.9

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc-ccc---------CccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH-KIK---------HVEEAGIVPGLKEEFVIIGENEADDSL  165 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~-~~~---------~~~~~~~~~G~~v~v~Vl~vd~~~~~i  165 (318)
                      .+++|++|.|+|+.+.+++++|+++....|++|+++++.. .+.         +..+. |++||.|.++|++++. ++.+
T Consensus        92 ~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~-l~vGDlV~ArVisv~~-~~~i  169 (308)
T 2nn6_H           92 IGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGF-LQEGDLISAEVQAVFS-DGAV  169 (308)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHH-SCSSCEECCEEEEEET-TTEE
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhccccceeecccchhhhhhhcc-CCCCCEEEEEEEEcCC-CCCE
Confidence            6789999999999999999999999778899999998652 221         12244 8999999999999984 6789


Q ss_pred             EEEeeeh
Q 021034          166 VLSLRMI  172 (318)
Q Consensus       166 ~lS~k~~  172 (318)
                      .||+|..
T Consensus       170 ~LStr~~  176 (308)
T 2nn6_H          170 SLHTRSL  176 (308)
T ss_dssp             EEECCSS
T ss_pred             EEEecCc
Confidence            9998853

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

Probab=97.87  E-value=5.7e-05  Score=65.25  Aligned_cols=65  Identities=15%  Similarity=0.094  Sum_probs=53.5

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc-------------------cCccccCcCCCCEEEEEEE
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI-------------------KHVEEAGIVPGLKEEFVII  156 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~-------------------~~~~~~~~~~G~~v~v~Vl  156 (318)
                      ...+|+++.|+|+++++.|+||+++ ..+|+++.+++..++.                   ++.... +++|+.|+++|.
T Consensus        78 ~p~~GEv~~G~Vs~vt~~GifV~lg-~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~-~~~Gd~VrvrV~  155 (203)
T 3ayh_B           78 RPFRGEVMLGKIKSCSEEGIRVTIS-FFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELY-FDIDEEIRFQIE  155 (203)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECS-SCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEE-CCTTCEEEEEEE
T ss_pred             ccCCCCEEEEEEEEEeccEEEEEEe-CceEEEEcHHhCCCCceECccCceEEeecccccccccCCcE-EcCCCEEEEEEE
Confidence            5678999999999999999999995 6899999999966442                   222333 899999999999


Q ss_pred             EEeCCC
Q 021034          157 GENEAD  162 (318)
Q Consensus       157 ~vd~~~  162 (318)
                      +++..+
T Consensus       156 ~v~~~~  161 (203)
T 3ayh_B          156 SEDFVD  161 (203)
T ss_dssp             EEEECC
T ss_pred             EEEccc
Confidence            988654

>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=97.77  E-value=9.3e-05  Score=74.67  Aligned_cols=66  Identities=14%  Similarity=0.293  Sum_probs=55.9

Q ss_pred             CCCc--EEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCC--c---CC-----c-----chh-cCCeEeEEEEEEecccC
Q 021034          186 SEDV--VVKGKVVGANKGGVVAEVE--GLRGFVPFSQISS--K---ST-----A-----EEL-LGKDLPLKFVEVDEEQS  245 (318)
Q Consensus       186 ~~G~--iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~--~---~~-----~-----~~~-vGq~v~~kVl~vd~~~~  245 (318)
                      +.|+  .++|+|++++++|+||++.  |+.||||.|++++  .   .+     +     ..+ +||.|+++|.++|.+++
T Consensus       557 ~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~vd~~~~  636 (644)
T 2id0_A          557 KAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRMETR  636 (644)
T ss_dssp             GTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETTTT
T ss_pred             ccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEEEEEeCCCC
Confidence            4788  9999999999999999993  8999999999974  1   10     1     224 79999999999999999


Q ss_pred             eEeeeh
Q 021034          246 RLVLSN  251 (318)
Q Consensus       246 ~i~lS~  251 (318)
                      +|.+++
T Consensus       637 ~I~~~l  642 (644)
T 2id0_A          637 SIIARP  642 (644)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            999875

>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=97.75  E-value=6.8e-05  Score=66.29  Aligned_cols=66  Identities=21%  Similarity=0.291  Sum_probs=56.8

Q ss_pred             CCCcEEEEEEEE----EEcCeEEEEECC----EEEEEeCcccCCcCCcchh-cCCeEeEEEEEEeccc--CeEeeehhhh
Q 021034          186 SEDVVVKGKVVG----ANKGGVVAEVEG----LRGFVPFSQISSKSTAEEL-LGKDLPLKFVEVDEEQ--SRLVLSNRKA  254 (318)
Q Consensus       186 ~~G~iv~g~V~~----v~~~G~~V~i~g----l~gfip~s~ls~~~~~~~~-vGq~v~~kVl~vd~~~--~~i~lS~K~~  254 (318)
                      ..|++|+|+|.+    +.++.++|+++.    .+|+||.+++..+.   .| .|+.+++.|++++.+.  .++.||+...
T Consensus         6 r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqip~E---~~~~GDrIkayV~~V~~~~~gpqIiLSRt~p   82 (251)
T 2asb_A            6 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPGE---SYEHGNRLRCYVVGVTRGAREPLITLSRTHP   82 (251)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSCTTC---CCCTTCEEEEEEEEEECCSSSCEEEEESSCH
T ss_pred             cCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcCCCc---cCCCCCEEEEEEEEEEcCCCCCEEEEEeccH
Confidence            489999999999    899999999985    99999999987542   34 7999999999998764  5799998764

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=97.74  E-value=4.5e-05  Score=71.10  Aligned_cols=66  Identities=21%  Similarity=0.288  Sum_probs=56.6

Q ss_pred             CCCcEEEEEEEE----EEcCeEEEEECC----EEEEEeCcccCCcCCcchh-cCCeEeEEEEEEecccC--eEeeehhhh
Q 021034          186 SEDVVVKGKVVG----ANKGGVVAEVEG----LRGFVPFSQISSKSTAEEL-LGKDLPLKFVEVDEEQS--RLVLSNRKA  254 (318)
Q Consensus       186 ~~G~iv~g~V~~----v~~~G~~V~i~g----l~gfip~s~ls~~~~~~~~-vGq~v~~kVl~vd~~~~--~i~lS~K~~  254 (318)
                      ..|++|+|+|.+    +.+++++|++|+    .+|+||.+++..+.   .| +|+.|+|.|++++.+.+  .|.||+...
T Consensus       129 r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~EqiP~E---~~~~GDrVkvyV~~V~~~~kgpqI~LSRT~p  205 (366)
T 1k0r_A          129 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPGE---SYEHGNRLRCYVVGVTRGAREPLITLSRTHP  205 (366)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSCTTC---CCCTTCEEEEEEEEEECCSSSCEEEEESSCH
T ss_pred             cCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcCCCc---cCCCCCEEEEEEEEEecCCCccEEEEEeCCh
Confidence            389999999999    999999999986    99999999988642   34 79999999999997644  588998654

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

Probab=97.69  E-value=0.00011  Score=64.06  Aligned_cols=68  Identities=18%  Similarity=0.057  Sum_probs=54.5

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc--------------cCccccCcCCCCEEEEEEEEEeCC
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI--------------KHVEEAGIVPGLKEEFVIIGENEA  161 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~--------------~~~~~~~~~~G~~v~v~Vl~vd~~  161 (318)
                      ....|+++.|+|++++++|+||++.+..+|+++.+++..++.              ++-... +++|+.|+++|.+++..
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 KPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLY-FDVNEKIRFRIEREVFV  156 (218)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEE-ECTTCEEEEEEEEEEEC
T ss_pred             cCCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcE-EcCCCEEEEEEEEEEcc
Confidence            567899999999999999999999556899999999865432              112223 88999999999999876


Q ss_pred             CCe
Q 021034          162 DDS  164 (318)
Q Consensus       162 ~~~  164 (318)
                      ++.
T Consensus       157 ~~~  159 (218)
T 2ckz_B          157 DVK  159 (218)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            653

>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=97.41  E-value=0.00025  Score=72.80  Aligned_cols=64  Identities=16%  Similarity=0.314  Sum_probs=47.2

Q ss_pred             cEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccC--CcC-------------C-----cchh-cCCeEeEEEEEEecc--
Q 021034          189 VVVKGKVVGANKGGVVAEVE--GLRGFVPFSQIS--SKS-------------T-----AEEL-LGKDLPLKFVEVDEE--  243 (318)
Q Consensus       189 ~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls--~~~-------------~-----~~~~-vGq~v~~kVl~vd~~--  243 (318)
                      +.+.|+|+++.++|+||.+.  |+.|+||.++++  +..             +     ...+ +||+|+|+|+.+|.+  
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            79999999999999999995  899999999995  210             1     1234 799999999999987  


Q ss_pred             -cCeEeeehh
Q 021034          244 -QSRLVLSNR  252 (318)
Q Consensus       244 -~~~i~lS~K  252 (318)
                       +++|.||+|
T Consensus       751 ~~~kI~lslk  760 (760)
T 2vnu_D          751 SKRKAELLLK  760 (760)
T ss_dssp             -CCEEEC---
T ss_pred             cCCcEEEEeC
Confidence             689999986

>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=97.38  E-value=0.00034  Score=71.88  Aligned_cols=69  Identities=13%  Similarity=0.042  Sum_probs=50.4

Q ss_pred             CEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccc--cccc-----------cC----ccccCcCCCCEEEEEEEEEeCC-
Q 021034          101 TKVKGTVFCTDNRGALVDITA-KSSAYLPTQEAC--IHKI-----------KH----VEEAGIVPGLKEEFVIIGENEA-  161 (318)
Q Consensus       101 ~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls--~~~~-----------~~----~~~~~~~~G~~v~v~Vl~vd~~-  161 (318)
                      +...|+|+++.++|+||.+.. +.+|++|+++++  ..+.           .+    .... +++||.|+|+|+.+|.+ 
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            799999999999999999965 799999999996  3221           12    1344 89999999999999987 


Q ss_pred             --CCeEEEEee
Q 021034          162 --DDSLVLSLR  170 (318)
Q Consensus       162 --~~~i~lS~k  170 (318)
                        ++++.+|+|
T Consensus       750 ~~~~kI~lslk  760 (760)
T 2vnu_D          750 TSKRKAELLLK  760 (760)
T ss_dssp             --CCEEEC---
T ss_pred             ccCCcEEEEeC
Confidence              589999875

>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1

Probab=97.34  E-value=0.00037  Score=58.65  Aligned_cols=56  Identities=14%  Similarity=0.118  Sum_probs=49.2

Q ss_pred             cccCeEEEEEEEEEEcceEEEEECC--eEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          262 LGIGSVVIGTVQSLKPYGAFIDIGG--INGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~~G~fV~i~g--v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .++||+|.|.|..+..++++|+++.  ..|++|.+.+. ....+....|++||.|.|+|
T Consensus         5 P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~-g~~k~~r~~l~~GDlV~ArV   62 (175)
T 2ja9_A            5 PSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFP-NASKKNRPTLQVGDLVYARV   62 (175)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSST-TCCSSSCCCCCTTCEEEEEE
T ss_pred             CCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCC-chhhhhhccCCCCCEEEEEE
Confidence            3579999999999999999999996  99999999886 33466778899999999986

>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=97.27  E-value=0.00012  Score=67.04  Aligned_cols=58  Identities=17%  Similarity=0.315  Sum_probs=47.7

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcc----cc------cCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHD----RV------ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~----~~------~~~~~~~~~Gq~V~v~V  318 (318)
                      ..++|++|.|.|+.++++|+||+++ ...|++|.|+++++    |.      .+..+.|++||.|.|+|
T Consensus        92 ~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArV  160 (308)
T 2nn6_H           92 IGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEV  160 (308)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEE
T ss_pred             CCCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEE
Confidence            4568999999999999999999999 68999999999763    22      13457899999999986

>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=97.22  E-value=0.00077  Score=61.12  Aligned_cols=73  Identities=16%  Similarity=-0.033  Sum_probs=61.1

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~  171 (318)
                      -.++|++|.|+|+++....+.|+|+....|+||.+++.. ..++..+. |++||.|.++|++.+. ++.+.|||-.
T Consensus       124 iP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~G-atk~~r~~-f~~GDlV~ArV~s~~~-~~~~eLsc~~  196 (289)
T 2nn6_G          124 VPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEG-ATKRNRPN-VQVGDLIYGQFVVANK-DMEPEMVCID  196 (289)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSC-CSSCSSSS-SCTTCEEEEEEEECCT-TSCCEEECSB
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcCc-chhhhhhh-cCCCCEEEEEEEEcCC-CCceEEEecc
Confidence            578999999999999999999999988899999998763 23444555 9999999999999874 4568889854

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

Probab=97.19  E-value=0.00052  Score=72.09  Aligned_cols=70  Identities=13%  Similarity=0.037  Sum_probs=57.3

Q ss_pred             CCEEEEEEEEEECCeEEEEeCC-CeEEEEeCcccc--cccc-----------cC----ccccCcCCCCEEEEEEEEEeCC
Q 021034          100 GTKVKGTVFCTDNRGALVDITA-KSSAYLPTQEAC--IHKI-----------KH----VEEAGIVPGLKEEFVIIGENEA  161 (318)
Q Consensus       100 G~iv~G~V~~i~~~G~~V~i~~-~~~g~lp~sEls--~~~~-----------~~----~~~~~~~~G~~v~v~Vl~vd~~  161 (318)
                      |+...|+|+++.++|+||.+.. +.+|++|+++++  +++.           .+    .... +++||.|+|+|..++..
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            9999999999999999999965 799999999996  3321           11    2344 89999999999998863


Q ss_pred             ---CCeEEEEee
Q 021034          162 ---DDSLVLSLR  170 (318)
Q Consensus       162 ---~~~i~lS~k  170 (318)
                         ++++.||+|
T Consensus       966 ~~~~~kI~Lslk  977 (977)
T 2wp8_J          966 ITSKRKAELLLK  977 (977)
T ss_dssp             SSCCCCCCEEEC
T ss_pred             ccCCCceEEEeC
Confidence               378999886

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

Probab=97.19  E-value=0.00039  Score=73.03  Aligned_cols=66  Identities=15%  Similarity=0.323  Sum_probs=54.5

Q ss_pred             CCcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccC--CcC-------------C-----cchh-cCCeEeEEEEEEecc
Q 021034          187 EDVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQIS--SKS-------------T-----AEEL-LGKDLPLKFVEVDEE  243 (318)
Q Consensus       187 ~G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls--~~~-------------~-----~~~~-vGq~v~~kVl~vd~~  243 (318)
                      .|+.+.|+|+++.++|+||.+.  |+.|+||.++|+  +..             .     ...+ +||+|+++|..+|.+
T Consensus       886 ~ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~VkV~~vd~~  965 (977)
T 2wp8_J          886 NESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDP  965 (977)
T ss_dssp             TTCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEEECCCCCS
T ss_pred             cceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCCEEEEEEEEEcCc
Confidence            3889999999999999999995  899999999996  221             1     1224 799999999999874


Q ss_pred             ---cCeEeeehh
Q 021034          244 ---QSRLVLSNR  252 (318)
Q Consensus       244 ---~~~i~lS~K  252 (318)
                         +++|.||+|
T Consensus       966 ~~~~~kI~Lslk  977 (977)
T 2wp8_J          966 ITSKRKAELLLK  977 (977)
T ss_dssp             SSCCCCCCEEEC
T ss_pred             ccCCCceEEEeC
Confidence               478999976

>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=95.85  E-value=0.012  Score=53.20  Aligned_cols=56  Identities=20%  Similarity=0.100  Sum_probs=49.2

Q ss_pred             cccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          262 LGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       262 l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      .++|++|-|.|+.++...+.|+|+ -..|++|.+++. ....+....|++||-|.|+|
T Consensus       125 P~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~-Gatk~~r~~f~~GDlV~ArV  181 (289)
T 2nn6_G          125 PVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFE-GATKRNRPNVQVGDLIYGQF  181 (289)
T ss_dssp             CCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSS-CCSSCSSSSSCTTCEEEEEE
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcC-cchhhhhhhcCCCCEEEEEE
Confidence            468999999999999999999999 789999999876 33456778899999999986

>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae}

Probab=94.64  E-value=0.14  Score=44.12  Aligned_cols=70  Identities=11%  Similarity=0.101  Sum_probs=50.7

Q ss_pred             cCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccc-----------cCcCCCCEEEEEEEEEeCCCC
Q 021034           95 FNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEE-----------AGIVPGLKEEFVIIGENEADD  163 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~-----------~~~~~G~~v~v~Vl~vd~~~~  163 (318)
                      .....|+++.|+|.++.+.|+.+-+.+-..+++|...+...+.-++.+           ..-++|+.|+++|.+++..++
T Consensus       125 FrPf~GevL~G~V~~~s~~~Ig~~~~G~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~~~~~~~~  204 (214)
T 2rf4_A          125 WQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGR  204 (214)
T ss_dssp             ECCCTTCEEEEEECCCCSSCEEEEETTTEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEEEEECCSS
T ss_pred             EecCCCCEEEEEEEEECCCcEEEEEeCCEEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEEEEEecCC
Confidence            357799999999999999888776655678999999885432211111           012469999999999986554


Q ss_pred             e
Q 021034          164 S  164 (318)
Q Consensus       164 ~  164 (318)
                      .
T Consensus       205 ~  205 (214)
T 2rf4_A          205 V  205 (214)
T ss_dssp             S
T ss_pred             E
Confidence            4

>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=92.90  E-value=0.7  Score=34.92  Aligned_cols=57  Identities=9%  Similarity=-0.018  Sum_probs=47.2

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc-----cC-ccccCcCCCCEEEEE
Q 021034           97 SELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI-----KH-VEEAGIVPGLKEEFV  154 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~-----~~-~~~~~~~~G~~v~v~  154 (318)
                      ...|....|.|.++.+.++.|.+.++..+.||.+.|.+..-     +. +++. +++|+.|.++
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            34589999999999999999999777888899999998642     33 5555 8999999887

>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=92.06  E-value=0.39  Score=36.40  Aligned_cols=54  Identities=13%  Similarity=0.076  Sum_probs=46.6

Q ss_pred             cCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccc-----cC-cccccCCCCEEEEE
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV-----AD-IATVLQPGDTLKVC  317 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~-----~~-~~~~~~~Gq~V~v~  317 (318)
                      .|+.+.+.|.++++.++-|.+. |-.+.|+.+.|.|-+-     .. +++.+++||.|.|+
T Consensus        33 ~~~~~~AvV~~v~~~~~~v~~~~g~~~~l~~~~~~WA~~~~~~~~~~~~~~l~~GdvI~V~   93 (106)
T 3d0f_A           33 SDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAHRFLSNDPKIGEKRIRPGALIRVK   93 (106)
T ss_dssp             TTTCEEEEEEEEETTEEEEEETTSCEEEECGGGGSTTGGGTTTCTTTGGGSCCTTEEEEEE
T ss_pred             cCCeEEEEEEEeCCCeEEEEEcCCCeEEEcHHHChhhhhcccccccchhccCCCCCEEEEE
Confidence            4889999999999999999996 7888899999999753     34 67789999999875

>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=89.44  E-value=0.96  Score=38.85  Aligned_cols=60  Identities=10%  Similarity=0.068  Sum_probs=45.4

Q ss_pred             CCCcEEEEEEEEEEcCeEEEE-ECCEEEEEeCcccCCc--CCc--------------chhcCCeEeEEEEEEecccC
Q 021034          186 SEDVVVKGKVVGANKGGVVAE-VEGLRGFVPFSQISSK--STA--------------EELLGKDLPLKFVEVDEEQS  245 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~-i~gl~gfip~s~ls~~--~~~--------------~~~vGq~v~~kVl~vd~~~~  245 (318)
                      ..|+++.|+|..+++.|+-+- ++-..+|||...+...  .++              ...+|++|+++|..++.+.+
T Consensus       128 f~GevL~G~V~~~s~~~Ig~~~~G~Fn~~Ip~~~ip~~~~f~~~~~~~~~~~wv~~~~~~ig~~IRFrV~~~~~~~~  204 (214)
T 2rf4_A          128 QVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGR  204 (214)
T ss_dssp             CTTCEEEEEECCCCSSCEEEEETTTEEEEECSTTSCSSCBCCCCSCC-CCCCCBCSSCCBCCSEEEEEEEEEECCSS
T ss_pred             CCCCEEEEEEEEECCCcEEEEEeCCEEEEEcHHHCCCcccccccccccCCCceEcCCCCCCCCEEEEEEEEEEecCC
Confidence            489999999999999888764 4668899999988532  110              11269999999999986544

>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=86.61  E-value=1.6  Score=34.29  Aligned_cols=88  Identities=14%  Similarity=0.010  Sum_probs=58.6

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeCCCe--EEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehhhh
Q 021034           98 ELGTKVKGTVFCTDNRGALVDITAKS--SAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQYE  175 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~~~~--~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~~  175 (318)
                      +.|.-.+|+|..+.+++++|.+.+..  .--+|.+++-........ ..|.+||+|+|.-    ..+..           
T Consensus        13 ~~G~~y~a~V~~v~~d~~~V~f~n~w~~~~~vp~~~vRlpP~~~~~-~~f~~gd~VEV~~----~~~d~-----------   76 (128)
T 3h8z_A           13 SNGAFYKGFVKDVHEDSVTIFFENNWQSERQIPFGDVRLPPPADYN-KEITEGDEVEVYS----RANEQ-----------   76 (128)
T ss_dssp             TTSCEEEEEEEEECSSEEEEEETTCTTCCEEEEGGGEECCCCC-----CCCTTCEEEEEE----CC--------------
T ss_pred             CCCCEEEEEEEEEeCCcEEEEEccccCcceEechhhEEcCCCcccc-cCCCCCCEEEEEe----cCCCC-----------
Confidence            45999999999999999999996543  457888887653322222 2388999999844    11110           


Q ss_pred             HHHHHHhhhcCCCcEEEEEEEEEEcCeEEEEECCEE
Q 021034          176 LAWERCRQLQSEDVVVKGKVVGANKGGVVAEVEGLR  211 (318)
Q Consensus       176 ~~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~gl~  211 (318)
                                ++--.-.|+|+.+...=++|+..|.+
T Consensus        77 ----------ep~gWw~a~I~~~kg~f~~V~y~~~~  102 (128)
T 3h8z_A           77 ----------EPCGWWLARVRMMKGDFYVIEYAACD  102 (128)
T ss_dssp             ----------CCCEEEEEEEEEEETTEEEEEETTC-
T ss_pred             ----------CcCccEEEEEEEeeCCEEEEEEcCCC
Confidence                      12337889998888777778875433

>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=85.30  E-value=2  Score=33.77  Aligned_cols=54  Identities=17%  Similarity=0.187  Sum_probs=38.8

Q ss_pred             cCeEEEEEEEEEEcceEEEEECC---eEEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIGG---INGLLHVSQISHDRVADIATVLQPGDTLKVC  317 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~g---v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~  317 (318)
                      .|.-++|+|+.+.+.+++|.+.+   -.--+|.+++.-.........|.+||+|+|.
T Consensus        14 ~G~~y~a~V~~v~~d~~~V~f~n~w~~~~~vp~~~vRlpP~~~~~~~f~~gd~VEV~   70 (128)
T 3h8z_A           14 NGAFYKGFVKDVHEDSVTIFFENNWQSERQIPFGDVRLPPPADYNKEITEGDEVEVY   70 (128)
T ss_dssp             TSCEEEEEEEEECSSEEEEEETTCTTCCEEEEGGGEECCCCC----CCCTTCEEEEE
T ss_pred             CCCEEEEEEEEEeCCcEEEEEccccCcceEechhhEEcCCCcccccCCCCCCEEEEE
Confidence            38999999999999999999973   2345666666543333344679999999985

>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=84.68  E-value=3.2  Score=39.91  Aligned_cols=59  Identities=10%  Similarity=0.065  Sum_probs=42.6

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034           98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~  169 (318)
                      ..|+..+|.|+.+..          ..|+++++++... .. .... +++||.|+|+|.++|..++.+.+..
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 QPERVWDAVVVDRRG----------AQATLLIPDLAFD-VQ-VNTP-AAPGTALQVQFADIDLPQMRVRARS  460 (469)
T ss_dssp             CTTCCEEEEEEEEET----------TEEEEEEGGGTEE-EE-EECC-CCTTCEEEEEEEEEETTTTEEEEEE
T ss_pred             CCCCEEEEEEEEEeC----------cEEEEEECCCCeE-Ee-cCCc-CCCCCEEEEEEEEEccCCCEEEEEE
Confidence            589999998876442          3567777776543 11 1222 8999999999999999998886643

>4b9x_A TDRD1, tudor domain-containing protein 1; replication; 2.80A {Mus musculus}

Probab=84.65  E-value=18  Score=30.81  Aligned_cols=136  Identities=9%  Similarity=0.013  Sum_probs=85.8

Q ss_pred             cCCCCEEEEEEEEEeCCCCeEEEEeeehhh----hHHHHHHhhh--------------------c-CCCcEEEEEEEEEE
Q 021034          145 IVPGLKEEFVIIGENEADDSLVLSLRMIQY----ELAWERCRQL--------------------Q-SEDVVVKGKVVGAN  199 (318)
Q Consensus       145 ~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~----~~~~~~~~~~--------------------~-~~G~iv~g~V~~v~  199 (318)
                      +.+|+.++|.|..+... +.+.+-......    +.-...+.+.                    + ..|....|.|.++.
T Consensus        13 l~~~~~~~V~Vt~v~sP-~~Fyvq~~~~~~~~~L~~L~~~l~~~~~~~~~~~~~~~~G~~c~a~~~~d~~WyRa~V~~~~   91 (226)
T 4b9x_A           13 FTVDETVDVVVCMMYSP-GEFYCHFLKDDALEKLDDLNQSLADYCAQKPPNGFKAEIGRPCCAFFSGDGNWYRALVKEIL   91 (226)
T ss_dssp             CCTTCEEEEEEEEEEET-TEEEEEECCTTHHHHHHHHHHHHHHHTSSSCC--CCCCTTCEEEEEETTTTEEEEEEEEEEC
T ss_pred             cCCCCEEEEEEEEEeCC-CEEEEEEcCCchHHHHHHHHHHHHHHHhcCCCCCCCCCCCCEEEEEECCCCeEEEEEEEEEC
Confidence            78999999999998754 556554432211    1111122211                    1 13567889999986


Q ss_pred             cCe-EEEEE-C-CEEEEEeCcccCCc-CCcchhcCCeEeEEEEEEecccCeEeeehhhhhhhhHhhcccCeEEEEEEEEE
Q 021034          200 KGG-VVAEV-E-GLRGFVPFSQISSK-STAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSL  275 (318)
Q Consensus       200 ~~G-~~V~i-~-gl~gfip~s~ls~~-~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~~~~l~~G~~v~G~V~~i  275 (318)
                      +.+ +-|.+ + |-...+|.++|-.- ..+..+-.|-++|++-.+.+..+.  -|.  ...+.+.++-.|..+.+.|..+
T Consensus        92 ~~~~~~V~~vDyGn~~~v~~~~l~~l~~~f~~lP~qA~~c~L~~v~p~~~~--w~~--ea~~~f~~l~~~k~l~~~V~~~  167 (226)
T 4b9x_A           92 PSGNVKVHFVDYGNVEEVTTDQLQAILPQFLLLPFQGMQCWLVDIQPPNKH--WTK--EATARFQACVVGLKLQARVVEI  167 (226)
T ss_dssp             SSSEEEEECTTTCCEEEEEGGGEECCCGGGSSSCBCCEEEEESSEECSSSS--CCH--HHHHHHHHHHTTCCEEEEEEEE
T ss_pred             CCCeEEEEEEecCCEEEEEHHHhccChHHHcccccceEEEEEecEECCCCC--CCH--HHHHHHHHHHCCCeEEEEEEEE
Confidence            554 44554 4 77888998886632 222233478899998777664331  111  1123456677799999999999


Q ss_pred             EcceEEEEEC
Q 021034          276 KPYGAFIDIG  285 (318)
Q Consensus       276 ~~~G~fV~i~  285 (318)
                      .+.++.|.+.
T Consensus       168 ~~~~~~V~L~  177 (226)
T 4b9x_A          168 TANGVGVELT  177 (226)
T ss_dssp             CSSCEEEEEE
T ss_pred             eCCeEEEEEE
Confidence            9999888873

>3cam_A Cold-shock domain family protein; cold shock protein, chain SWAP, STRU genomics, oxford protein production facility, OPPF, gene RE; 2.60A {Neisseria meningitidis MC58}

Probab=82.78  E-value=9  Score=26.22  Aligned_cols=49  Identities=12%  Similarity=0.149  Sum_probs=35.5

Q ss_pred             EEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034          104 KGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus       104 ~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~  157 (318)
                      +|+|...++   +|.+-.-.++.+-|+|.+.+.....+.     +..||.|++.+..
T Consensus         3 ~G~Vk~fn~~kGfGFI~~~~gg~dvFvH~s~i~~~g~~~-----l~~G~~V~f~~~~   54 (67)
T 3cam_A            3 TGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINMEGFKT-----LKEGQRVSFDVTT   54 (67)
T ss_dssp             EEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCGGGGSS-----CCTTCEEEEEEEE
T ss_pred             CEEEEEEECCCCeEEEecCCCCccEEEEHHHccccCCCC-----CCCCCEEEEEEEE
Confidence            699999875   355544455689999999996432222     6789999998854

>1wfq_A UNR protein; beta-barrel, translational regulation, RNA chaperone, RNA/DN binding, QB fold, greek-KEY topology, structur genomics; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=81.09  E-value=14  Score=26.93  Aligned_cols=56  Identities=7%  Similarity=0.097  Sum_probs=41.0

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEe-CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i-~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~  157 (318)
                      .....+...|+|...++..=|+.- .++-+-|+|.+.+... .+    . +..||.|++.+..
T Consensus        12 ~~s~~~~~~G~Vkwf~KGfGFI~~ddgg~DVFvH~s~i~~~-~~----~-L~~G~~V~F~v~~   68 (89)
T 1wfq_A           12 GTSAALRETGVIEKLLTSYGFIQCSERQARLFFHCSQYNGN-LQ----D-LKVGDDVEFEVSS   68 (89)
T ss_dssp             SSSCCCEEEEEEEEECSSEEEEEETTTTEEEEEETTTCSSC-TT----T-CCTTCCEEEEEEE
T ss_pred             CCCcccccceEEEEEeCCeeEEecCCCCccEEEEhHHhhCc-cC----C-CCCCCEEEEEEEE
Confidence            345567899999999764445555 4458999999998654 21    2 7899999998854

>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=81.02  E-value=7.3  Score=28.55  Aligned_cols=64  Identities=11%  Similarity=0.101  Sum_probs=42.7

Q ss_pred             cCCCCCCEEEEEEEEEECCeEEEEe-CC-CeEEEEeCc-ccccccccCccccCcCCCCEEEEEEEEEeCC
Q 021034           95 FNSELGTKVKGTVFCTDNRGALVDI-TA-KSSAYLPTQ-EACIHKIKHVEEAGIVPGLKEEFVIIGENEA  161 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~G~~V~i-~~-~~~g~lp~s-Els~~~~~~~~~~~~~~G~~v~v~Vl~vd~~  161 (318)
                      .++.+|++.+|.|. +.++-.+|.+ ++ +.+|+|-.. .+-.+...+.++.  -+|.++.++|+.+|.-
T Consensus        28 ~~~~~g~VtkGiVy-~kd~~fyV~L~dY~glEaii~dYvnv~~dr~~klkkk--LVGKtIkVqVIRvD~l   94 (102)
T 1jjg_A           28 MDLSPGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKER--LVGRVIKTRVVRADGL   94 (102)
T ss_dssp             CCCCSSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHH--HTTCEEEEEEEEECSS
T ss_pred             cccCCCceEeeEEE-EeCCEEEEEecCCCCceeeeehhhhhhHHHHHHHHHH--hcCceEEEEEEEeccE
Confidence            47889999999665 5666777888 33 688887532 1122223333332  3799999999998853

>4b9w_A TDRD1, tudor domain-containing protein 1; replication; HET: 2MR; 2.10A {Mus musculus}

Probab=80.87  E-value=23  Score=29.44  Aligned_cols=135  Identities=9%  Similarity=0.015  Sum_probs=84.4

Q ss_pred             cCCCCEEEEEEEEEeCCCCeEEEEeeehhh----hHHHHHHhhh--------------------c-CCCcEEEEEEEEEE
Q 021034          145 IVPGLKEEFVIIGENEADDSLVLSLRMIQY----ELAWERCRQL--------------------Q-SEDVVVKGKVVGAN  199 (318)
Q Consensus       145 ~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~~----~~~~~~~~~~--------------------~-~~G~iv~g~V~~v~  199 (318)
                      +.+|+.++|.|..+... +.+.+-......    +.-...+.+.                    + ..|....|.|.++.
T Consensus        13 l~~~~~~~V~Vt~v~sP-~~Fyvq~~~~~~~~~l~~L~~~l~~~~~~~~~~~~~~~~G~~c~a~~~~d~~wyRa~V~~~~   91 (201)
T 4b9w_A           13 FTVDETVDVVVCMMYSP-GEFYCHFLKDDALEKLDDLNQSLADYCAQKPPNGFKAEIGRPCCAFFSGDGNWYRALVKEIL   91 (201)
T ss_dssp             CCTTCEEEEEEEEEEET-TEEEEEECCTTHHHHHHHHHHHHHHHHHSSSCCCCCCCTTCEEEEEETTTTEEEEEEEEEEC
T ss_pred             cCCCCEEEEEEEEEeCC-CEEEEEECCCchHHHHHHHHHHHHHHHhcCCCCCCCCCCCCEEEEEECCCCeEEEEEEEEEC
Confidence            78999999999998754 556554432211    1111122110                    1 13567889999986


Q ss_pred             cCe-EEEEE-C-CEEEEEeCcccCCc-CCcchhcCCeEeEEEEEEecccCeEeeehhhhhhhhHhhcccCeEEEEEEEEE
Q 021034          200 KGG-VVAEV-E-GLRGFVPFSQISSK-STAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSL  275 (318)
Q Consensus       200 ~~G-~~V~i-~-gl~gfip~s~ls~~-~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~~~~l~~G~~v~G~V~~i  275 (318)
                      +.+ +-|.+ + |-...+|.+++-.- ..+..+-.|-++|++-.+.+....  -|.  ...+.+.++-.|..+.+.|..+
T Consensus        92 ~~~~~~V~~vDyG~~~~v~~~~l~~l~~~f~~lP~qA~~c~L~~v~p~~~~--w~~--ea~~~f~~l~~~k~l~~~V~~~  167 (201)
T 4b9w_A           92 PSGNVKVHFVDYGNVEEVTTDQLQAILPQFLLLPFQGMQCWLVDIQPPNKH--WTK--EATARFQACVVGLKLQARVVEI  167 (201)
T ss_dssp             TTSCEEEEETTTCCEEEECGGGEEECCGGGGSSCBCCEEEEESSEECSSSS--CCH--HHHHHHHHHHTTCCEEEEEEEE
T ss_pred             CCCeEEEEEEccCCEEEEEHHHhccChHhHcccchhhEEEEEcCEEcCCCC--CCH--HHHHHHHHHHCCCEEEEEEEEE
Confidence            554 55555 4 77788888876532 223333478889998777654332  111  1123456666789999999999


Q ss_pred             EcceEEEEE
Q 021034          276 KPYGAFIDI  284 (318)
Q Consensus       276 ~~~G~fV~i  284 (318)
                      .+.++.|.+
T Consensus       168 ~~~~~~V~L  176 (201)
T 4b9w_A          168 TANGVGVEL  176 (201)
T ss_dssp             ETTEEEEEE
T ss_pred             eCCEEEEEE
Confidence            998888876

>3i2z_B RNA chaperone, negative regulator of CSPA transcription; beta barrel, DNA binding protein/transcription, cytoplasm, gene regulation; 1.10A {Salmonella typhimurium} SCOP: b.40.4.5 PDB: 2l15_A 1mjc_A 3mef_A

Probab=80.70  E-value=12  Score=25.94  Aligned_cols=51  Identities=20%  Similarity=0.283  Sum_probs=36.9

Q ss_pred             EEEEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034          102 KVKGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus       102 iv~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~  157 (318)
                      ...|+|...++   +|.+-.-.++-+-|+|.+.+.....+.     +..||.|++.+..
T Consensus         5 ~~~G~Vk~fn~~kGfGFI~~~~g~~dvFvH~s~i~~~g~~~-----l~~G~~V~f~~~~   58 (71)
T 3i2z_B            5 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKT-----LAEGQRVEFEITN   58 (71)
T ss_dssp             CEEEEEEEEETTTTEEEEEETTCCCCEEEEGGGBCCSSCCC-----CCTTCEEEEEEEE
T ss_pred             cccEEEEEEECCCCcEEEecCCCCccEEEEhHHcccccCcC-----CCCCCEEEEEEEE
Confidence            46799999975   455554455578999999986542221     6789999998854

---

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	318
d1e3pa2	62	b.40.4.5 (A:656-717) S1 RNA-binding domain of poly	2e-09
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	2e-09
d1y14b1	91	b.40.4.5 (B:81-171) C-terminal domain of RNA polym	2e-07
d1go3e1	106	b.40.4.5 (E:79-184) C-terminal domain of RNA polym	2e-07
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	3e-07
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	5e-07
d3bzka4	94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	1e-05
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	2e-05
d2c35b1	94	b.40.4.5 (B:78-171) C-terminal domain of RNA polym	3e-05
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	3e-05
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	4e-05
d2ahob2	84	b.40.4.5 (B:1-84) Eukaryotic initiation factor 2al	1e-04
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	1e-04
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	4e-04

>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 = 51.3 bits (123), Expect = 2e-09
 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 5/52 (9%)

Query: 270 GTVQSLKPYGAFIDI-GGINGLLHVSQISHD----RVADIATVLQPGDTLKV 316
           G+V     +GAF+ +  G +GLLH+SQI       RV ++  VL  G  ++V
Sbjct: 1   GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQV 52

>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 = 51.3 bits (123), Expect = 2e-09
 Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           A++ +G V  G V  +  +GAF+ IG G  GL+H+SQI+  RV  +   LQ G  + V
Sbjct: 1   AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPV 58

>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 = 46.0 bits (109), Expect = 2e-07
 Identities = 12/63 (19%), Positives = 21/63 (33%), Gaps = 10/63 (15%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA----------DIATVLQPGDT 313
            G VV GTV S   +G  + +G +   +    +  D                 V+     
Sbjct: 3   KGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSR 62

Query: 314 LKV 316
           ++V
Sbjct: 63  IRV 65

>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 = 46.6 bits (110), Expect = 2e-07
 Identities = 14/38 (36%), Positives = 25/38 (65%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV 301
           +  ++ G V  +  +G+F+ +G ++GL+HVSQI  D V
Sbjct: 3   MYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYV 40

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.7 bits (108), Expect = 3e-07
 Identities = 9/64 (14%), Positives = 26/64 (40%), Gaps = 11/64 (17%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQIS----------HDRVADIATVLQPGD 312
           +G +V+G +  ++     ++    ++ +L +S ++           +    +   LQ GD
Sbjct: 8   VGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGD 67

Query: 313 TLKV 316
            +  
Sbjct: 68  LISA 71

>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 = 44.9 bits (106), Expect = 5e-07
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 5/58 (8%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV----ADIATVLQPGDTLKV 316
            G VVIG +QS+     F+DI      +L V             D+ ++L+ GD +K 
Sbjct: 7   AGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKA 64

>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 = 41.0 bits (96), Expect = 1e-05
 Identities = 23/57 (40%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKV 316
            L  G V+ G V ++  +GAF+DIG   +GL+H+S +S   V D   V++ GD +KV
Sbjct: 15  DLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKV 71

>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 = 34.1 bits (78), 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 = 40.7 bits (95), Expect = 2e-05
 Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 3/56 (5%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +  VV+  V+S+   GA++ +     I G++ +S++S  R+  I  +++ G    V
Sbjct: 13  VEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECV 68

>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 = 39.9 bits (93), Expect = 3e-05
 Identities = 13/65 (20%), Positives = 23/65 (35%), Gaps = 12/65 (18%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA------------DIATVLQPG 311
            G VV   V  +   G F +IG ++  +    I  +               D   V+Q  
Sbjct: 4   KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQD 63

Query: 312 DTLKV 316
           D +++
Sbjct: 64  DEIRL 68

>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 = 39.8 bits (93), Expect = 3e-05
 Identities = 12/54 (22%), Positives = 17/54 (31%), Gaps = 2/54 (3%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKV 316
            G  VIG V +       +D+GG     L                +Q GD +  
Sbjct: 6   KGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEG-ATKRNRPNVQVGDLIYG 58

>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 = 39.2 bits (91), Expect = 4e-05
 Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 1/39 (2%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRV 301
           I  +VIG V+ ++ YG  +DI       L  S +    +
Sbjct: 7   INDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSI 45

>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 = 38.1 bits (88), Expect = 1e-04
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 3/56 (5%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI---GGINGLLHVSQISHDRVADIATVLQPGDTLKV 316
            G ++I TV+ +  YG+++ +   GG+   L  S++S   V +I  VL+    + V
Sbjct: 11  EGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIV 66

>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 = 38.3 bits (89), Expect = 1e-04
 Identities = 7/54 (12%), Positives = 15/54 (27%), Gaps = 1/54 (1%)

Query: 264 IGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKV 316
           +   VIG +         + +    + +        +        LQ GD +  
Sbjct: 7   VNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYA 60

>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 = 36.5 bits (84), Expect = 4e-04
 Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHD-RVADIATVLQPGDTLKV 316
           +G VVIG ++ +   G  +DI       L VS+            VL  GD +  
Sbjct: 5   VGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIA 59

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	318
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.71
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.68
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.63
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.6
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.57
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.53
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.53
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.49
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.49
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.45
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.44
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.43
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.35
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.33
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	99.27
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.26
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.26
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.21
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.15
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.15
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	99.09
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.9
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.88
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.81
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.81
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	98.78
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	98.76
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.76
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.73
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.71
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.63
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.53
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	98.43
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.4
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.12
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	98.08
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.79
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.77
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	97.63
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.51
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	91.26
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	90.66
d1mjca_	69	Major cold shock protein {Escherichia coli [TaxId:	89.64
d1jjga_	102	Viral structural mimic of eIF2alpha {Myxoma virus,	88.97
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	88.08
d3d31a1	119	Sulfate/molybdate ABC transporter, ATP-binding pro	87.9
d1luza_	85	Viral structural mimic of eIF2alpha {Vaccinia viru	87.0
d1h95a_	79	Y-box protein 1 cold shock domain (YB1-CSD) {Human	84.9
d1wfqa_	89	Cold shock domain protein E1 (UNR) {Human (Homo sa	83.13
d1g6pa_	66	Major cold shock protein {Thermotoga maritima [Tax	81.28

>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=99.71  E-value=2.2e-17  Score=124.69  Aligned_cols=90  Identities=22%  Similarity=0.297  Sum_probs=82.9

Q ss_pred             CCHHHHHHHHhhhccCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeC
Q 021034           81 FTLEEFHSALEKYDFNSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENE  160 (318)
Q Consensus        81 ~s~~~~~~~~~~~~~~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~  160 (318)
                      |...+|++.++.+. ++++|+++.|+|.++.++|+||+++++.+||||.+|+++.+..++++. |++||.+.|+|+++|+
T Consensus         1 fk~a~~~~~ie~~~-~~k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~-~~vGq~v~~~V~~id~   78 (94)
T d3bzka4           1 FKTAEFQEGVESLK-DLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEV-VKAGDIVKVKVMEVDI   78 (94)
T ss_dssp             CCHHHHHHTCCCGG-GCCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSCHHHH-CCTTCEEEEEEEEEET
T ss_pred             CchhHHHhhhhHHh-cCCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccChhhh-hccCcEEEEEEEEEEC
Confidence            44567777777665 899999999999999999999999989999999999999999999998 9999999999999999


Q ss_pred             CCCeEEEEeeeh
Q 021034          161 ADDSLVLSLRMI  172 (318)
Q Consensus       161 ~~~~i~lS~k~~  172 (318)
                      +++++.||+|..
T Consensus        79 ~~~~i~LS~K~~   90 (94)
T d3bzka4          79 PRNRVGLSMRMS   90 (94)
T ss_dssp             TTTEEEEESCTT
T ss_pred             CCCEEEEEEecc
Confidence            999999999975

>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=99.68  E-value=2.7e-17  Score=119.30  Aligned_cols=75  Identities=16%  Similarity=0.241  Sum_probs=71.0

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      ++++|++++|+|.++.++|+||+++++.+||+|.+|+++.+..+|++. |++||+++|+|+++|+ ++++.||+|++
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            688999999999999999999999988999999999999999999998 9999999999999985 57899999974

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=7.3e-16  Score=114.31  Aligned_cols=74  Identities=22%  Similarity=0.227  Sum_probs=58.5

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEeC--CCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034           97 SELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i~--~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~  171 (318)
                      .++|+++.|+|.++.++|+||++.  ++.+||+|.+|+++.+..++.+. |++||.++|+|+++|++++++.||+|+
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 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKL-IRIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC-------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEE-eecccEEEEEEEEEECCCCEEEEEeeC
Confidence            368999999999999999999995  47999999999999999999998 999999999999999999999999985

>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=99.60  E-value=1e-15  Score=112.94  Aligned_cols=75  Identities=19%  Similarity=0.217  Sum_probs=65.8

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC--CCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDIT--AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~--~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~  171 (318)
                      ..++|++++|+|.++.++|+||++.  ++.+||+|.+|+++.+..++.+. |++||+++|+|+++|++++++.||+|+
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            4578999999999999999999996  47999999999999999999998 999999999999999999999999985

>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=99.57  E-value=5.3e-16  Score=112.36  Aligned_cols=59  Identities=39%  Similarity=0.714  Sum_probs=56.8

Q ss_pred             hhcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          260 AQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       260 ~~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      +++++|++++|+|+++++||+||+|+ ++.||+|.++++|.++.+|++.|++||+|+|+|
T Consensus         1 ad~kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~V   60 (76)
T d1sroa_           1 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKV   60 (76)
T ss_dssp             CCCCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEE
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEE
Confidence            36899999999999999999999998 999999999999999999999999999999986

>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=99.53  E-value=2.2e-14  Score=105.39  Aligned_cols=76  Identities=21%  Similarity=0.193  Sum_probs=68.6

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccc-ccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHK-IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~-~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      ..++|+++.|+|.++.++|+||+++++..||||.+|+++.. ..++.+. |++||.+.|+|+++|+ ++++.||+|...
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            46899999999999999999999999999999999999754 6778887 9999999999999985 678999999854

>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=99.53  E-value=2e-15  Score=118.72  Aligned_cols=87  Identities=22%  Similarity=0.195  Sum_probs=76.6

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC-CCeEEEEeCccccccc-ccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDIT-AKSSAYLPTQEACIHK-IKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~-~~~~g~lp~sEls~~~-~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      ++++|+++.|+|.++.++|+||+|+ .+++||||.+|+++.+ .++|.+. |++||.++|+|+++|+.++++.||+|+..
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 6799999999999864 6678776 99999999999999999999999999987


Q ss_pred             hhHHHHHHhh
Q 021034          174 YELAWERCRQ  183 (318)
Q Consensus       174 ~~~~~~~~~~  183 (318)
                      ....|....+
T Consensus        97 ~~~~~~~~~~  106 (119)
T d1wi5a_          97 VSTAIATEQQ  106 (119)
T ss_dssp             SCCCCCCSSC
T ss_pred             hhhhhhhhhh
Confidence            7555544433

>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=99.49  E-value=5.5e-14  Score=103.96  Aligned_cols=68  Identities=22%  Similarity=0.375  Sum_probs=56.3

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEEC---CEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEVE---GLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRK  253 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i~---gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~  253 (318)
                      +.|++++|+|+++.++|+||++.   |++||+|.+++++.  .++.+.  +||.|+|+|+++|++++++.||+|+
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 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             CCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEEECCCCEEEEEeeC
Confidence            47999999999999999999994   79999999999987  345554  7999999999999999999999985

>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=99.49  E-value=1.9e-14  Score=108.27  Aligned_cols=77  Identities=27%  Similarity=0.376  Sum_probs=67.4

Q ss_pred             HHHHHhhhcCCCcEEEEEEEEEEcCeEEEEEC-CEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeeh
Q 021034          177 AWERCRQLQSEDVVVKGKVVGANKGGVVAEVE-GLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSN  251 (318)
Q Consensus       177 ~~~~~~~~~~~G~iv~g~V~~v~~~G~~V~i~-gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~  251 (318)
                      .++.+++. ++|++++|+|+++.++|+||+++ |+.||+|.+++++.  .++.+.  +||.|+|+|+++|++++++.||+
T Consensus         9 ~ie~~~~~-k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~~i~LS~   87 (94)
T d3bzka4           9 GVESLKDL-KPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSM   87 (94)
T ss_dssp             TCCCGGGC-CTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEES
T ss_pred             hhhHHhcC-CCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEE
Confidence            34445554 69999999999999999999997 99999999999987  356554  79999999999999999999999


Q ss_pred             hhh
Q 021034          252 RKA  254 (318)
Q Consensus       252 K~~  254 (318)
                      |++
T Consensus        88 K~~   90 (94)
T d3bzka4          88 RMS   90 (94)
T ss_dssp             CTT
T ss_pred             ecc
Confidence            975

>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=9.3e-14  Score=102.23  Aligned_cols=68  Identities=25%  Similarity=0.431  Sum_probs=59.7

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEEC---CEEEEEeCcccCCc--CCcchh--cCCeEeEEEEEEecccCeEeeehhh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEVE---GLRGFVPFSQISSK--STAEEL--LGKDLPLKFVEVDEEQSRLVLSNRK  253 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i~---gl~gfip~s~ls~~--~~~~~~--vGq~v~~kVl~vd~~~~~i~lS~K~  253 (318)
                      ++|++++|+|++++++|+||+++   |++||+|.+++++.  .++.++  +||+++|+|+++|++++++.||+|+
T Consensus        10 ~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2          10 SEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             CTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEEcC
Confidence            47999999999999999999994   89999999999987  445544  7999999999999999999999985

>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=99.44  E-value=9.7e-14  Score=103.05  Aligned_cols=76  Identities=16%  Similarity=0.117  Sum_probs=67.6

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccccc----CccccCcCCCCEEEEEEEEEeCCCCeEEEEeee
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK----HVEEAGIVPGLKEEFVIIGENEADDSLVLSLRM  171 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~----~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~  171 (318)
                      ..++|+++.|+|.++.++|+||+++++.+||||.+|+++.+.+    ++.++ +++||.+.|+|+++|+ ++++.||+|.
T Consensus         4 ~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~-~~vGd~V~~kV~~vd~-~~~i~Ls~k~   81 (88)
T d2z0sa1           4 VPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSL-LKVGDYIKAKVVAFDK-TRSPLLTVQG   81 (88)
T ss_dssp             CCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTS-SCTTCEEEEEEEEECT-TSCEEEECCS
T ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcccccccccchhhh-cccCcEEEEEEEEECC-CCCEEEEEec
Confidence            5789999999999999999999999899999999999987654    45566 8999999999999985 5789999997


Q ss_pred             hh
Q 021034          172 IQ  173 (318)
Q Consensus       172 ~~  173 (318)
                      ..
T Consensus        82 ~~   83 (88)
T d2z0sa1          82 EG   83 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            63

>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=99.43  E-value=2e-13  Score=101.13  Aligned_cols=76  Identities=24%  Similarity=0.161  Sum_probs=67.8

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccccc---CccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK---HVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~---~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      ..++|+++.|+|+++.++|+||+++++.+|+||.+|+++.+..   ++.+. |++||.+.|+|+++|+ ++++.||+|..
T Consensus         4 ~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~-~~~Gd~v~~kV~~vd~-~~~i~LS~k~~   81 (87)
T d2je6i1           4 YPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRY-LDVGDYVIARIENFDR-SIDPVLSVKGK   81 (87)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSS-CCTTCEEEEEEEEEET-TEEEEEECCST
T ss_pred             cCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceeccccccchh-hcccceEEEEEEEECC-CCCEEEEEecC
Confidence            5789999999999999999999999899999999999987654   45566 9999999999999995 57999999875


Q ss_pred             h
Q 021034          173 Q  173 (318)
Q Consensus       173 ~  173 (318)
                      .
T Consensus        82 ~   82 (87)
T d2je6i1          82 D   82 (87)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.35  E-value=2.1e-12  Score=98.94  Aligned_cols=83  Identities=13%  Similarity=0.116  Sum_probs=68.4

Q ss_pred             CCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc-----------cCccccCcCCCCEEEEEEEEEeCCCCe--
Q 021034           98 ELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI-----------KHVEEAGIVPGLKEEFVIIGENEADDS--  164 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~-----------~~~~~~~~~~G~~v~v~Vl~vd~~~~~--  164 (318)
                      ++|++++|+|+++.++|+||+++ +++||+|.+++++.+.           .++.+. |++||.+.|+|+++|.+.++  
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 5999999999998765           355566 99999999999999988765  


Q ss_pred             ---EEEEeeehhhhHHHHHHhh
Q 021034          165 ---LVLSLRMIQYELAWERCRQ  183 (318)
Q Consensus       165 ---i~lS~k~~~~~~~~~~~~~  183 (318)
                         +.||+|+... .+|+.+.+
T Consensus        80 ~~~i~ls~K~~~~-~~~e~~~~  100 (106)
T d1go3e1          80 GSKIALTMRQPYL-GKLEWIEE  100 (106)
T ss_dssp             -CEEEEECCSTTC-EEHHHHHH
T ss_pred             CceeecccccCCC-Ccchhhhh
Confidence               7789888765 35555443

>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=99.33  E-value=8.6e-13  Score=96.69  Aligned_cols=56  Identities=27%  Similarity=0.371  Sum_probs=52.9

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCccc-ccCcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR-VADIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~-~~~~~~~~~~Gq~V~v~V  318 (318)
                      ++|++|.|+|++++++|+||+|+ ++.||+|.++++|.+ ..++.+.|++||.|+|+|
T Consensus         4 k~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV   61 (83)
T d2ba0a1           4 SVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKV   61 (83)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEE
Confidence            67999999999999999999999 899999999999975 678999999999999986

>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=99.27  E-value=1.4e-12  Score=102.08  Aligned_cols=72  Identities=18%  Similarity=0.305  Sum_probs=63.8

Q ss_pred             cCCCcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCc---CCcc-hh-cCCeEeEEEEEEecccCeEeeehhhhhh
Q 021034          185 QSEDVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSK---STAE-EL-LGKDLPLKFVEVDEEQSRLVLSNRKAMA  256 (318)
Q Consensus       185 ~~~G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~---~~~~-~~-vGq~v~~kVl~vd~~~~~i~lS~K~~l~  256 (318)
                      +++|++++|+|+++.++|+||+++  +++||||.+++++.   .++. .+ +||.|+|+|+++|++++++.||+|++..
T Consensus        19 l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~k~~~~   97 (119)
T d1wi5a_          19 LKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV   97 (119)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCCCCS
T ss_pred             cCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEEecHHHh
Confidence            469999999999999999999995  89999999999964   3443 44 7999999999999999999999998754

>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=99.26  E-value=7e-12  Score=95.98  Aligned_cols=74  Identities=20%  Similarity=0.318  Sum_probs=60.8

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCcC-------------Ccch-h-cCCeEeEEEEEEecccCe----
Q 021034          186 SEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKS-------------TAEE-L-LGKDLPLKFVEVDEEQSR----  246 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~~-------------~~~~-~-vGq~v~~kVl~vd~~~~~----  246 (318)
                      +.|++++|+|++++++|+||++++++||+|.++|++..             ++.+ + +||.|+|+|+++|.++++    
T Consensus         2 ~~gei~~g~V~~v~~~G~FVel~~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~~~~~~~~   81 (106)
T d1go3e1           2 EMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKRGS   81 (106)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC-----C
T ss_pred             CCCCEEEEEEEEEeeeEEEEEeeCeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchhhccccCc
Confidence            47999999999999999999999999999999999752             2223 3 799999999999988876    


Q ss_pred             -EeeehhhhhhhhH
Q 021034          247 -LVLSNRKAMADSQ  259 (318)
Q Consensus       247 -i~lS~K~~l~~~~  259 (318)
                       +.||+|+....++
T Consensus        82 ~i~ls~K~~~~~~~   95 (106)
T d1go3e1          82 KIALTMRQPYLGKL   95 (106)
T ss_dssp             EEEEECCSTTCEEH
T ss_pred             eeecccccCCCCcc
Confidence             7889988655433

>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=99.26  E-value=6.7e-14  Score=96.85  Aligned_cols=49  Identities=39%  Similarity=0.680  Sum_probs=29.6

Q ss_pred             EEEEEEEcceEEEEEC-CeEEEEecCCcCcc----cccCcccccCCCCEEEEEC
Q 021034          270 GTVQSLKPYGAFIDIG-GINGLLHVSQISHD----RVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       270 G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~----~~~~~~~~~~~Gq~V~v~V  318 (318)
                      |+|++|++||+||+|+ |++||||+|+|+|.    ++.+|++.|++||+|+|+|
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV   54 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEI   54 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC-------------------CCSSCBCCCCC
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEE
Confidence            7899999999999998 99999999999864    6889999999999999876

>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=99.21  E-value=4.1e-12  Score=93.81  Aligned_cols=56  Identities=27%  Similarity=0.431  Sum_probs=51.7

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCccccc---CcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVA---DIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~---~~~~~~~~Gq~V~v~V  318 (318)
                      ++|++|.|+|.+++++|+||+++ ++.||+|.++++|.+..   ++.+.|++||.|.|+|
T Consensus         6 k~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV   65 (87)
T d2je6i1           6 KINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARI   65 (87)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceeccccccchhhcccceEEEEE
Confidence            57999999999999999999998 99999999999998654   5778999999999986

>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=99.15  E-value=8e-12  Score=92.44  Aligned_cols=56  Identities=30%  Similarity=0.441  Sum_probs=51.8

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCccccc----CcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVA----DIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~----~~~~~~~~Gq~V~v~V  318 (318)
                      ++|++|.|+|.+++++|+||+|+ ++.||+|.++++|.+..    ++.+.|++||.|+|+|
T Consensus         6 k~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV   66 (88)
T d2z0sa1           6 QAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKV   66 (88)
T ss_dssp             CTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEE
Confidence            57999999999999999999999 89999999999998764    6778899999999986

>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=99.15  E-value=1.6e-11  Score=92.03  Aligned_cols=76  Identities=13%  Similarity=0.096  Sum_probs=64.3

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccc----------cccCccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIH----------KIKHVEEAGIVPGLKEEFVIIGENEADDSL  165 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~----------~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i  165 (318)
                      ..++|++|.|+|+++.++|++|+++...+|+||++++++.          ...++.+. |++||.|.|+|++++. ++++
T Consensus         5 ~P~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~-~~~Gd~V~~kV~~v~~-dg~i   82 (95)
T d2nn6h1           5 IGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGF-LQEGDLISAEVQAVFS-DGAV   82 (95)
T ss_dssp             CCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHH-SCSSCEECCEEEEEET-TTEE
T ss_pred             cCCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchhhhhhhhh-cccccEEEEEEEEECC-CCCE
Confidence            5789999999999999999999999889999999999653          22344556 9999999999999986 6899


Q ss_pred             EEEeeehh
Q 021034          166 VLSLRMIQ  173 (318)
Q Consensus       166 ~lS~k~~~  173 (318)
                      .||+|.+.
T Consensus        83 ~Ls~r~~~   90 (95)
T d2nn6h1          83 SLHTRSLK   90 (95)
T ss_dssp             EEECCSST
T ss_pred             EEEecccc
Confidence            99998753

>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=99.09  E-value=1.1e-12  Score=90.64  Aligned_cols=57  Identities=21%  Similarity=0.285  Sum_probs=35.7

Q ss_pred             EEEEEEECCeEEEEeCCCeEEEEeCccccc----ccccCccccCcCCCCEEEEEEEEEeCCC
Q 021034          105 GTVFCTDNRGALVDITAKSSAYLPTQEACI----HKIKHVEEAGIVPGLKEEFVIIGENEAD  162 (318)
Q Consensus       105 G~V~~i~~~G~~V~i~~~~~g~lp~sEls~----~~~~~~~~~~~~~G~~v~v~Vl~vd~~~  162 (318)
                      |+|.++.++||||+++++.+||||+|||++    .++.+|++. +++||+++|+|+++|+++
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            789999999999999989999999999985    367889988 999999999999999654

>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=98.90  E-value=1.8e-09  Score=79.88  Aligned_cols=55  Identities=22%  Similarity=0.283  Sum_probs=49.5

Q ss_pred             cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccc----------cCcccccCCCCEEEEEC
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV----------ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~----------~~~~~~~~~Gq~V~v~V  318 (318)
                      .|+++.|+|++++++|+||+++.++||+|+++|++++.          .+....|+.||.|++||
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV   67 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKI   67 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEEcCeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEE
Confidence            59999999999999999999999999999999998754          34566799999999986

>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=98.88  E-value=2.6e-09  Score=78.37  Aligned_cols=75  Identities=16%  Similarity=-0.044  Sum_probs=66.1

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      ..++|++|-|+|+++..++++||++....|+||.+++. ...++..+. +++||.+.|+|.+++ .++.+.|||..+.
T Consensus         3 ~P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~-g~~k~~r~~-l~~GD~V~arV~~v~-~~~~~~Lscvd~~   77 (88)
T d2nn6g1           3 VPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFE-GATKRNRPN-VQVGDLIYGQFVVAN-KDMEPEMVCIDSC   77 (88)
T ss_dssp             CCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSS-CCSSCSSSS-SCTTCEEEEEEEECC-TTSCCEEECSBTT
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcC-ccccccCcc-cCCCCEEEEEEEEeC-CCCCEEEEEEccc
Confidence            56899999999999999999999999999999999995 455666666 999999999999997 4678999998764

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=98.81  E-value=1.3e-08  Score=74.48  Aligned_cols=68  Identities=12%  Similarity=0.078  Sum_probs=57.3

Q ss_pred             CCCEEEEEEEEEECCeEEEEe-CCCeEEEEeCccccccccc------------CccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034           99 LGTKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACIHKIK------------HVEEAGIVPGLKEEFVIIGENEADDSL  165 (318)
Q Consensus        99 ~G~iv~G~V~~i~~~G~~V~i-~~~~~g~lp~sEls~~~~~------------~~~~~~~~~G~~v~v~Vl~vd~~~~~i  165 (318)
                      .|+..+|+|+++.++|+||++ ..+.+||+|.++|.+++..            +.+.. |++||+++|+|+++|++++++
T Consensus         3 ~~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~-~~~Gd~V~V~v~~vd~~~r~I   81 (87)
T d2ix0a3           3 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETV-YKVTDVIDVTIAEVRMETRSI   81 (87)
T ss_dssp             SCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEE-EETTCEEEEEEEEEETTTTEE
T ss_pred             CCCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCCCceEEEeccceEEEEEEcccEE-EECCCEEEEEEEEEecccCeE
Confidence            478899999999999999999 4579999999999875432            12234 899999999999999999998


Q ss_pred             EE
Q 021034          166 VL  167 (318)
Q Consensus       166 ~l  167 (318)
                      .+
T Consensus        82 ~~   83 (87)
T d2ix0a3          82 IA   83 (87)
T ss_dssp             EE
T ss_pred             EE
Confidence            64

>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=98.81  E-value=1.7e-08  Score=70.97  Aligned_cols=66  Identities=23%  Similarity=0.162  Sum_probs=56.4

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC--eEEEEe
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD--SLVLSL  169 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~--~i~lS~  169 (318)
                      .-+.|++++|+|.++++++++|+++ +.+|+||.+|..      |.+. |++|+.+.|.|.+++...+  ++.||+
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            3468999999999999999999998 599999999864      5566 9999999999999876543  577775

>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=98.78  E-value=8.1e-10  Score=82.51  Aligned_cols=56  Identities=16%  Similarity=0.330  Sum_probs=48.1

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCccc----------ccCcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDR----------VADIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~----------~~~~~~~~~~Gq~V~v~V  318 (318)
                      ++|++|.|+|++++++|+||+++ +..|++|.|+++|.+          ..++.+.|++||.|.|+|
T Consensus         7 ~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV   73 (95)
T d2nn6h1           7 EVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEV   73 (95)
T ss_dssp             CSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEE
T ss_pred             CCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEE
Confidence            47999999999999999999999 899999999998742          345677899999999986

>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=98.76  E-value=1.7e-08  Score=73.77  Aligned_cols=62  Identities=18%  Similarity=0.342  Sum_probs=53.1

Q ss_pred             CcEEEEEEEEEEcCeEEEEEC--CEEEEEeCcccCCcC---C-----------cc-hh-cCCeEeEEEEEEecccCeEee
Q 021034          188 DVVVKGKVVGANKGGVVAEVE--GLRGFVPFSQISSKS---T-----------AE-EL-LGKDLPLKFVEVDEEQSRLVL  249 (318)
Q Consensus       188 G~iv~g~V~~v~~~G~~V~i~--gl~gfip~s~ls~~~---~-----------~~-~~-vGq~v~~kVl~vd~~~~~i~l  249 (318)
                      ++.++|+|++++++|+||++.  +++||+|.++|.+..   +           .+ .| +||+|+++|+++|+++++|.+
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            578999999999999999994  799999999998641   1           12 24 799999999999999999875

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.76  E-value=2.3e-08  Score=73.76  Aligned_cols=67  Identities=18%  Similarity=0.124  Sum_probs=56.6

Q ss_pred             CCCEEEEEEEEEECCeEEEEeCCCeEEEEeCccccccccc----------CccccCcCCCCEEEEEEEEEeCCCCeEEE
Q 021034           99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIK----------HVEEAGIVPGLKEEFVIIGENEADDSLVL  167 (318)
Q Consensus        99 ~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~----------~~~~~~~~~G~~v~v~Vl~vd~~~~~i~l  167 (318)
                      .|+++.|+|++++++|+||+++ ..+||+|.++|.+++.-          +..+. ++.|+.|+++|++++.+.+++.+
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg-~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~-~~~Gd~VrvkV~~v~~~~~~i~~   79 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVG-PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDV-ITIKSRIRVKIEGCISQVSSIHA   79 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTCEECC-----CEECSSCE-ECTTCEEEEEEEEEEEETTEEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEEc-CeEEEEEhhhcCcceEEccccceeEecccCeE-EeCCCEEEEEEEEEecccCccEE
Confidence            6999999999999999999997 58999999999875442          22333 88999999999999998887644

>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=98.73  E-value=2e-08  Score=73.90  Aligned_cols=76  Identities=12%  Similarity=-0.060  Sum_probs=67.1

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeehh
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMIQ  173 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~~  173 (318)
                      ..++|++|-|+|.++..++++|+|++...|+||.++..+...++.... +.+||.|.|+|.+++. ++.+.|||+.+.
T Consensus         4 ~P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g~~k~~r~~-l~~GDlV~arV~~v~~-~~~~~Lsc~~~~   79 (90)
T d2ja9a1           4 IPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPT-LQVGDLVYARVCTAEK-ELEAEIECFDST   79 (90)
T ss_dssp             CCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSSSCCC-CCTTCEEEEEEEECCT-TSCCEEESSCTT
T ss_pred             cCCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCccccccCCc-cCCCCEEEEEEEEECC-CCCEEEEEeccc
Confidence            468999999999999999999999988999999888777777777776 9999999999999984 678999998764

>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=98.71  E-value=1.5e-08  Score=75.32  Aligned_cols=55  Identities=24%  Similarity=0.393  Sum_probs=49.0

Q ss_pred             cCeEEEEEEEEEEcceEEEEECCeEEEEecCCcCcccc------------cCcccccCCCCEEEEEC
Q 021034          264 IGSVVIGTVQSLKPYGAFIDIGGINGLLHVSQISHDRV------------ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       264 ~G~~v~G~V~~i~~~G~fV~i~gv~Glv~~s~ls~~~~------------~~~~~~~~~Gq~V~v~V  318 (318)
                      .|+++.|+|++++++|+||+++.++||+|+++++++..            .+....|+.||.|++||
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV   70 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKI   70 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEecCceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEE
Confidence            49999999999999999999999999999999998852            34456799999999986

>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=98.63  E-value=1e-07  Score=70.62  Aligned_cols=66  Identities=14%  Similarity=0.170  Sum_probs=55.2

Q ss_pred             CCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccc------------cCccccCcCCCCEEEEEEEEEeCCCCeEE
Q 021034           99 LGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKI------------KHVEEAGIVPGLKEEFVIIGENEADDSLV  166 (318)
Q Consensus        99 ~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~------------~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~  166 (318)
                      .|++++|+|.+++++|+||+++ ..+||+|.++|.+++.            ++.... ++.|+.|+++|++++.+.+++.
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg-~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~-~~~Gd~VrvkV~~v~~~~~~I~   81 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIV-IQQDDEIRLKIVGTRVDKNDIF   81 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSE-EETTCEEEEEEEEEEEETTEEE
T ss_pred             CCCEEEEEEEEEEeeEEEEEec-CceEEEEhhhcCcceeecccccceEEEcccceEE-EeCCCEEEEEEEEEecCcCcce
Confidence            6999999999999999999997 5899999999987642            111222 7899999999999988888764

>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=98.53  E-value=3.6e-07  Score=63.97  Aligned_cols=63  Identities=11%  Similarity=0.158  Sum_probs=53.9

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEECCEEEEEeCcccCCcCCcchh-cCCeEeEEEEEEecccC--eEeeeh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEEL-LGKDLPLKFVEVDEEQS--RLVLSN  251 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~vd~~~~--~i~lS~  251 (318)
                      ..|++++|+|..+.+++++|++++..|+||.++...+..   | .|+.|+|.|.+++...+  .|.||+
T Consensus         7 ~~geiv~G~V~r~~~~~~~Vdlg~~eaiLp~~eqip~E~---~~~Gdrik~~i~~V~~~~kgpqI~lSR   72 (72)
T d1hh2p1           7 LKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWIPGEE---IKAGDLVKVYIIDVVKTTKGPKILVSR   72 (72)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTEEEEEEGGGSCTTCC---CCTTCEEEEEEEEEEEETTEEEEEEES
T ss_pred             ccCcEEEEEEEEEcCCCEEEEECCcEEECCHHHcCCCCC---CCCCCEEEEEEEEEEEcCCCCeEEEeC
Confidence            489999999999999999999999999999999775432   3 79999999999986654  477774

>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=98.43  E-value=2.8e-07  Score=65.21  Aligned_cols=65  Identities=20%  Similarity=0.225  Sum_probs=53.6

Q ss_pred             CCCCEEEEEEEEEECC----eEEEEeC---CCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEEeCCCC--eEEEE
Q 021034           98 ELGTKVKGTVFCTDNR----GALVDIT---AKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGENEADD--SLVLS  168 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~----G~~V~i~---~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~--~i~lS  168 (318)
                      +.|+++.|+|.++..+    .++|++|   ++.+|+||.+|.      -|.|. |++||.+.|.|.+++...+  +++||
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------VPGES-YEHGNRLRCYVVGVTRGAREPLITLS   75 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGS------CTTCC-CCTTCEEEEEEEEEECCSSSCEEEEE
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHc------CCCcc-cCCCCEEEEEEEEEEecCCCCEEEEe
Confidence            5799999999998754    3899997   469999999886      35666 9999999999999986543  68887


Q ss_pred             e
Q 021034          169 L  169 (318)
Q Consensus       169 ~  169 (318)
                      +
T Consensus        76 R   76 (76)
T d2asba1          76 R   76 (76)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=98.40  E-value=2.2e-07  Score=67.86  Aligned_cols=55  Identities=20%  Similarity=0.107  Sum_probs=50.6

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ++|++|-|+|.+++.+|+||+++ ...|++|.+++++ +..+....|++||.|.|+|
T Consensus         5 ~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~g-~~k~~r~~l~~GD~V~arV   60 (88)
T d2nn6g1           5 VKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEG-ATKRNRPNVQVGDLIYGQF   60 (88)
T ss_dssp             CSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSC-CSSCSSSSSCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcCc-cccccCcccCCCCEEEEEE
Confidence            57999999999999999999999 8999999999964 6778888899999999986

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=98.12  E-value=1.9e-06  Score=62.95  Aligned_cols=56  Identities=13%  Similarity=0.054  Sum_probs=52.4

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ++|++|-|+|.+++..|.||+|+ ...|++|.++..+....+....|.+||.|.|+|
T Consensus         6 ~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV   62 (90)
T d2ja9a1           6 SVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARV   62 (90)
T ss_dssp             CTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEE
T ss_pred             CCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCccccccCCccCCCCEEEEEE
Confidence            57999999999999999999999 789999999988888888899999999999987

>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=98.08  E-value=7.8e-06  Score=63.29  Aligned_cols=77  Identities=16%  Similarity=0.126  Sum_probs=62.8

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeC--------CCeEEEEeCcccc--cccccCccccCcCCCCEEEEEEEEEeCCCCeE
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDIT--------AKSSAYLPTQEAC--IHKIKHVEEAGIVPGLKEEFVIIGENEADDSL  165 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~--------~~~~g~lp~sEls--~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i  165 (318)
                      -.++|++|.|+|+++.+..++|++.        ....|+++.++..  +.+..++.+. |++||.|.++|++..+.+..+
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            3578999999999999999999993        2467899998884  3344456676 999999999999998766679


Q ss_pred             EEEeeehh
Q 021034          166 VLSLRMIQ  173 (318)
Q Consensus       166 ~lS~k~~~  173 (318)
                      .||.+...
T Consensus        83 ~Lst~~~~   90 (125)
T d2nn6i1          83 LLTTAENE   90 (125)
T ss_dssp             EEECCSSS
T ss_pred             EEEecCCC
Confidence            99987753

>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=97.79  E-value=3.1e-05  Score=54.38  Aligned_cols=63  Identities=21%  Similarity=0.288  Sum_probs=50.6

Q ss_pred             CCCcEEEEEEEEEEcC----eEEEEEC----CEEEEEeCcccCCcCCcchh-cCCeEeEEEEEEecccC--eEeeeh
Q 021034          186 SEDVVVKGKVVGANKG----GVVAEVE----GLRGFVPFSQISSKSTAEEL-LGKDLPLKFVEVDEEQS--RLVLSN  251 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~----G~~V~i~----gl~gfip~s~ls~~~~~~~~-vGq~v~~kVl~vd~~~~--~i~lS~  251 (318)
                      +.|++++|+|..+..+    -++|+++    +.+|+||.++...+..   | .|+.++|.|.+++...+  .|.||+
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqip~E~---y~~Gdrik~~i~~V~~~~kGp~IilSR   76 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPGES---YEHGNRLRCYVVGVTRGAREPLITLSR   76 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSCTTCC---CCTTCEEEEEEEEEECCSSSCEEEEES
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcCCCcc---cCCCCEEEEEEEEEEecCCCCEEEEeC
Confidence            4799999999998654    3899995    5999999999776533   3 79999999999986544  577774

>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=97.77  E-value=4.6e-05  Score=54.93  Aligned_cols=70  Identities=19%  Similarity=0.276  Sum_probs=53.9

Q ss_pred             CEEEEEEEEEEC--CeEEEEeCCCeEEEEeCccccccccc---------CccccCcCCCCEEEEEEEEEeCCCCeEEEEe
Q 021034          101 TKVKGTVFCTDN--RGALVDITAKSSAYLPTQEACIHKIK---------HVEEAGIVPGLKEEFVIIGENEADDSLVLSL  169 (318)
Q Consensus       101 ~iv~G~V~~i~~--~G~~V~i~~~~~g~lp~sEls~~~~~---------~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~  169 (318)
                      .++.|+|.++.+  ++||||+|....||||.+|+...+..         +.++. ++.||.+-|-|.+-...+.-..||.
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  69999999999999999998754432         22334 7899999999987554455566665


Q ss_pred             ee
Q 021034          170 RM  171 (318)
Q Consensus       170 k~  171 (318)
                      .-
T Consensus        81 ~I   82 (87)
T d1smxa_          81 FI   82 (87)
T ss_dssp             CC
T ss_pred             EE
Confidence            43

>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=97.63  E-value=2.6e-05  Score=60.20  Aligned_cols=56  Identities=20%  Similarity=0.326  Sum_probs=48.4

Q ss_pred             ccCeEEEEEEEEEEcceEEEEEC---------CeEEEEecCCcCc--ccccCcccccCCCCEEEEEC
Q 021034          263 GIGSVVIGTVQSLKPYGAFIDIG---------GINGLLHVSQISH--DRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       263 ~~G~~v~G~V~~i~~~G~fV~i~---------gv~Glv~~s~ls~--~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ++|++|.|.|+++++..++|++.         .+.|++|.+++..  ....++.+.|++||.|.|+|
T Consensus         6 ~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~V   72 (125)
T d2nn6i1           6 DVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKV   72 (125)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEE
T ss_pred             CCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEE
Confidence            47999999999999999999993         3789999999854  34557889999999999986

>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=97.51  E-value=7.8e-05  Score=53.64  Aligned_cols=53  Identities=26%  Similarity=0.555  Sum_probs=44.9

Q ss_pred             eEEEEEEEEEEc--ceEEEEEC-CeEEEEecCCcCcccc---------cCcccccCCCCEEEEEC
Q 021034          266 SVVIGTVQSLKP--YGAFIDIG-GINGLLHVSQISHDRV---------ADIATVLQPGDTLKVCL  318 (318)
Q Consensus       266 ~~v~G~V~~i~~--~G~fV~i~-gv~Glv~~s~ls~~~~---------~~~~~~~~~Gq~V~v~V  318 (318)
                      .++.|+|.+|.|  .++||+++ +-.||+|.+++.+...         .+..+.+++||.|-|.|
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV   66 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQI   66 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEE
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccceeeeccccccccccchhhhccCCCeEEEEE
Confidence            478999999998  78999999 9999999999887543         24567799999998875

>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=91.26  E-value=0.41  Score=31.67  Aligned_cols=49  Identities=22%  Similarity=0.228  Sum_probs=39.8

Q ss_pred             CCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEEE
Q 021034           96 NSELGTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIGE  158 (318)
Q Consensus        96 ~~~~G~iv~G~V~~i~~~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~v  158 (318)
                      ..++|++=+|-+.+..+.|++||+|-.-.+++-  +            .+.+|+.+.|+|+++
T Consensus         7 ~p~vGEiReG~~~rr~~~g~~vDiGlD~la~~k--~------------~~~~~~r~tfrIvs~   55 (71)
T d1k3ra1           7 KPVTGEYRQGLTVKRVKKGTLVDIGADKLALCR--E------------KLTVNRIMSFRVVRL   55 (71)
T ss_dssp             SCCTTCEEEEEEEEECSSSEEEESSSSCEEECS--S------------CCCSSCEEEEEEEEC
T ss_pred             CCcccceeeEEEEEecCCcEEEEecCCceeeee--c------------ccccCcEEEEEEEEc
Confidence            468999999999999999999999854444422  1            177899999999886

>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=90.66  E-value=0.83  Score=31.01  Aligned_cols=73  Identities=11%  Similarity=0.207  Sum_probs=51.2

Q ss_pred             CCCCCEEEEEEEEEECCeEEEEeC-C-CeEEEEeCc-ccccccccCccccCcCCCCEEEEEEEEEeCCCCeEEEEeeeh
Q 021034           97 SELGTKVKGTVFCTDNRGALVDIT-A-KSSAYLPTQ-EACIHKIKHVEEAGIVPGLKEEFVIIGENEADDSLVLSLRMI  172 (318)
Q Consensus        97 ~~~G~iv~G~V~~i~~~G~~V~i~-~-~~~g~lp~s-Els~~~~~~~~~~~~~~G~~v~v~Vl~vd~~~~~i~lS~k~~  172 (318)
                      ..+|++.+|.|. +.++-.+|.+. . +.+|+|-.+ .+-.+...+.++.  -+|.+++++|+.+|.-+|.+-+..|+.
T Consensus         6 PnigdVtkGiVy-~kd~~fyV~L~dY~g~ea~l~dy~~~~~d~~~klk~k--LVGKtIkvqVIR~d~lKGYIDVr~~~~   81 (85)
T d1luza_           6 PNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDK--LVGKTVKVKVIRVDYTKGYIDVNYKRM   81 (85)
T ss_dssp             CCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHH--HTTCEEEEEEEEEETTTTEEEEEEEEE
T ss_pred             CCCCceeeeEEE-EeCCEEEEEecCCCCceEEeeehhhhhhHHHHHHHHH--hcCceEEEEEEEEcceeeEEEehhhhh
Confidence            358999999765 55666778883 3 688887532 1212222333332  389999999999999999999988764

>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=89.64  E-value=1.3  Score=29.17  Aligned_cols=50  Identities=18%  Similarity=0.162  Sum_probs=36.0

Q ss_pred             EEEEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEE
Q 021034          102 KVKGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVII  156 (318)
Q Consensus       102 iv~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl  156 (318)
                      .++|+|.-.++   +|.+..-.++-+.|+|.+.+.....+.     +.+||.|++.+.
T Consensus         3 r~~G~Vk~f~~~kGfGFI~~d~g~~diFvH~s~l~~~~~~~-----L~~G~~V~f~~~   55 (69)
T d1mjca_           3 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKS-----LDEGQKVSFTIE   55 (69)
T ss_dssp             CEEEEEEEEETTTTEEEEEETTSCCCEEEEGGGBCCTTTCC-----CCTTCEEEEEEE
T ss_pred             CEEEEEEEEeCCCCEEEEEEcCCCccEEEEhHHhcccCCCc-----CCCCCEEEEEEE
Confidence            47899998864   455554455578999999986543221     678999999874

>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=88.97  E-value=0.6  Score=32.55  Aligned_cols=62  Identities=11%  Similarity=0.116  Sum_probs=42.4

Q ss_pred             cCCCCCCEEEEEEEEEECCeEEEEe-CC-CeEEEEeC-cccccccccCccccCcCCCCEEEEEEEEEe
Q 021034           95 FNSELGTKVKGTVFCTDNRGALVDI-TA-KSSAYLPT-QEACIHKIKHVEEAGIVPGLKEEFVIIGEN  159 (318)
Q Consensus        95 ~~~~~G~iv~G~V~~i~~~G~~V~i-~~-~~~g~lp~-sEls~~~~~~~~~~~~~~G~~v~v~Vl~vd  159 (318)
                      .++.+|++.+|.|. +.++-++|.+ ++ +.+|+|-. -.+-.+...+..+.  -+|.++.++|+.+|
T Consensus        28 ~~~~~G~V~kGiVy-~rd~~fyV~L~dY~g~eail~dY~n~~~dr~~klkkk--LVGKTIkVqVIRvD   92 (102)
T d1jjga_          28 MDLSPGSVHEGIVY-FKDGIFKVRLLGYEGHECILLDYLNYRQDTLDRLKER--LVGRVIKTRVVRAD   92 (102)
T ss_dssp             CCCCSSCEEEEEEE-EETTEEEEECTTTSSCEEEECTTCCSSCCCCCHHHHH--HTTCEEEEEEEEEC
T ss_pred             cccCCCcEeeeEEE-EeCCEEEEEecCCCCceeeeeehhhhhHHHHHHHHHH--hcCceEEEEEEEec
Confidence            47889999999664 6667778888 33 67887543 22222333333332  38999999999998

>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=88.08  E-value=0.48  Score=31.29  Aligned_cols=45  Identities=18%  Similarity=0.173  Sum_probs=35.7

Q ss_pred             hcccCeEEEEEEEEEEcceEEEEEC-CeEEEEecCCcCcccccCcccccCCCCEEEEEC
Q 021034          261 QLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLKVCL  318 (318)
Q Consensus       261 ~l~~G~~v~G~V~~i~~~G~fV~i~-gv~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~V  318 (318)
                      ..++|++-+|++.+....|+||++| +--++|.             ..|++|+.+++||
T Consensus         7 ~p~vGEiReG~~~rr~~~g~~vDiGlD~la~~k-------------~~~~~~~r~tfrI   52 (71)
T d1k3ra1           7 KPVTGEYRQGLTVKRVKKGTLVDIGADKLALCR-------------EKLTVNRIMSFRV   52 (71)
T ss_dssp             SCCTTCEEEEEEEEECSSSEEEESSSSCEEECS-------------SCCCSSCEEEEEE
T ss_pred             CCcccceeeEEEEEecCCcEEEEecCCceeeee-------------cccccCcEEEEEE
Confidence            4678999999999999999999997 6555542             2477888887775

>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=87.90  E-value=3.2  Score=29.20  Aligned_cols=101  Identities=23%  Similarity=0.291  Sum_probs=63.0

Q ss_pred             EEEEEEEEEEcCeEEEEECCEEEEEeCcccCCcCCcchhcCCeEeEEEEEEecccCeEeeehhhhhhhhHhhcccCeEEE
Q 021034          190 VVKGKVVGANKGGVVAEVEGLRGFVPFSQISSKSTAEELLGKDLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVI  269 (318)
Q Consensus       190 iv~g~V~~v~~~G~~V~i~gl~gfip~s~ls~~~~~~~~vGq~v~~kVl~vd~~~~~i~lS~K~~l~~~~~~l~~G~~v~  269 (318)
                      ++.|+|.+..++.+.+++++.....|.. +.        .|+.+.   +.+.|+  .+.++....      .-.....+.
T Consensus         4 ~l~g~v~~~~~~~~~v~~~~~~l~~~~~-~~--------~g~~v~---~~iRPE--~i~l~~~~~------~~~~~N~l~   63 (119)
T d3d31a1           4 VLKGRVISAEQGLLRIRVGEVVIDAAGD-ME--------VGDQVY---AFLRPE--NIALSKSST------QSSIRNSLQ   63 (119)
T ss_dssp             EEEEEEEEEETTEEEEEETTEEEEEESS-CC--------TTCEEE---EEECGG--GEEEESSCC------CBSCSEEEE
T ss_pred             EEEEEEEEecCCEEEEEECCEEEECCCC-CC--------CCCEEE---EEEchH--Hcccccccc------ccccceEEE
Confidence            6899999999999999999887766531 11        477665   345554  355543211      111234799


Q ss_pred             EEEEEEEcceEEEEEC---C--eEEEEecCCcCcccccCcccccCCCCEEEEE
Q 021034          270 GTVQSLKPYGAFIDIG---G--INGLLHVSQISHDRVADIATVLQPGDTLKVC  317 (318)
Q Consensus       270 G~V~~i~~~G~fV~i~---g--v~Glv~~s~ls~~~~~~~~~~~~~Gq~V~v~  317 (318)
                      |+|..+...|..+.+.   |  +...+.....       -...+++||+|.+.
T Consensus        64 g~V~~~~~~G~~~~v~l~~g~~~~~~v~~~~~-------~~~~l~~G~~V~v~  109 (119)
T d3d31a1          64 GRVTEAWVLGALVRVKVDCGVPLNVLITRRSA-------EEMELSPGVQIYAR  109 (119)
T ss_dssp             EEEEEEEECSSEEEEEEESSSEEEEEEETTHH-------HHSCCCTTCEEEEE
T ss_pred             EEEEEEEECCCeEEEEEEeCCEEEEEEecCch-------hhcCcCCCCEEEEE
Confidence            9999999988655553   3  3333322111       12248899999875

>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=87.00  E-value=1.6  Score=29.53  Aligned_cols=67  Identities=16%  Similarity=0.235  Sum_probs=47.4

Q ss_pred             CCCcEEEEEEEEEEcCeEEEEE---CCEEEEEeCcccCCc---CCcc-hhcCCeEeEEEEEEecccCeEeeehhh
Q 021034          186 SEDVVVKGKVVGANKGGVVAEV---EGLRGFVPFSQISSK---STAE-ELLGKDLPLKFVEVDEEQSRLVLSNRK  253 (318)
Q Consensus       186 ~~G~iv~g~V~~v~~~G~~V~i---~gl~gfip~s~ls~~---~~~~-~~vGq~v~~kVl~vd~~~~~i~lS~K~  253 (318)
                      ..|++.+|.|.. .++-+.|.+   +|++|++-..---.-   .+++ +++|.+|+++|+.+|.-++-|-++.|.
T Consensus         7 nigdVtkGiVy~-kd~~fyV~L~dY~g~ea~l~dy~~~~~d~~~klk~kLVGKtIkvqVIR~d~lKGYIDVr~~~   80 (85)
T d1luza_           7 NAGDVIKGRVYE-KDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKLVGKTVKVKVIRVDYTKGYIDVNYKR   80 (85)
T ss_dssp             CTTCEEEEEEEE-ETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHHTTCEEEEEEEEEETTTTEEEEEEEE
T ss_pred             CCCceeeeEEEE-eCCEEEEEecCCCCceEEeeehhhhhhHHHHHHHHHhcCceEEEEEEEEcceeeEEEehhhh
Confidence            578999998864 455667887   388998863321111   1233 458999999999999988888877653

>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=84.90  E-value=3  Score=28.05  Aligned_cols=56  Identities=20%  Similarity=0.194  Sum_probs=38.1

Q ss_pred             CEEEEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034          101 TKVKGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus       101 ~iv~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~  157 (318)
                      ..+.|+|.-.++   +|.+..-.++-+-|+|.+.+........-.. +..||.|++.+..
T Consensus         7 ~r~~G~VKwfn~~KGfGFI~~ddg~~DvFvH~s~i~~~g~~~~~~~-L~~G~~V~f~~~~   65 (79)
T d1h95a_           7 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRS-VGDGETVEFDVVE   65 (79)
T ss_dssp             EEEEEEEEEEETTTTEEEEEEGGGTEEEEEEGGGBCSCCCSCCSCS-CCSSCEEEEEEEE
T ss_pred             CcccEEEEEEcCCCCeEEEEECCCCccEEEEhhHcccCCCcceeee-cCCCCEEEEEEEe
Confidence            468899998874   3555444556889999999965421111111 6789999998854

>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=83.13  E-value=5.3  Score=27.36  Aligned_cols=54  Identities=7%  Similarity=0.060  Sum_probs=40.7

Q ss_pred             CCCCEEEEEEEEEECCeEEEEe-CCCeEEEEeCcccccccccCccccCcCCCCEEEEEEEE
Q 021034           98 ELGTKVKGTVFCTDNRGALVDI-TAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVIIG  157 (318)
Q Consensus        98 ~~G~iv~G~V~~i~~~G~~V~i-~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl~  157 (318)
                      ..+...+|+|....+..=|+.- .+.-+-|+|.+++....     .. +.+||.|++.+..
T Consensus        14 ~~~~r~~G~I~~~~~gfGFI~~~~~~~dvF~H~s~~~~~~-----~~-l~~G~~VeF~v~~   68 (89)
T d1wfqa_          14 SAALRETGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNL-----QD-LKVGDDVEFEVSS   68 (89)
T ss_dssp             SCCCEEEEEEEEECSSEEEEEETTTTEEEEEETTTCSSCT-----TT-CCTTCCEEEEEEE
T ss_pred             CccceEEEEEEEecCccceEEeCCCCceEEEEeehhhccC-----Cc-ccCCCEEEEEEEE
Confidence            4688889999999775556665 44578999999985321     12 7899999999854

>d1g6pa_ b.40.4.5 (A:) Major cold shock protein {Thermotoga maritima [TaxId: 2336]}

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: Thermotoga maritima [TaxId: 2336]

Probab=81.28  E-value=1.9  Score=28.01  Aligned_cols=47  Identities=19%  Similarity=0.255  Sum_probs=33.3

Q ss_pred             EEEEEEEEC---CeEEEEeCCCeEEEEeCcccccccccCccccCcCCCCEEEEEEE
Q 021034          104 KGTVFCTDN---RGALVDITAKSSAYLPTQEACIHKIKHVEEAGIVPGLKEEFVII  156 (318)
Q Consensus       104 ~G~V~~i~~---~G~~V~i~~~~~g~lp~sEls~~~~~~~~~~~~~~G~~v~v~Vl  156 (318)
                      +|+|...++   +|.+.. ..+-+-|+|.+.+......    . +.+|+.|.+.+.
T Consensus         2 ~G~Vk~f~~~kGfGFI~~-~~g~diFvH~s~l~~~g~~----~-l~~G~~V~f~~~   51 (66)
T d1g6pa_           2 RGKVKWFDSKKGYGFITK-DEGGDVFVHWSAIEMEGFK----T-LKEGQVVEFEIQ   51 (66)
T ss_dssp             CEEEEEEETTTTEEEEEE-TTSCBCBBCSSSSCCSSCC----C-CCSSSEEEEEEE
T ss_pred             eEEEEEEeCCCCeeEEEe-cCCceEEEEhHHhcccCCC----c-CCCCCEEEEEEE
Confidence            689998865   456554 4445899999998643222    1 678999999873