Citrus Sinensis ID: 019315

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340---
Protein Sequence
MQTPVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccEEcccccccccccccccccccccccEEEEEEEEEccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccHHHHcccccccccccccHHHHHHccccccccccccccccHHHHccccccccccccccEEEEEEEEEcccEEEEEccccccccEEccccccccHHHHHHHHHHHcccccccEEEEEEEEEccccEEEEcccccccccccccccEEEEEEEEEcccccEEEEHHHHHHHHHHHHHHHHHHccccEEEEEEEEEEcEEEEEEccEEEEEEccccccccccHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEEEccccccccEEEEccccccccccccccccccccccEEEccEEEEEccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccEEEEEccccccEEEEEEEEccccEEEEEccccHHHHHHHHHHccccHHHHHHHHHcccccHHHccccccEEEEEccccccccccccccccEEcccEEEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHccccEEEEEEEEccccEEEEEccHHcccccHHHHcccccHHHHHHccc
Coil and Loop (DISEMBL)
MQTPVQACKSFTFtllnsapplstcsfvqngnakyplqqsrkfhSFAASFRFLRSThivfcsqkdvfddlssaqfpenveneglegneelellnkpnlvpisngvasevdkksekpdeeealapflkffkprdsaeeveeegsevgvsresidvddkvgedkvsveyyepkpgdFVIGVVVSgnenkldvNVGADLLGTmltkevlplYDKEMDFLLCDLKKDAEEFMVRgkmgivkdddaiamsggsgpgrpvveTGTVLFAEVLGrtlsgrpllsTRRLFRKMAWHRVRQIKQLnepievkftewntggllTRIEGLRAFLPKAELLSRVNNFTELKEKVS
Flexible Loop (DISEMBL)
MQTPVQACKSFTFtllnsapplSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVasevdkksekpdeeealapflkffkprDSAEeveeegsevgvsresidvddkvgeDKVSveyyepkpgdFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVlgrtlsgrpllstrRLFRKMAWHRVRQikqlnepievkftewntgGLLTRIEGLRAFlpkaellsrvnnftelkekvs
Low Complexity Region (SEG)
MQTPVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPenveneglegneelellnkpnlvpISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAeeveeegsevgvsresIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVS
Disordered region (IsUnstruct)
******ACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDL********************************************************************************************VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA********RPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNF********
Disordered Region (DISOPRED)
*******CKSFTFTLLNSAPPLSTCSFVQN******************SFRFLRSTHIVFCS**************************************************************FL*************************************SVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFT*LKE***
Disordered Region (DISEMBL)
MQTPVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVA************EEALAPFLKFFKPR*****************ESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVS
Disordered Region (DISPRO)
***PVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLS****************E*LE***KPNLVP***************PDEEEALAPFLKFFKPR****************************DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAI******GPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEK**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQTPVQACKSFTFTLLNSAPPLSTCSFVQNGNAKYPLQQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSAQFPENVENEGLEGNEELELLNKPNLVPISNGVASEVDKKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESIDVDDKVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVS
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	343	2.2.26 [Sep-21-2011]
P73530	328	30S ribosomal protein S1	N/A	no	0.174	0.182	0.4	1e-05
P46228	307	30S ribosomal protein S1	yes	no	0.174	0.195	0.4	2e-05
O33698	295	30S ribosomal protein S1	no	no	0.166	0.193	0.385	2e-05
P51345	263	30S ribosomal protein S1,	N/A	no	0.183	0.239	0.343	0.0001
P29344	411	30S ribosomal protein S1,	N/A	no	0.192	0.160	0.343	0.0003
P74142	305	30S ribosomal protein S1	N/A	no	0.180	0.203	0.306	0.0007

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

 Score = 50.8 bits (120), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 34/60 (56%)

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

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 = 50.4 bits (119), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 35/60 (58%)

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

Binds mRNA.

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

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

 Score = 50.4 bits (119), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 37/57 (64%)

Query: 272 GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL 328
           G+  +S R L  + AW RV ++++  + ++VK T  N GG+   +EGLRAF+P++ L
Sbjct: 90  GQVTVSLRALALEQAWTRVAELQEGGQTVQVKVTGSNKGGVTADLEGLRAFIPRSHL 146

Binds mRNA.

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

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

 Score = 48.1 bits (113), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 40/67 (59%), Gaps = 4/67 (5%)

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

Query: 331 RVNNFTE 337
             NNF++
Sbjct: 146 --NNFSK 150

Porphyra purpurea (taxid: 2787)

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

 Score = 46.6 bits (109), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 43/67 (64%), Gaps = 1/67 (1%)

Query: 275 LLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNN 334
           +LS R++  ++AW R RQ++  +  ++ K    N GG++  +EGLR F+P +++ S+ ++
Sbjct: 162 ILSLRQIQYELAWERCRQLQAEDVVVKGKIVGANKGGVVALVEGLRGFVPFSQISSK-SS 220

Query: 335 FTELKEK 341
             EL EK
Sbjct: 221 AEELLEK 227

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

 Score = 45.1 bits (105), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 39/62 (62%)

Query: 272 GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR 331
           G+  LS R+L  + +W  + ++++  + +E+  T  N GG++  +EGLR F+P++ L+ +
Sbjct: 91  GQVRLSRRQLQIQQSWENLAELEESGKTLEMVVTGTNKGGVVGDVEGLRGFIPRSHLMHK 150

Query: 332 VN 333
            N
Sbjct: 151 DN 152

Binds mRNA.

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

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	343
255572295	476	conserved hypothetical protein [Ricinus	0.836	0.602	0.741	1e-118
359495207	513	PREDICTED: uncharacterized protein LOC10	0.924	0.617	0.666	1e-114
449446381	530	PREDICTED: 30S ribosomal protein S1 homo	0.842	0.545	0.708	1e-110
297739376	435	unnamed protein product [Vitis vinifera]	0.705	0.556	0.741	1e-101
449527959	529	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.839	0.544	0.657	3e-99
224066601	486	predicted protein [Populus trichocarpa]	0.886	0.625	0.566	8e-97
356534027	513	PREDICTED: uncharacterized protein LOC10	0.860	0.575	0.637	9e-96
297839005	501	predicted protein [Arabidopsis lyrata su	0.787	0.538	0.619	5e-93
334183835	500	small subunit ribosomal protein S1 [Arab	0.787	0.54	0.620	3e-92
62320614	336	RIBOSOMAL PROTEIN [Arabidopsis thaliana]	0.787	0.803	0.620	1e-91

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

 Score =  432 bits (1111), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 215/290 (74%), Positives = 252/290 (86%), Gaps = 3/290 (1%)

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

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

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

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

Query: 294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKVS 343
           K+LNEPIEV+ TEWNTGGLLTRIEGLRAFLPKAEL++RV NF ELKE VS
Sbjct: 257 KELNEPIEVRITEWNTGGLLTRIEGLRAFLPKAELMNRVKNFKELKENVS 306

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  416 bits (1069), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 228/342 (66%), Positives = 263/342 (76%), Gaps = 25/342 (7%)

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

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

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

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

Query: 241 AIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPI 300
           A  +S     G PVVETGTVLFAEVLGRTLSGRPLLSTRR FR++AWHRVRQIKQLNEPI
Sbjct: 239 A--LSRVPMQGSPVVETGTVLFAEVLGRTLSGRPLLSTRRFFRRIAWHRVRQIKQLNEPI 296

Query: 301 EVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKV 342
           EV+ TEWNTGGLLTRIEGLRAFLPKAELL+RV +FTELKE V
Sbjct: 297 EVRITEWNTGGLLTRIEGLRAFLPKAELLNRVKSFTELKENV 338

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  404 bits (1039), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 207/292 (70%), Positives = 244/292 (83%), Gaps = 3/292 (1%)

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

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

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

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

Query: 291 RQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKV 342
           RQIK L+EPIEVK +EWNTGGLLTRIEGLRAFLPKAELL+RVNNFTELKE V
Sbjct: 309 RQIKGLDEPIEVKISEWNTGGLLTRIEGLRAFLPKAELLNRVNNFTELKENV 360

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  374 bits (959), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 192/259 (74%), Positives = 218/259 (84%), Gaps = 17/259 (6%)

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

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

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

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

Query: 324 PKAELLSRVNNFTELKEKV 342
           PKAELL+RV +FTELKE V
Sbjct: 242 PKAELLNRVKSFTELKENV 260

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  367 bits (943), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 192/292 (65%), Positives = 232/292 (79%), Gaps = 4/292 (1%)

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

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

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

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

Query: 291 RQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSRVNNFTELKEKV 342
           RQIK L+EPIEVK +EWNTGGLLTRIEGLRAFLPKAELL+RVNNFTELKE V
Sbjct: 308 RQIKGLDEPIEVKISEWNTGGLLTRIEGLRAFLPKAELLNRVNNFTELKENV 359

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  360 bits (923), Expect = 8e-97,   Method: Compositional matrix adjust.
 Identities = 204/360 (56%), Positives = 246/360 (68%), Gaps = 56/360 (15%)

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

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

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

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

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

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

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  356 bits (913), Expect = 9e-96,   Method: Compositional matrix adjust.
 Identities = 204/320 (63%), Positives = 238/320 (74%), Gaps = 25/320 (7%)

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

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

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

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

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

Query: 323 LPKAELLSRVNNFTELKEKV 342
           LPKAEL+ R N+FTELKE V
Sbjct: 325 LPKAELVKRANSFTELKENV 344

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  347 bits (890), Expect = 5e-93,   Method: Compositional matrix adjust.
 Identities = 189/305 (61%), Positives = 224/305 (73%), Gaps = 35/305 (11%)

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

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

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

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

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

Query: 338 LKEKV 342
           LKE V
Sbjct: 325 LKENV 329

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  345 bits (884), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 188/303 (62%), Positives = 223/303 (73%), Gaps = 33/303 (10%)

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

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

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

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

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

Query: 340 EKV 342
           E V
Sbjct: 326 ENV 328

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|62320614|dbj|BAD95265.1| RIBOSOMAL PROTEIN [Arabidopsis thaliana]

 Score =  343 bits (879), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 188/303 (62%), Positives = 223/303 (73%), Gaps = 33/303 (10%)

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

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

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

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

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

Query: 340 EKV 342
           E V
Sbjct: 326 ENV 328

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00005394001	SubName- Full=Chromosome undetermined scaffold_151, whole genome shotgun sequence; (507 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00033518001	SubName- Full=Chromosome chr5 scaffold_67, whole genome shotgun sequence; (390 aa)			•	•				•	0.420

---

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	343
PRK00087	647	PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl d	9e-08
cd04465	67	cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec	1e-07
COG0539	541	COG0539, RpsA, Ribosomal protein S1 [Translation,	3e-07
PRK07400	318	PRK07400, PRK07400, 30S ribosomal protein S1; Revi	1e-06
PRK06676	390	PRK06676, rpsA, 30S ribosomal protein S1; Reviewed	6e-06
PRK06299	565	PRK06299, rpsA, 30S ribosomal protein S1; Reviewed	6e-04
PRK07899	486	PRK07899, rpsA, 30S ribosomal protein S1; Reviewed	0.003

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

 Score = 53.4 bits (129), Expect = 9e-08
 Identities = 46/187 (24%), Positives = 79/187 (42%), Gaps = 46/187 (24%)

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

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

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

Query: 335 FTELKEK 341
            +E K +
Sbjct: 429 LSEYKGQ 435

Length = 647

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

 Score = 47.8 bits (115), Expect = 1e-07
 Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 297 NEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LSRVNNFTELKEKV 342
            E +E K TE   GGL+  IEG+RAFLP +++ L  V +  E   K 
Sbjct: 1   GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEYVGKE 47

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Length = 67

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

 Score = 51.5 bits (124), Expect = 3e-07
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 272 GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL-LS 330
           G  +LS R+  R+ AW ++ +  +  E +E K T    GGL   IEG+RAFLP + + + 
Sbjct: 81  GELVLSRRKAERERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEGVRAFLPGSLVDVR 140

Query: 331 RVNNFTELKEKV 342
            V +   L  K 
Sbjct: 141 PVRDLDPLIGKE 152

Length = 541

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

 Score = 49.4 bits (118), Expect = 1e-06
 Identities = 24/60 (40%), Positives = 36/60 (60%)

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

Length = 318

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

 Score = 47.2 bits (113), Expect = 6e-06
 Identities = 36/91 (39%), Positives = 51/91 (56%), Gaps = 4/91 (4%)

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

Query: 313 LTRIEGLRAFLPKAELLS--RVNNFTELKEK 341
           +  +EG+R F+P A L+S   V +F++ K K
Sbjct: 122 VVDVEGVRGFIP-ASLISTRFVEDFSDFKGK 151

Length = 390

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

 Score = 41.3 bits (98), Expect = 6e-04
 Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 1/71 (1%)

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

Query: 331 RVNNFTELKEK 341
            V +   L+ K
Sbjct: 150 PVRDTDPLEGK 160

Length = 565

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

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

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

Query: 313 LTRIEGLRAFLP 324
           +  I GLR FLP
Sbjct: 139 ILDI-GLRGFLP 149

Length = 486

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	343
PRK07400	318	30S ribosomal protein S1; Reviewed	99.92
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	99.91
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.89
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.88
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.87
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	99.87
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	99.84
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	99.84
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.83
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	99.79
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	99.78
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.78
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	99.69
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	99.68
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	99.67
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	99.64
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	99.58
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	99.49
PRK07400	318	30S ribosomal protein S1; Reviewed	99.47
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.06
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	98.94
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	98.88
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	98.86
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.84
PRK08582	139	hypothetical protein; Provisional	98.78
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	98.78
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.71
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	98.64
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	98.63
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	98.57
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	98.56
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	98.56
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.54
PRK07252	120	hypothetical protein; Provisional	98.49
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	98.48
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	98.47
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.47
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	98.46
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	98.43
PRK05807	136	hypothetical protein; Provisional	98.42
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.41
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	98.39
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.35
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.35
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.31
PRK08059	123	general stress protein 13; Validated	98.31
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	98.28
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	98.27
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.25
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	98.22
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.17
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.13
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	98.11
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.11
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.1
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.08
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.07
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	98.05
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.03
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	98.01
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.94
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	97.92
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	97.89
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	97.89
PRK09202	470	nusA transcription elongation factor NusA; Validat	97.88
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	97.88
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	97.79
PHA02945	88	interferon resistance protein; Provisional	97.77
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	97.71
TIGR01953	341	NusA transcription termination factor NusA. This m	97.69
PRK09202	470	nusA transcription elongation factor NusA; Validat	97.68
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	97.52
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	97.48
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.47
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	97.46
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	97.46
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	97.45
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	97.44
COG2183	780	Tex Transcriptional accessory protein [Transcripti	97.42
PRK12327	362	nusA transcription elongation factor NusA; Provisi	97.41
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	97.36
TIGR01953	341	NusA transcription termination factor NusA. This m	97.32
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	97.3
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	97.3
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	97.29
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	97.27
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	97.26
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	97.24
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	97.2
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	97.2
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	97.2
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	97.14
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	97.1
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	97.09
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	97.08
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	97.04
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	96.99
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	96.98
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	96.97
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	96.97
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	96.95
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	96.92
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	96.92
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	96.83
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	96.8
COG1098	129	VacB Predicted RNA binding protein (contains ribos	96.75
PRK08582	139	hypothetical protein; Provisional	96.7
PRK05807	136	hypothetical protein; Provisional	96.68
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	96.65
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	96.62
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	96.59
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	96.56
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	96.56
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	96.48
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	96.36
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.35
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	96.3
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	96.25
PRK08059	123	general stress protein 13; Validated	96.16
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	96.1
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	96.07
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	96.01
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	95.97
PRK07252	120	hypothetical protein; Provisional	95.96
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.94
PHA02945	88	interferon resistance protein; Provisional	95.88
KOG2916	304	consensus Translation initiation factor 2, alpha s	95.81
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	95.8
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	95.75
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	95.69
PRK11642	813	exoribonuclease R; Provisional	95.65
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	95.63
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	95.62
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	95.57
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	95.48
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	95.48
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	95.45
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.43
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.39
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	95.35
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	95.32
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	95.27
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	95.24
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	94.68
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	94.59
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	94.59
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	94.53
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	93.94
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	93.74
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	93.43
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	93.11
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	91.58
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	91.48
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	91.06
PF09883	225	DUF2110: Uncharacterized protein conserved in arch	90.99
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	90.96
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	90.58
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	90.53
KOG4078	173	consensus Putative mitochondrial ribosomal protein	89.63
PRK11642	813	exoribonuclease R; Provisional	87.58
PRK12328	374	nusA transcription elongation factor NusA; Provisi	87.58
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	87.24
PRK11712	489	ribonuclease G; Provisional	86.48
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	86.38
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	85.7
KOG3013	301	consensus Exosomal 3'-5' exoribonuclease complex,	84.25
PRK10811	1068	rne ribonuclease E; Reviewed	83.34
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	83.33
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	81.87

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.92  E-value=2.4e-24  Score=209.38  Aligned_cols=137  Identities=28%  Similarity=0.356  Sum_probs=120.0

Q ss_pred             hhHHHHhhcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeee
Q 019315          157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV  236 (343)
Q Consensus       157 ~dFa~lLe~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i  236 (343)
                      ++|+++|+++.+++++|++|+|+|++++++|+|||||+|++|+||++|+++.+...                        
T Consensus        16 ~~f~~~le~~~~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~------------------------   71 (318)
T PRK07400         16 EDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEG------------------------   71 (318)
T ss_pred             HHHHHHHHhhHhhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccC------------------------
Confidence            68999998766779999999999999999999999999999999999998532100                        


Q ss_pred             cCCcceeccCCCCCCCCceeccceEEEEEEee-cCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEE
Q 019315          237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR  315 (343)
Q Consensus       237 ~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~-de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVe  315 (343)
                             +       .....+|+.+.+.|+.. +++++++||+|++....+|+++++++++|.+|+|+|++++++|++|+
T Consensus        72 -------~-------~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~  137 (318)
T PRK07400         72 -------P-------EEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVR  137 (318)
T ss_pred             -------H-------HHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHhccCCCEEEEEEEEEECCeEEEE
Confidence                   0       11235677888888875 46789999999998889999999999999999999999999999999


Q ss_pred             ECCeEEEEeCCccccC
Q 019315          316 IEGLRAFLPKAELLSR  331 (343)
Q Consensus       316 IeGlrgFIP~SQl~~r  331 (343)
                      ++|++||||.||++.+
T Consensus       138 l~Gv~gfip~s~ls~~  153 (318)
T PRK07400        138 IEGLRGFIPGSHISTR  153 (318)
T ss_pred             ECCEEEEEEHHHcCcc
Confidence            9999999999999986

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

Probab=99.91  E-value=4.3e-24  Score=219.41  Aligned_cols=145  Identities=30%  Similarity=0.340  Sum_probs=125.4

Q ss_pred             hhHHHHhh---cccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhccee
Q 019315          157 KVGEDKVS---VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKM  233 (343)
Q Consensus       157 ~dFa~lLe---~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV  233 (343)
                      .+|+++|.   .+.+.+++|++|+|+|++|.+++|+||||+|++|+||++||+....                       
T Consensus         3 ~~f~~~~~~~~~~~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~~~~-----------------------   59 (541)
T COG0539           3 EEFAELFEESDKSDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPV-----------------------   59 (541)
T ss_pred             hhHHHHHHhhhcchhccCCCCEEEEEEEEEeCCeEEEEecCccccEeEHHHhccccc-----------------------
Confidence            34555554   3457899999999999999999999999999999999999983210                       


Q ss_pred             eeecCCcceeccCCCCCCCCceeccceEEEEEEee-cCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCee
Q 019315          234 GIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL  312 (343)
Q Consensus       234 ~~i~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~-de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGl  312 (343)
                                        ..++.+|+.+.+.|+.. +++|.++||++++.+..+|+++++++++|++|+|+|++.+|||+
T Consensus        60 ------------------~~~~~~gd~v~v~v~~~e~~~g~~~lS~~k~~~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~  121 (541)
T COG0539          60 ------------------EDVVQVGDEVEVLVLRVEDGEGELVLSRRKAERERAWEKLEEAFENGEIVEGKITGKVKGGL  121 (541)
T ss_pred             ------------------cceecCCCEEEEEEEEEecCCceEEeeHHHHHHHHhHHHHHHHHhcCCeEEEEEEEEecCcE
Confidence                              01346677788888753 56689999999999999999999999999999999999999999


Q ss_pred             EEEECCeEEEEeCCccccC-CCChhhhcccC
Q 019315          313 LTRIEGLRAFLPKAELLSR-VNNFTELKEKV  342 (343)
Q Consensus       313 iVeIeGlrgFIP~SQl~~r-v~nleel~g~v  342 (343)
                      +|+++|+|||||+||++.| ++|+++|+|+.
T Consensus       122 ~Vdi~gvr~FlP~S~v~~r~v~d~~~~~Gk~  152 (541)
T COG0539         122 TVDIEGVRAFLPGSLVDVRPVRDLDPLIGKE  152 (541)
T ss_pred             EEEECCEEEeccHHHhcccccccccccCCce
Confidence            9999999999999999998 79999999874

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.89  E-value=7.4e-23  Score=209.01  Aligned_cols=146  Identities=27%  Similarity=0.358  Sum_probs=126.9

Q ss_pred             hhHHHHhhcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeee
Q 019315          157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV  236 (343)
Q Consensus       157 ~dFa~lLe~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i  236 (343)
                      ++|+++++.....+++|++|+|+|++|++++++||||+|++|+||++|+++....       +                 
T Consensus        20 e~f~~~~e~~~~~~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~-------~-----------------   75 (486)
T PRK07899         20 EDFLAAIDKTIKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDV-------D-----------------   75 (486)
T ss_pred             HHHHHHHHHHHhcCCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccccC-------C-----------------
Confidence            6899999877788999999999999999999999999999999999999843100       0                 


Q ss_pred             cCCcceeccCCCCCCCCceeccceEEEEEEee-cCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEE
Q 019315          237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTR  315 (343)
Q Consensus       237 ~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~-de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVe  315 (343)
                             .       ...+++|+++.+.|+.. +.+|+++||+|++....+|++++++++.|.+|+|+|++++++|++|+
T Consensus        76 -------~-------~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~~~~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vd  141 (486)
T PRK07899         76 -------P-------NEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILD  141 (486)
T ss_pred             -------h-------hhcCCCCCEEEEEEEEEECCCCeEEEEehhhcccchHHHHHHHhcCCCEEEEEEEEEECCeEEEE
Confidence                   0       12246788899999875 46789999999999889999999999999999999999999999999


Q ss_pred             ECCeEEEEeCCccccC-CCChhhhccc
Q 019315          316 IEGLRAFLPKAELLSR-VNNFTELKEK  341 (343)
Q Consensus       316 IeGlrgFIP~SQl~~r-v~nleel~g~  341 (343)
                      + |++||||.||++.+ ++++++++|+
T Consensus       142 l-Gi~gflP~Sel~~~~~~~~~~~vGq  167 (486)
T PRK07899        142 I-GLRGFLPASLVEMRRVRDLQPYIGQ  167 (486)
T ss_pred             E-CCEEEEEhhHhcccccCChhhcCCC
Confidence            9 89999999999987 6778888775

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.88  E-value=1.4e-21  Score=201.08  Aligned_cols=144  Identities=23%  Similarity=0.265  Sum_probs=125.4

Q ss_pred             hhHHHHhhccc--CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceee
Q 019315          157 KVGEDKVSVEY--YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMG  234 (343)
Q Consensus       157 ~dFa~lLe~~~--~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~  234 (343)
                      ++|++||+++.  +.+++|++|+|+|+++++++++||||+|++|+||.+|++...                         
T Consensus        13 ~~f~~~l~~~~~~~~~~~G~~v~G~V~~v~~~~~~Vdig~k~~g~lp~~e~~~~~-------------------------   67 (565)
T PRK06299         13 ESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQ-------------------------   67 (565)
T ss_pred             HHHHHHHHhhcccccCCCCCEEEEEEEEEECCEEEEEeCCCeEEEEEHHHhcCcc-------------------------
Confidence            78999998765  668999999999999999999999999999999999997310                         


Q ss_pred             eecCCcceeccCCCCCCCCceeccceEEEEEEee-cCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeE
Q 019315          235 IVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLL  313 (343)
Q Consensus       235 ~i~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~-de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGli  313 (343)
                         .             .....+|+++.+.|+.. +.+|+++||+|++.....|+++.++++.|++|+|+|++++++|++
T Consensus        68 ---~-------------~~~~~vG~~i~~~V~~~~~~~~~i~lS~k~~~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~  131 (565)
T PRK06299         68 ---G-------------ELEVKVGDEVEVYVERIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGFT  131 (565)
T ss_pred             ---c-------------cccCCCCCEEEEEEEEEECCCCcEEEechHHHHHHHHHHHHHHhhCCCEEEEEEEEEECCEEE
Confidence               0             01235677888888875 466899999999999999999999999999999999999999999


Q ss_pred             EEECCeEEEEeCCccccC-CCChhhhccc
Q 019315          314 TRIEGLRAFLPKAELLSR-VNNFTELKEK  341 (343)
Q Consensus       314 VeIeGlrgFIP~SQl~~r-v~nleel~g~  341 (343)
                      |+++|++||||+||++.+ .++++.++|+
T Consensus       132 V~~~g~~gfip~s~~~~~~~~~~~~~vG~  160 (565)
T PRK06299        132 VDLNGVEAFLPGSQVDVRPVRDTDPLEGK  160 (565)
T ss_pred             EEECCEEEEEEHHHccCcCCCChHHhCCC
Confidence            999999999999999987 5677766664

>TIGR00717 rpsA ribosomal protein S1

Probab=99.87  E-value=2.3e-21  Score=196.82  Aligned_cols=142  Identities=22%  Similarity=0.320  Sum_probs=122.4

Q ss_pred             hhHHHHhhcc--cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceee
Q 019315          157 KVGEDKVSVE--YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMG  234 (343)
Q Consensus       157 ~dFa~lLe~~--~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~  234 (343)
                      ++|++||+++  ...+++|++|+|+|+++++++++||+|+|++|+||++|++..                          
T Consensus         1 ~~f~~~~~~~~~~~~~~~G~~v~g~V~~i~~~~~~v~~g~k~~g~i~~~E~~~~--------------------------   54 (516)
T TIGR00717         1 ESFAQLLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDA--------------------------   54 (516)
T ss_pred             ChHHHHHhhhcccccCCCCCEEEEEEEEEECCEEEEEcCCCcEEEEEHHHhcCC--------------------------
Confidence            4799999765  346899999999999999999999999999999999999721                          


Q ss_pred             eecCCcceeccCCCCCCCCceeccceEEEEEEee-cCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeE
Q 019315          235 IVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLL  313 (343)
Q Consensus       235 ~i~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~-de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGli  313 (343)
                                       ....++|+++.+.|+.. ++.|++.||++++.+...|+++++++++|.+|+|+|++++++|++
T Consensus        55 -----------------~~~~~vGd~i~~~V~~~~~~~g~i~lS~~~~~~~~~~~~l~~a~~~g~~v~g~V~~~~~~g~~  117 (516)
T TIGR00717        55 -----------------PLEIQVGDEVEVYLDRVEDRFGETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFI  117 (516)
T ss_pred             -----------------ccCCCCCCEEEEEEEEEeCCCCcEEEEHHHhhhhHHHHHHHHHhhCCCeEEEEEEEEECCEEE
Confidence                             01235677888888864 467999999999998899999999999999999999999999999


Q ss_pred             EEECCeEEEEeCCccccC-CCChhhhccc
Q 019315          314 TRIEGLRAFLPKAELLSR-VNNFTELKEK  341 (343)
Q Consensus       314 VeIeGlrgFIP~SQl~~r-v~nleel~g~  341 (343)
                      |+++|++||||.||++.+ .++.+.++|+
T Consensus       118 V~i~g~~~flP~s~~~~~~~~~~~~~vG~  146 (516)
T TIGR00717       118 VDLNGVEAFLPGSQVDVKPIKDLDSLIGK  146 (516)
T ss_pred             EEECCEEEEEeHHHhcCcccCchhhhCCC
Confidence            999999999999999876 4566666654

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.

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

Probab=99.87  E-value=7.5e-22  Score=202.93  Aligned_cols=163  Identities=20%  Similarity=0.188  Sum_probs=140.0

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccc----------cchhh------------------hhh
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYD----------KEMDF------------------LLC  218 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~----------ke~e~------------------l~~  218 (343)
                      ...+++|++|+|+|.+|+++|+|||||+ .+|++|++|++|.+.          +++..                  +.-
T Consensus       187 ~~~l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~  265 (541)
T COG0539         187 LNKLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEE  265 (541)
T ss_pred             HhcCCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhccc
Confidence            4679999999999999999999999987 999999999997641          12211                  122


Q ss_pred             hhhhhh-----hHhhhcceeeeecCCcc-eeccCCCCCCCCceecc--------------ceEEEEEEeec-CCCceEEe
Q 019315          219 DLKKDA-----EEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVVETG--------------TVLFAEVLGRT-LSGRPLLS  277 (343)
Q Consensus       219 d~~k~~-----ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~eiG--------------d~v~~eVl~~d-e~G~I~LS  277 (343)
                      |+|...     .+..+.|+|++++++|+ |++..+++||+|+++++              +++.++|+..+ +++||+||
T Consensus       266 dPw~~i~~~~~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~  345 (541)
T COG0539         266 DPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLG  345 (541)
T ss_pred             CcHHHHhhhcCCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEee
Confidence            233222     24789999999999999 99999999999999655              77889999876 67999999


Q ss_pred             HHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315          278 TRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR  331 (343)
Q Consensus       278 ~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r  331 (343)
                      +|++. .+||+.+.+.|+.|..|+|+|+++.+.|++|.++ |++||++.|++++.
T Consensus       346 iKq~~-~~pw~~~~~~~~~g~~v~g~v~~~t~~g~fv~le~gidG~vh~~d~sw~  399 (541)
T COG0539         346 LKQLK-ENPWEEFADKHPVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWD  399 (541)
T ss_pred             ehhhh-cChhhhhhhhcCCCCeEEEEEeeecccceEEccCCCccceEEHHhcCcc
Confidence            99999 5999999999999999999999999999999995 59999999999975

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=99.84  E-value=3.8e-20  Score=188.90  Aligned_cols=142  Identities=20%  Similarity=0.189  Sum_probs=119.2

Q ss_pred             hhHHHHhhcccC----CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcce
Q 019315          157 KVGEDKVSVEYY----EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGK  232 (343)
Q Consensus       157 ~dFa~lLe~~~~----~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGk  232 (343)
                      ++|+++|+++.+    .+++|++|+|+|++|++++++||||+|++|+||++|+....                       
T Consensus        15 ~~f~~~l~~~~~~~~~~~~~G~~v~G~V~~v~~~~v~Vdig~k~eg~ip~~e~~~~~-----------------------   71 (491)
T PRK13806         15 ESFAELLEAYEGERKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDAD-----------------------   71 (491)
T ss_pred             HHHHHHHHhhhhhccccCCCCCEEEEEEEEEECCEEEEEECCCcEEEEEHHHhcCcc-----------------------
Confidence            689999987643    38999999999999999999999999999999999986210                       


Q ss_pred             eeeecCCcceeccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCee
Q 019315          233 MGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGL  312 (343)
Q Consensus       233 V~~i~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGl  312 (343)
                           .+             ....+|+++.+.|+..+ ++.+.||++.+ ....|+++.+++++|++|+|+|++++++|+
T Consensus        72 -----~~-------------~~~~~G~~i~~~Vi~~~-~~~~~lS~~~~-~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~  131 (491)
T PRK13806         72 -----GE-------------LTVAVGDEVELYVVSVN-GQEIRLSKALS-GQGGAAMLEEAYENGVPVEGKVTGTCKGGF  131 (491)
T ss_pred             -----cc-------------ccccCCCEEEEEEEEEc-CCEEEEEhHHh-hhhhHHHHHHHHhCCCEEEEEEEEEEcCCE
Confidence                 00             01256777888887654 35799998755 468999999999999999999999999999


Q ss_pred             EEEECCeEEEEeCCccccC-CCChhhhccc
Q 019315          313 LTRIEGLRAFLPKAELLSR-VNNFTELKEK  341 (343)
Q Consensus       313 iVeIeGlrgFIP~SQl~~r-v~nleel~g~  341 (343)
                      +|++.|++||||+||++.+ .++++.++|+
T Consensus       132 ~V~i~g~~~flP~s~~~~~~~~~~~~~vG~  161 (491)
T PRK13806        132 NVEVLGRRAFCPVSQIDLRYVEDPESYVGQ  161 (491)
T ss_pred             EEEECCEEEEEEHHHhccccCCChHHcCCC
Confidence            9999999999999999987 5777777664

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=99.84  E-value=3.1e-20  Score=200.32  Aligned_cols=176  Identities=22%  Similarity=0.215  Sum_probs=134.3

Q ss_pred             ccCCCCChhhhhhhhhhccCCCCChhHHhhhcccccccccccC-cCc-hhHHHHhhcc-cCCCCCCCEEEEEEEEEeCCe
Q 019315          111 KKSEKPDEEEALAPFLKFFKPRDSAEEVEEEGSEVGVSRESID-VDD-KVGEDKVSVE-YYEPKPGDFVIGVVVSGNENK  187 (343)
Q Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~-~dFa~lLe~~-~~~~k~GdiVeG~VVsI~~~g  187 (343)
                      -.+..++.+|.+.=.++..+.+---      |++.  +.++.+ .+. ---..|++++ +..+++|++|+|+|++|++++
T Consensus       265 iDts~l~ieevv~~i~~~~~~~~~~------~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~iV~G~Vv~i~~~~  336 (863)
T PRK12269        265 VDTSCLTIEEVCERIAREAHRRALW------GGER--SVENQEGKGTPLVPRQLQERYSFEAPEPGSVRMGTVVQVNAGT  336 (863)
T ss_pred             EECCCCCHHHHHHHHHHHHHhcccc------cccc--ccccccccCCCchhHHHHHhhccccCCCCCEEEEEEEEEECCE
Confidence            3456688888888888888753211      0000  000100 111 1123455544 577999999999999999999


Q ss_pred             EEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCCCceeccceEEEEEEe
Q 019315          188 LDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRPVVETGTVLFAEVLG  267 (343)
Q Consensus       188 v~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~  267 (343)
                      +|||||+|+||+||++|+...                                              .++|+++.+.|+.
T Consensus       337 v~VdiG~K~eGiI~~~E~~~~----------------------------------------------~kvGd~i~~~V~~  370 (863)
T PRK12269        337 VFVDIGGKSEGRVPVEEFEAP----------------------------------------------PKAGDGVRVYVER  370 (863)
T ss_pred             EEEEeCCCceEEeEHHHhccC----------------------------------------------CCCCCEEEEEEEE
Confidence            999999999999999998511                                              1456777888877


Q ss_pred             ecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEE--ecCeeEEEEC-CeEEEEeCCccccC-CCChhhhccc
Q 019315          268 RTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEW--NTGGLLTRIE-GLRAFLPKAELLSR-VNNFTELKEK  341 (343)
Q Consensus       268 ~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~--nKGGliVeIe-GlrgFIP~SQl~~r-v~nleel~g~  341 (343)
                      .+++| +.||++++.....|++++++|++|++|+|+|+++  +|||++|+++ |++||||+||++.+ .++++.++|+
T Consensus       371 ~~~~~-~~LS~~~~~~~~~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~~~~~~~~vG~  447 (863)
T PRK12269        371 VTPYG-PELSKTKADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPESLIGL  447 (863)
T ss_pred             EcCCc-eEEEehHhhhhHHHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhccccccchHHhCCC
Confidence            65556 8999999999999999999999999999999996  6799999995 89999999999977 5678777764

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.83  E-value=1.1e-19  Score=179.04  Aligned_cols=146  Identities=32%  Similarity=0.459  Sum_probs=123.9

Q ss_pred             hhHHHHhhcccCCCCCCCEEEEEEEEEeCCeEEEEe-CCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeee
Q 019315          157 KVGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNV-GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGI  235 (343)
Q Consensus       157 ~dFa~lLe~~~~~~k~GdiVeG~VVsI~~~gv~VDI-G~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~  235 (343)
                      ..|++++. ....+++|++|+|+|+++++++++||| |++.+|+||.+|+++...+                        
T Consensus         3 ~~~~~~~~-~~~~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~~------------------------   57 (390)
T PRK06676          3 EEFEESLN-SVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIE------------------------   57 (390)
T ss_pred             HHHHHHhh-hhhcccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhcccccc------------------------
Confidence            46888886 567899999999999999999999999 8899999999999742100                        


Q ss_pred             ecCCcceeccCCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEE
Q 019315          236 VKDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLT  314 (343)
Q Consensus       236 i~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliV  314 (343)
                        +     .       .....+|+.+.+.|+..+ +++++.||+|++....+|+++.++++.|++++|+|+++.++|++|
T Consensus        58 --~-----~-------~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V  123 (390)
T PRK06676         58 --D-----I-------NDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVV  123 (390)
T ss_pred             --C-----c-------ccccCCCCEEEEEEEEEECCCCCEEEEHHHhhhhhhHHHHHHhccCCCEEEEEEEEEECCeEEE
Confidence              0     0       112467888888888764 557899999999988999999999999999999999999999999


Q ss_pred             EECCeEEEEeCCccccC-CCChhhhccc
Q 019315          315 RIEGLRAFLPKAELLSR-VNNFTELKEK  341 (343)
Q Consensus       315 eIeGlrgFIP~SQl~~r-v~nleel~g~  341 (343)
                      +++|++||||.|+++.+ ..++++++|+
T Consensus       124 ~~~G~~gflp~~el~~~~~~~~~~~vG~  151 (390)
T PRK06676        124 DVEGVRGFIPASLISTRFVEDFSDFKGK  151 (390)
T ss_pred             EECCEEEEEEHHHcCCccCCChHHcCCC
Confidence            99999999999999876 5677777664

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=99.79  E-value=4.4e-19  Score=191.49  Aligned_cols=169  Identities=17%  Similarity=0.214  Sum_probs=138.3

Q ss_pred             HHhhcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCccc----------ccchhhhhhhh----------
Q 019315          161 DKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLY----------DKEMDFLLCDL----------  220 (343)
Q Consensus       161 ~lLe~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~----------~ke~e~l~~d~----------  220 (343)
                      +++++.+.++++|++|+|+|.++.++|+||+++ +.+||||++++++.+          ++++.+.+++.          
T Consensus       482 ~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LS  560 (863)
T PRK12269        482 QAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLS  560 (863)
T ss_pred             HHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEEC-CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEE
Confidence            334444567889999999999999999999996 689999999998543          12222222111          


Q ss_pred             --------hhh-----hhHhhhcceeeeecCCcc-eeccCCCCCCCCceec---------------cceEEEEEEeec-C
Q 019315          221 --------KKD-----AEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVVET---------------GTVLFAEVLGRT-L  270 (343)
Q Consensus       221 --------~k~-----~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~ei---------------Gd~v~~eVl~~d-e  270 (343)
                              |..     ..+.+++|+|+.++++|+ |.++.+++|++|++++               |+++.+.|+..+ +
T Consensus       561 lK~l~~~p~~~~~~~~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e  640 (863)
T PRK12269        561 LKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQ  640 (863)
T ss_pred             EeccccchhhhhhccCCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecc
Confidence                    111     134789999999999999 9999899999997654               467888898876 6


Q ss_pred             CCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          271 SGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       271 ~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      ++++.||+|++.. +||+.+.+.|+.|++|+|+|+++.++|++|++ +|++||||.|++++.
T Consensus       641 ~~rIsLS~K~l~~-~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~  701 (863)
T PRK12269        641 AGRVSLGLKQVTA-NPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWV  701 (863)
T ss_pred             cCceEEEehhccc-CchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhcc
Confidence            7899999999984 89999999999999999999999999999999 699999999999863

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=99.78  E-value=4.3e-19  Score=181.20  Aligned_cols=164  Identities=17%  Similarity=0.110  Sum_probs=135.4

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccc----------cchhhhh--hh---------------
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYD----------KEMDFLL--CD---------------  219 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~----------ke~e~l~--~d---------------  219 (343)
                      +..+++|++|+|+|+++.++|+||+++.+.+|+||++|+++.+.          +.+.+.+  +|               
T Consensus       197 ~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K  276 (491)
T PRK13806        197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIK  276 (491)
T ss_pred             HhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEeh
Confidence            34688999999999999999999999888999999999986431          1111111  11               


Q ss_pred             -----hhhh-----hhHhhhcceeeeecCCcc-eeccCCCCCCCCcee---------------ccceEEEEEEeec-CCC
Q 019315          220 -----LKKD-----AEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVVE---------------TGTVLFAEVLGRT-LSG  272 (343)
Q Consensus       220 -----~~k~-----~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~e---------------iGd~v~~eVl~~d-e~G  272 (343)
                           .|..     ..+..++|+|+.++++|+ |.++.+++||+|+++               +|+.+.+.|+..+ +++
T Consensus       277 ~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~  356 (491)
T PRK13806        277 QAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKR  356 (491)
T ss_pred             hhhcccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCC
Confidence                 1211     124789999999999999 999888999999655               4467788888776 678


Q ss_pred             ceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          273 RPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       273 ~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      +|.||+|++. ..||+.+.+.|+.|++|+|+|+++.+.|++|++ +|+.||||.|+++..
T Consensus       357 ri~Ls~K~~~-~~p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~  415 (491)
T PRK13806        357 RISLSLRDAE-GDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRA  415 (491)
T ss_pred             EEEEEEeecc-cChhHHhhhhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCcc
Confidence            9999999987 489999999999999999999999999999999 699999999999864

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

Probab=99.78  E-value=3.4e-18  Score=179.70  Aligned_cols=140  Identities=30%  Similarity=0.392  Sum_probs=119.7

Q ss_pred             hcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCccee
Q 019315          164 SVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA  243 (343)
Q Consensus       164 e~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~  243 (343)
                      +.....+++|++|+|+|++++++++|||+|++.+|+||++|+++...+                          +     
T Consensus       294 ~~~~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~--------------------------~-----  342 (647)
T PRK00087        294 NELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEIS--------------------------S-----  342 (647)
T ss_pred             HHHHhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccC--------------------------C-----
Confidence            455678999999999999999999999999999999999999842100                          0     


Q ss_pred             ccCCCCCCCCceeccceEEEEEEee-cCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEECCeEEE
Q 019315          244 MSGGSGPGRPVVETGTVLFAEVLGR-TLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAF  322 (343)
Q Consensus       244 Ig~~ieg~i~v~eiGd~v~~eVl~~-de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIeGlrgF  322 (343)
                      .       .....+|+.+.+.|+.. +++|++.||+|++....+|++++++++.|++++|+|++++++|++|+++|++||
T Consensus       343 ~-------~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~~~~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lggi~gf  415 (647)
T PRK00087        343 L-------KESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAF  415 (647)
T ss_pred             h-------hhccCCCCEEEEEEEEEECCCCcEEEEeehhcchhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECCEEEE
Confidence            0       12246788888888875 467899999999998899999999999999999999999999999999999999


Q ss_pred             EeCCccccC-CCChhhhccc
Q 019315          323 LPKAELLSR-VNNFTELKEK  341 (343)
Q Consensus       323 IP~SQl~~r-v~nleel~g~  341 (343)
                      ||.|+++.+ .+++..++|+
T Consensus       416 iP~sel~~~~~~d~~~~vG~  435 (647)
T PRK00087        416 LPASHVELGYVEDLSEYKGQ  435 (647)
T ss_pred             EEHHHhCccccCCHHHhCCC
Confidence            999999877 6777777664

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.69  E-value=5.8e-17  Score=165.93  Aligned_cols=158  Identities=20%  Similarity=0.253  Sum_probs=128.6

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCccc--------ccchhhhhh--hhh------------------
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLY--------DKEMDFLLC--DLK------------------  221 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~--------~ke~e~l~~--d~~------------------  221 (343)
                      ++.|++|+|+|+++.++|++|++|  ..||||.+++...+        ++.+.+.++  |..                  
T Consensus       120 ~e~g~~V~G~V~~v~k~G~~VdlG--i~gflP~Sel~~~~~~~~~~~vGq~V~vkVleid~~~~~ivLSrr~~l~~~~~~  197 (486)
T PRK07899        120 KEKDGVVTGTVIEVVKGGLILDIG--LRGFLPASLVEMRRVRDLQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSE  197 (486)
T ss_pred             hcCCCEEEEEEEEEECCeEEEEEC--CEEEEEhhHhcccccCChhhcCCCEEEEEEEEEECCCCEEEEEhHHHHHhhhHH
Confidence            467999999999999999999995  68999999987432        222222111  110                  


Q ss_pred             -------hhhhHhhhcceeeeecCCcc-eeccCCCCCCCCcee--------------ccceEEEEEEeec-CCCceEEeH
Q 019315          222 -------KDAEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVVE--------------TGTVLFAEVLGRT-LSGRPLLST  278 (343)
Q Consensus       222 -------k~~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~e--------------iGd~v~~eVl~~d-e~G~I~LS~  278 (343)
                             +...+.+++|+|+.++++|+ |.++ +++||+|+++              +|+.+.+.|+..+ ++++|.||+
T Consensus       198 ~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlg-gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSl  276 (486)
T PRK07899        198 VRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSL  276 (486)
T ss_pred             HHHHHHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEE
Confidence                   00124688999999999999 8896 5999998665              4567888888876 569999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          279 RRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       279 Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      |++. ..||+++.+.++.|++++|+|+++.+.|++|++ +|+.||+|.|++..+
T Consensus       277 K~~~-~dPw~~~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~  329 (486)
T PRK07899        277 KATQ-EDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAER  329 (486)
T ss_pred             eecc-ccchhhhHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcc
Confidence            9988 489999999999999999999999999999999 599999999999754

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.68  E-value=1.6e-16  Score=163.73  Aligned_cols=163  Identities=17%  Similarity=0.178  Sum_probs=133.7

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCccc----------ccchhhhh--hh---------------
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLY----------DKEMDFLL--CD---------------  219 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~----------~ke~e~l~--~d---------------  219 (343)
                      ...+++|++++|+|+++.++|+||++| +.+|+||++|+++..          ++.+.+.+  .|               
T Consensus       196 ~~~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~k~~~~  274 (565)
T PRK06299        196 LENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGE  274 (565)
T ss_pred             HhcCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEEEeccc
Confidence            356899999999999999999999998 899999999998542          11122111  11               


Q ss_pred             -hhhh-----hhHhhhcceeeeecCCcc-eeccCCCCCCCCce---------------eccceEEEEEEeec-CCCceEE
Q 019315          220 -LKKD-----AEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVV---------------ETGTVLFAEVLGRT-LSGRPLL  276 (343)
Q Consensus       220 -~~k~-----~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~---------------eiGd~v~~eVl~~d-e~G~I~L  276 (343)
                       +|..     ..+..+.|+|+.++++|+ +.++.+++|++|++               .+|+.+.+.|+..+ +++++.|
T Consensus       275 ~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~v~Glv~~sel~~~~~~~~~~~~~~~G~~v~v~V~~id~~~~~i~l  354 (565)
T PRK06299        275 DPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISL  354 (565)
T ss_pred             ChhHHHHhhCCCCCEEEEEEEEEeCCeEEEEeCCCCEEEEEHHHcCccccccCHHHhcCCCCEEEEEEEEEcCCCCEEEE
Confidence             1211     124788999999999999 89988899998854               35677888888876 5689999


Q ss_pred             eHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315          277 STRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR  331 (343)
Q Consensus       277 S~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r  331 (343)
                      |+|++. ..+|.++.+.++.|++|+|+|+++.+.|++|+++ |+.||||.|++++.
T Consensus       355 s~k~~~-~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~  409 (565)
T PRK06299        355 GLKQCK-ENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWD  409 (565)
T ss_pred             ehHHhc-cchhhhHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCcc
Confidence            999987 4899999988999999999999999999999995 89999999999853

>TIGR00717 rpsA ribosomal protein S1

Probab=99.67  E-value=3e-16  Score=159.60  Aligned_cols=163  Identities=15%  Similarity=0.152  Sum_probs=132.4

Q ss_pred             ccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccc----------cchhhh--hhhh-------------
Q 019315          166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYD----------KEMDFL--LCDL-------------  220 (343)
Q Consensus       166 ~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~----------ke~e~l--~~d~-------------  220 (343)
                      ....+++|++|+|+|+++.++|+||++| +.+|+||.+|+++...          +.+.+.  ..|.             
T Consensus       181 ~~~~l~~G~~v~g~V~~i~~~G~~V~l~-g~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~d~~~~~i~lS~k~~~  259 (516)
T TIGR00717       181 LLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLG  259 (516)
T ss_pred             HHHhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEEEECCCCcEEEEEEecc
Confidence            3457899999999999999999999997 5899999999984321          111111  1111             


Q ss_pred             ---hh-----hhhHhhhcceeeeecCCcc-eeccCCCCCCCCce---------------eccceEEEEEEeec-CCCceE
Q 019315          221 ---KK-----DAEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVV---------------ETGTVLFAEVLGRT-LSGRPL  275 (343)
Q Consensus       221 ---~k-----~~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~---------------eiGd~v~~eVl~~d-e~G~I~  275 (343)
                         |.     ...+..++|+|+.+.+.|+ |.++++++|++|++               .+|+.+.+.|+..+ +++++.
T Consensus       260 ~~p~~~~~~~~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~  339 (516)
T TIGR00717       260 EDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLS  339 (516)
T ss_pred             hhHHHHHHhhccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEE
Confidence               11     1124678999999999999 99998999999854               46678888888766 568999


Q ss_pred             EeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCcccc
Q 019315          276 LSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLS  330 (343)
Q Consensus       276 LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~  330 (343)
                      ||+|++. ..+|.++.+.++.|++++|+|+++.+.|++|+++ |++||+|.|++++
T Consensus       340 lS~k~~~-~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~  394 (516)
T TIGR00717       340 LGLKQCK-ANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISW  394 (516)
T ss_pred             EEehhcc-cCcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcC
Confidence            9999987 4899999998999999999999999999999996 8999999999975

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.

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=99.64  E-value=3.8e-16  Score=154.06  Aligned_cols=161  Identities=17%  Similarity=0.192  Sum_probs=129.5

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCccc--------ccchhhhhh--hhh----------------
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLY--------DKEMDFLLC--DLK----------------  221 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~--------~ke~e~l~~--d~~----------------  221 (343)
                      ..+++|++|+|+|+++.++|++|+++ +.+|+||++|+++..        ++.+.+.++  |..                
T Consensus       101 ~~~~~G~~v~g~V~~v~~~G~~V~~~-G~~gflp~~el~~~~~~~~~~~vG~~v~~~Vl~~d~~~~~i~lS~k~~~~~~~  179 (390)
T PRK06676        101 EKFEEGEVVEVKVTEVVKGGLVVDVE-GVRGFIPASLISTRFVEDFSDFKGKTLEVKIIELDPEKNRVILSRRAVVEEER  179 (390)
T ss_pred             HhccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCccCCChHHcCCCEEEEEEEEEECCCCEEEEEeHHHhhhhh
Confidence            34678999999999999999999995 459999999998432        122222221  110                


Q ss_pred             ---------hhhhHhhhcceeeeecCCcc-eeccCCCCCCCCceec--------------cceEEEEEEeec-CCCceEE
Q 019315          222 ---------KDAEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVVET--------------GTVLFAEVLGRT-LSGRPLL  276 (343)
Q Consensus       222 ---------k~~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~ei--------------Gd~v~~eVl~~d-e~G~I~L  276 (343)
                               +...+..++|+|..+++.|+ |.++ +++|++|.+++              |+.+.+.|+..+ ++++|.|
T Consensus       180 ~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~-~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~l  258 (390)
T PRK06676        180 AAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISL  258 (390)
T ss_pred             hhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeC-CeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEE
Confidence                     00124788999999999999 8885 58999987664              678888888875 5689999


Q ss_pred             eHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315          277 STRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR  331 (343)
Q Consensus       277 S~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r  331 (343)
                      |+|++. ..+|+.+.+.++.|++++|+|+++.+.|++|+++ |+.||+|.|++...
T Consensus       259 S~k~~~-~~~~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~  313 (390)
T PRK06676        259 SLKDTL-PGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHK  313 (390)
T ss_pred             EEeecc-cCccccchhhhcCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCcc
Confidence            999887 4799999889999999999999999999999994 89999999999754

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

Probab=99.58  E-value=4.9e-15  Score=155.96  Aligned_cols=165  Identities=19%  Similarity=0.214  Sum_probs=132.7

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccc--------cchhhhh--hhhh--h--------------
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYD--------KEMDFLL--CDLK--K--------------  222 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~--------ke~e~l~--~d~~--k--------------  222 (343)
                      .+++|++++|+|+++.++|++|++|. .+||||.+|+++...        +.+.+.+  .|..  .              
T Consensus       386 ~~~~G~iv~g~V~~v~~~G~~V~lgg-i~gfiP~sel~~~~~~d~~~~vG~~v~v~Vl~vd~e~~~~l~lS~k~~~~~~~  464 (647)
T PRK00087        386 AFENGEPVKGKVKEVVKGGLLVDYGG-VRAFLPASHVELGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEK  464 (647)
T ss_pred             HhhCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHhCccccCCHHHhCCCEEEEEEEEEEcCCCcEEEEEeHHHhhhhh
Confidence            46789999999999999999999986 999999999885421        1121111  1110  0              


Q ss_pred             ----------hhhHhhhcceeeeecCCcc-eeccCCCCCCCCcee--------------ccceEEEEEEeec-CCCceEE
Q 019315          223 ----------DAEEFMVRGKMGIVKDDDA-IAMSGGSGPGRPVVE--------------TGTVLFAEVLGRT-LSGRPLL  276 (343)
Q Consensus       223 ----------~~ee~~VeGkV~~i~~dga-V~Ig~~ieg~i~v~e--------------iGd~v~~eVl~~d-e~G~I~L  276 (343)
                                ...+..+.|+|..++++|+ |.+ ++++|++|+++              +|+.+.+.|+..+ +++++.|
T Consensus       465 ~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~l  543 (647)
T PRK00087        465 EKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSL  543 (647)
T ss_pred             hhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence                      0124688999999999999 888 67899998765              6678888888875 6789999


Q ss_pred             eHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChh
Q 019315          277 STRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFT  336 (343)
Q Consensus       277 S~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nle  336 (343)
                      |+|++. .++|+.+.+.++.|++++|+|+++.+.|++|++ +|+.||+|.|++... ..++.
T Consensus       544 S~K~~~-~~p~~~~~~~~~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~~  604 (647)
T PRK00087        544 SLKKLL-PDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPE  604 (647)
T ss_pred             Eeeccc-cChhhhhhhhccCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCHh
Confidence            999987 589999988899999999999999999999999 589999999999754 44443

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=99.49  E-value=2.3e-14  Score=140.11  Aligned_cols=129  Identities=16%  Similarity=0.112  Sum_probs=105.2

Q ss_pred             CCC-CCCEEEEEEEEEeCCeEEEEeC-C-CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceecc
Q 019315          169 EPK-PGDFVIGVVVSGNENKLDVNVG-A-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS  245 (343)
Q Consensus       169 ~~k-~GdiVeG~VVsI~~~gv~VDIG-~-KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig  245 (343)
                      .|. +|++|.|+|++|.++|+||+|+ | +.+|+||++|+++..                       +..        + 
T Consensus        13 ~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~r-----------------------i~~--------i-   60 (319)
T PTZ00248         13 KFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRR-----------------------IRS--------I-   60 (319)
T ss_pred             hCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccc-----------------------cCC--------H-
Confidence            344 7999999999999999999994 4 799999999999642                       111        1 


Q ss_pred             CCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEec-CeeEEE------E-
Q 019315          246 GGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNT-GGLLTR------I-  316 (343)
Q Consensus       246 ~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nK-GGliVe------I-  316 (343)
                            ..++++|+++.+.|+..+ ++|+|.||+|++.. .+|..+.+.|+.|.+|+++|..+.+ .|+.++      . 
T Consensus        61 ------~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~-~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~  133 (319)
T PTZ00248         61 ------NKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSP-EDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIW  133 (319)
T ss_pred             ------HHhcCCCCEEEEEEEEEeCCCCEEEEEeeeccc-chHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHH
Confidence                  234578888999999865 67999999999995 6999999999999999999999954 899887      3 


Q ss_pred             CCeEEEEeCCccccC-CCChh
Q 019315          317 EGLRAFLPKAELLSR-VNNFT  336 (343)
Q Consensus       317 eGlrgFIP~SQl~~r-v~nle  336 (343)
                      .++++|.+.+++... +.+.+
T Consensus       134 pl~~~~gh~y~af~~~v~~~~  154 (319)
T PTZ00248        134 PLYKKYGHALDALKEALTNPD  154 (319)
T ss_pred             HHHHhcCCHHHHHHHHhcCch
Confidence            578999998887543 44444

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=99.47  E-value=7.8e-13  Score=129.05  Aligned_cols=121  Identities=19%  Similarity=0.149  Sum_probs=97.5

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG  249 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie  249 (343)
                      ++.|++|+|+|++++++|++|+++ +.+||||.+++++...+                                      
T Consensus       116 ~~~~~~V~g~V~~~~~~G~~V~l~-Gv~gfip~s~ls~~~~~--------------------------------------  156 (318)
T PRK07400        116 QKEDATVRSEVFATNRGGALVRIE-GLRGFIPGSHISTRKPK--------------------------------------  156 (318)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCccCCc--------------------------------------
Confidence            456999999999999999999996 79999999999853100                                      


Q ss_pred             CCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEECCeEEEEeCCcc
Q 019315          250 PGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL  328 (343)
Q Consensus       250 g~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl  328 (343)
                         . .-+|..+.+.|+..+ +++++.||+|++...    ...+.++.|++|+|+|+++...|++|++.|+.||||.|++
T Consensus       157 ---~-~~vG~~i~~kVl~id~~~~~i~lS~K~~~~~----~~~~~~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisel  228 (318)
T PRK07400        157 ---E-ELVGEELPLKFLEVDEERNRLVLSHRRALVE----RKMNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEI  228 (318)
T ss_pred             ---c-ccCCCEEEEEEEEEEcccCEEEEEhhHhhhh----hhhccCCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHc
Confidence               0 024566778888776 568999999876642    3345678999999999999999999999999999999999


Q ss_pred             ccC-CCChhh
Q 019315          329 LSR-VNNFTE  337 (343)
Q Consensus       329 ~~r-v~nlee  337 (343)
                      +.. +.++.+
T Consensus       229 s~~~~~~~~~  238 (318)
T PRK07400        229 SHEHIETPHS  238 (318)
T ss_pred             ccccccChhh
Confidence            875 444443

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

Probab=99.06  E-value=3.4e-10  Score=97.53  Aligned_cols=77  Identities=19%  Similarity=0.193  Sum_probs=64.0

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS  248 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i  248 (343)
                      +++.|++++|+|+.|+++||||++..+..|+||++|++..+       +.|+                            
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~f-------VkdI----------------------------   46 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGF-------VKDI----------------------------   46 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhh-------HHhH----------------------------
Confidence            57899999999999999999999988788999999998432       1111                            


Q ss_pred             CCCCCceeccceEEEEEEeecCCCceEEeHHHHHH
Q 019315          249 GPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFR  283 (343)
Q Consensus       249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~  283 (343)
                         -+...+|+++.++|+.++++|+|.||+|.+..
T Consensus        47 ---~d~L~vG~eV~vKVl~ide~GKisLSIr~~~e   78 (129)
T COG1098          47 ---HDHLKVGQEVKVKVLDIDENGKISLSIRKLEE   78 (129)
T ss_pred             ---HHHhcCCCEEEEEEEeeccCCCcceehHHhhh
Confidence               12346788999999999999999999999885

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

Probab=98.94  E-value=6.6e-09  Score=79.20  Aligned_cols=73  Identities=26%  Similarity=0.258  Sum_probs=57.7

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS  248 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i  248 (343)
                      +++.|++++|+|.+++++|+||+++.+.+|+||++|+.+....                          .          
T Consensus         1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~--------------------------~----------   44 (74)
T PF00575_consen    1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRID--------------------------D----------   44 (74)
T ss_dssp             -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEES--------------------------S----------
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCcccc--------------------------c----------
Confidence            3689999999999999999999999999999999999842100                          0          


Q ss_pred             CCCCCceeccceEEEEEEeec-CCCceEEeHH
Q 019315          249 GPGRPVVETGTVLFAEVLGRT-LSGRPLLSTR  279 (343)
Q Consensus       249 eg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~K  279 (343)
                        ......+|+.+.+.|+..+ +.+++.||+|
T Consensus        45 --~~~~~~~G~~v~v~v~~vd~~~~~i~lS~k   74 (74)
T PF00575_consen   45 --PSEVYKIGQTVRVKVIKVDKEKGRIRLSLK   74 (74)
T ss_dssp             --SHGTCETTCEEEEEEEEEETTTTEEEEEST
T ss_pred             --cccccCCCCEEEEEEEEEECCCCeEEEEEC
Confidence              0123467788888998865 6688999975

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 ....

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

Probab=98.88  E-value=6.6e-09  Score=81.95  Aligned_cols=81  Identities=28%  Similarity=0.315  Sum_probs=61.9

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      |.+++|++|+|+|+++.+++++|+++++.+|++|++|+++..   +     +.           .+.        .+   
T Consensus         2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~---~-----~~-----------~~~--------~~---   51 (86)
T cd05789           2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPR---T-----DE-----------DEL--------NM---   51 (86)
T ss_pred             CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCC---C-----cc-----------chH--------HH---
Confidence            457899999999999999999999999999999999997310   0     00           000        01   


Q ss_pred             CCCCCCceeccceEEEEEEeecCCCceEEeHHHHH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLF  282 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~  282 (343)
                          .....+|+.+.+.|+..++++++.||+++..
T Consensus        52 ----~~~l~vGd~i~~~V~~~~~~~~i~LS~~~~~   82 (86)
T cd05789          52 ----RSYLDEGDLIVAEVQSVDSDGSVSLHTRSLK   82 (86)
T ss_pred             ----HhhCCCCCEEEEEEEEECCCCCEEEEeCccc
Confidence                1234778889999998876699999987753

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".

>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=98.86  E-value=9.8e-09  Score=80.20  Aligned_cols=73  Identities=21%  Similarity=0.233  Sum_probs=56.4

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG  249 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie  249 (343)
                      +++|++|+|+|.+++++|+||+++.+.+|++|++|+++...+..                                   .
T Consensus         1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~-----------------------------------~   45 (74)
T cd05705           1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDP-----------------------------------S   45 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccCh-----------------------------------h
Confidence            57899999999999999999999999999999999985420000                                   0


Q ss_pred             CCCCceeccceEEEEEEeec-CCCceEEe
Q 019315          250 PGRPVVETGTVLFAEVLGRT-LSGRPLLS  277 (343)
Q Consensus       250 g~i~v~eiGd~v~~eVl~~d-e~G~I~LS  277 (343)
                      .+...+.+|+.+.+.|+..+ ++++|.||
T Consensus        46 ~~~~~~~~G~~v~~kVl~id~~~~~i~LS   74 (74)
T cd05705          46 LYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             hHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            00134577888889999875 56888886

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.

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

Probab=98.84  E-value=1.5e-08  Score=79.43  Aligned_cols=75  Identities=25%  Similarity=0.332  Sum_probs=59.9

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      |.+++||+|.|+|+++++++++|||+++.+|++|.++++....++                               +   
T Consensus         2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~-------------------------------~---   47 (82)
T cd04454           2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKE-------------------------------I---   47 (82)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHH-------------------------------H---
Confidence            457899999999999999999999999999999999997321000                               0   


Q ss_pred             CCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr  280 (343)
                          .+.+++||.+.+.|+..+.++++.||.+.
T Consensus        48 ----~~~~~~GD~i~~~V~~~~~~~~i~LS~~~   76 (82)
T cd04454          48 ----RKSLQPGDLILAKVISLGDDMNVLLTTAD   76 (82)
T ss_pred             ----HhcCCCCCEEEEEEEEeCCCCCEEEEECC
Confidence                12347788899999987655899999865

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".

>PRK08582 hypothetical protein; Provisional

Probab=98.78  E-value=1.9e-08  Score=87.92  Aligned_cols=82  Identities=18%  Similarity=0.133  Sum_probs=66.9

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS  248 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i  248 (343)
                      .+++|++|+|+|+.|++.|+||+|+.+.+|+||++|+++.+                       +.   +     +    
T Consensus         2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~-----------------------v~---~-----~----   46 (139)
T PRK08582          2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNY-----------------------VK---D-----I----   46 (139)
T ss_pred             CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCccc-----------------------cc---c-----c----
Confidence            47799999999999999999999999999999999998431                       00   0     0    


Q ss_pred             CCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHH
Q 019315          249 GPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHR  289 (343)
Q Consensus       249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~  289 (343)
                         ..+..+|+.+.+.|+.++.+|+|.||++++.. .+|..
T Consensus        47 ---~~~l~vGD~VkvkV~~id~~gkI~LSlk~~~~-~~~~~   83 (139)
T PRK08582         47 ---NDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKD-RPKRQ   83 (139)
T ss_pred             ---ccccCCCCEEEEEEEEECCCCcEEEEEEeccc-Cchhh
Confidence               12357788899999988767999999999974 78864

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

Probab=98.78  E-value=2.9e-08  Score=75.12  Aligned_cols=69  Identities=28%  Similarity=0.277  Sum_probs=54.8

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR  252 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i  252 (343)
                      |++|+|+|+++.+++++|+++.+.+|++|.+|+++...+.                               +       .
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~-------------------------------~-------~   42 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIEN-------------------------------G-------E   42 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCC-------------------------------H-------h
Confidence            8999999999999999999999999999999998431000                               0       1


Q ss_pred             CceeccceEEEEEEeec-CCCceEEeHH
Q 019315          253 PVVETGTVLFAEVLGRT-LSGRPLLSTR  279 (343)
Q Consensus       253 ~v~eiGd~v~~eVl~~d-e~G~I~LS~K  279 (343)
                      ....+|+.+.+.|+..+ +++++.||+|
T Consensus        43 ~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687          43 DEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             HcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            22467788888888765 6689999974

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=98.71  E-value=6.8e-08  Score=73.61  Aligned_cols=36  Identities=25%  Similarity=0.499  Sum_probs=33.4

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       171 k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      +.|++|+|+|++++++++|||+|+ ++|+||.+|+++
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~~   37 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQIP   37 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCCC
Confidence            469999999999999999999986 999999999973

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.

>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=98.64  E-value=1.2e-07  Score=74.25  Aligned_cols=69  Identities=17%  Similarity=0.138  Sum_probs=55.5

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeC-CCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNVG-ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS  248 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDIG-~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i  248 (343)
                      ++.|++|.|+|.+|+++|++||+| .+.+||||.+|+++.                                        
T Consensus         2 l~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~----------------------------------------   41 (74)
T cd05694           2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF----------------------------------------   41 (74)
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc----------------------------------------
Confidence            678999999999999999999998 478999999999731                                        


Q ss_pred             CCCCCceeccceEEEEEEeec-CCCceEEeHHHHH
Q 019315          249 GPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLF  282 (343)
Q Consensus       249 eg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~  282 (343)
                          ....+|+.+.+.|+..+ +++++.||.|++.
T Consensus        42 ----~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~~   72 (74)
T cd05694          42 ----SKLKVGQLLLCVVEKVKDDGRVVSLSADPSK   72 (74)
T ss_pred             ----cccCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence                01245667778888765 6678999988754

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.

>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=98.63  E-value=1.3e-07  Score=74.26  Aligned_cols=77  Identities=22%  Similarity=0.141  Sum_probs=59.7

Q ss_pred             hcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCccee
Q 019315          164 SVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA  243 (343)
Q Consensus       164 e~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~  243 (343)
                      ...+..++.|+++.|+|+++.++|+||+++.+.+|++|++|+++.+.                       .   +     
T Consensus         6 ~~~~~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~-----------------------~---~-----   54 (83)
T cd04461           6 PTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFV-----------------------T---D-----   54 (83)
T ss_pred             hhhHHhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccc-----------------------c---C-----
Confidence            34456789999999999999999999999888999999999974310                       0   0     


Q ss_pred             ccCCCCCCCCceeccceEEEEEEeec-CCCceEEeH
Q 019315          244 MSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLST  278 (343)
Q Consensus       244 Ig~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~  278 (343)
                      +       .....+|+.+.+.|+..+ +.+++.||.
T Consensus        55 ~-------~~~~~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461          55 P-------SFGFKKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             H-------HHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence            0       123467788888888765 568999883

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

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

Probab=98.57  E-value=2.2e-07  Score=72.23  Aligned_cols=71  Identities=20%  Similarity=0.188  Sum_probs=55.2

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR  252 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i  252 (343)
                      |++|+|+|+++.++|+||.++.+.+|+||++++++.. ...+    +                               ..
T Consensus         1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~-~~~~----~-------------------------------~~   44 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDV-SVLE----H-------------------------------PE   44 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCcc-cccc----C-------------------------------HH
Confidence            8999999999999999999999999999999997421 0000    0                               01


Q ss_pred             CceeccceEEEEEEeec-CCCceEEeHH
Q 019315          253 PVVETGTVLFAEVLGRT-LSGRPLLSTR  279 (343)
Q Consensus       253 ~v~eiGd~v~~eVl~~d-e~G~I~LS~K  279 (343)
                      ....+|+.+.+.|+..+ ++.+|.||+|
T Consensus        45 ~~~~vG~~v~~kV~~id~~~~~i~Ls~k   72 (73)
T cd05703          45 KKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             HhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            23467888999999876 6689999974

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.

>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=98.56  E-value=2.8e-07  Score=69.63  Aligned_cols=69  Identities=23%  Similarity=0.191  Sum_probs=53.8

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR  252 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i  252 (343)
                      |++++|+|+++.++|+||+++.+.+|++|++++++.+.       .+                        .       .
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~-------~~------------------------~-------~   42 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFI-------KD------------------------P-------E   42 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhc-------CC------------------------H-------H
Confidence            89999999999999999999888999999999973210       00                        0       1


Q ss_pred             CceeccceEEEEEEeec-CCCceEEeHH
Q 019315          253 PVVETGTVLFAEVLGRT-LSGRPLLSTR  279 (343)
Q Consensus       253 ~v~eiGd~v~~eVl~~d-e~G~I~LS~K  279 (343)
                      ....+|+.+.+.|+..+ +++++.||+|
T Consensus        43 ~~~~~G~~i~v~v~~~d~~~~~i~ls~k   70 (70)
T cd05698          43 EHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             HcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            12466788888888865 5689999964

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.

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

Probab=98.56  E-value=2.7e-07  Score=71.31  Aligned_cols=71  Identities=18%  Similarity=0.202  Sum_probs=55.8

Q ss_pred             CCCCCEEEEEEEEEeC-CeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315          170 PKPGDFVIGVVVSGNE-NKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS  248 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~-~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i  248 (343)
                      +++|++|.|+|+++.+ .|++|+++.+.+|++|++++++.+.+.                               +    
T Consensus         1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~-------------------------------~----   45 (72)
T cd05704           1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTEN-------------------------------P----   45 (72)
T ss_pred             CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCC-------------------------------H----
Confidence            4689999999999986 799999999999999999998532100                               0    


Q ss_pred             CCCCCceeccceEEEEEEeecCCCceEEeHH
Q 019315          249 GPGRPVVETGTVLFAEVLGRTLSGRPLLSTR  279 (343)
Q Consensus       249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS~K  279 (343)
                         .+++.+|+.+.++|++.+. +++.||+|
T Consensus        46 ---~~~~~~Gd~v~~kV~~~~~-~~i~LSl~   72 (72)
T cd05704          46 ---LEGFKPGKIVRCCILSKKD-GKYQLSLR   72 (72)
T ss_pred             ---HHhCCCCCEEEEEEEEecC-CEEEEEeC
Confidence               1234677888899988755 89999974

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=98.54  E-value=6.6e-07  Score=69.04  Aligned_cols=71  Identities=25%  Similarity=0.324  Sum_probs=54.3

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEe-CCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNV-GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS  248 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDI-G~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i  248 (343)
                      ++.|++++|+|+++.++|+||++ |.+.+|++|++|+++..   +.                       .     .    
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~---~~-----------------------~-----~----   45 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCR---VD-----------------------D-----P----   45 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCc---cc-----------------------C-----H----
Confidence            35799999999999999999999 43479999999998431   00                       0     0    


Q ss_pred             CCCCCceeccceEEEEEEeecCCCceEEeH
Q 019315          249 GPGRPVVETGTVLFAEVLGRTLSGRPLLST  278 (343)
Q Consensus       249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS~  278 (343)
                         ..+..+|+.+.+.|+..+.++++.||+
T Consensus        46 ---~~~~~~Gd~v~vkv~~vd~~~ki~ls~   72 (73)
T cd05686          46 ---SEVVDVGEKVWVKVIGREMKDKMKLSL   72 (73)
T ss_pred             ---hhEECCCCEEEEEEEEECCCCcEEEEe
Confidence               123467888889998877666899985

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.

>PRK07252 hypothetical protein; Provisional

Probab=98.49  E-value=3.2e-07  Score=78.42  Aligned_cols=80  Identities=18%  Similarity=0.254  Sum_probs=64.2

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCC
Q 019315          171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGP  250 (343)
Q Consensus       171 k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg  250 (343)
                      ++|+++.|+|++|.++|+||+++.+.+|++|++++++..                       +.   .     +      
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~-----------------------~~---~-----~------   44 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGF-----------------------ID---N-----I------   44 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCcc-----------------------cc---C-----h------
Confidence            579999999999999999999988899999999997421                       00   0     0      


Q ss_pred             CCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHH
Q 019315          251 GRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWH  288 (343)
Q Consensus       251 ~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe  288 (343)
                       .....+|+.+.+.|+..+ +.+++.||.+++....+|.
T Consensus        45 -~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~~~~~~~~   82 (120)
T PRK07252         45 -HQLLKVGEEVLVQVVDFDEYTGKASLSLRTLEEEKQHF   82 (120)
T ss_pred             -hhccCCCCEEEEEEEEEeCCCCEEEEEEeecccCcccc
Confidence             123467888888998876 5799999999998877775

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=98.48  E-value=3e-07  Score=100.47  Aligned_cols=94  Identities=18%  Similarity=0.082  Sum_probs=74.0

Q ss_pred             hhcccCCCCCCCEEE-EEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcc
Q 019315          163 VSVEYYEPKPGDFVI-GVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDA  241 (343)
Q Consensus       163 Le~~~~~~k~GdiVe-G~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dga  241 (343)
                      ++..+..++.|++++ |+|++|.++|+||+|..+.+|+||++|+++.+.                       .+      
T Consensus       744 I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv-----------------------~~------  794 (891)
T PLN00207        744 ISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWL-----------------------AK------  794 (891)
T ss_pred             HHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccc-----------------------cC------
Confidence            344445688999995 699999999999999888999999999985320                       00      


Q ss_pred             eeccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhh
Q 019315          242 IAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQ  295 (343)
Q Consensus       242 V~Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e  295 (343)
                        +       ..++++|+.+.++|++.+..|+|.||+|++. .+||++.....+
T Consensus       795 --~-------~dv~kvGD~V~VkVi~ID~~grI~LSlK~l~-~~Pw~~~~~~~~  838 (891)
T PLN00207        795 --P-------EDAFKVGDRIDVKLIEVNDKGQLRLSRRALL-PEANSEKSSQKQ  838 (891)
T ss_pred             --H-------HHhcCCCCEEEEEEEEECCCCcEEEEEeccc-cCchhhhhhhhh
Confidence              0       1235778889999998887899999999986 589998876543

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

Probab=98.47  E-value=2.9e-07  Score=69.44  Aligned_cols=45  Identities=44%  Similarity=0.635  Sum_probs=39.0

Q ss_pred             CCcEEEEEEEEecCeeEEEECCeEEEEeCCccccC-CCChhhhccc
Q 019315          297 NEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR-VNNFTELKEK  341 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~r-v~nleel~g~  341 (343)
                      |++|+|+|++++++|++|+++|++||||.||++.+ .+++.+++|+
T Consensus         1 G~iv~g~V~~v~~~G~~v~l~g~~gfip~s~~~~~~~~~~~~~vG~   46 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEYVGK   46 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCChHHhCCC
Confidence            68999999999999999999999999999999865 5566666554

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

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

Probab=98.47  E-value=9.4e-07  Score=67.35  Aligned_cols=72  Identities=24%  Similarity=0.284  Sum_probs=56.3

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG  249 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie  249 (343)
                      +++|++|.|+|.++.+++++|+++.+.+|++|.+++++.+..                          .     .     
T Consensus         1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~--------------------------~-----~-----   44 (73)
T cd05706           1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSE--------------------------A-----L-----   44 (73)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCcccc--------------------------c-----c-----
Confidence            368999999999999999999999899999999999743100                          0     0     


Q ss_pred             CCCCceeccceEEEEEEeec-CCCceEEeHH
Q 019315          250 PGRPVVETGTVLFAEVLGRT-LSGRPLLSTR  279 (343)
Q Consensus       250 g~i~v~eiGd~v~~eVl~~d-e~G~I~LS~K  279 (343)
                        .....+|+.+.+.|+..+ .++++.||+|
T Consensus        45 --~~~~~~Gd~v~~~V~~~d~~~~~i~ls~~   73 (73)
T cd05706          45 --PYKFKKNDIVRACVLSVDVPNKKIALSLR   73 (73)
T ss_pred             --ccccCCCCEEEEEEEEEeCCCCEEEEEEC
Confidence              123467888889998765 4688999863

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.

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

Probab=98.46  E-value=5.3e-07  Score=68.07  Aligned_cols=71  Identities=18%  Similarity=0.184  Sum_probs=55.4

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR  252 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i  252 (343)
                      |++|.|+|+++.+++++|+++.+.+|++|.+++++.+..                          +     +       .
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~--------------------------~-----~-------~   42 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVE--------------------------D-----A-------T   42 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCcccc--------------------------C-----H-------H
Confidence            799999999999999999999899999999999843100                          0     0       1


Q ss_pred             CceeccceEEEEEEeec-CCCceEEeHHHH
Q 019315          253 PVVETGTVLFAEVLGRT-LSGRPLLSTRRL  281 (343)
Q Consensus       253 ~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl  281 (343)
                      ....+|+.+.+.|+..+ .++++.||+|++
T Consensus        43 ~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~~   72 (73)
T cd05691          43 ERFKVGDEVEAKITNVDRKNRKISLSIKAK   72 (73)
T ss_pred             HccCCCCEEEEEEEEEeCCCCEEEEEEEEc
Confidence            22467788888888766 458899998764

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.

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

Probab=98.43  E-value=1.1e-06  Score=67.09  Aligned_cols=73  Identities=23%  Similarity=0.271  Sum_probs=55.3

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCC--CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNVGA--DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDIG~--KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      ++.|+++.|+|+++.++|+||++..  +.+|++|.+|+++.+..                          .     +   
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~--------------------------~-----~---   46 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIR--------------------------S-----I---   46 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccC--------------------------C-----H---
Confidence            4689999999999999999999963  48999999999743100                          0     0   


Q ss_pred             CCCCCCceeccceEEEEEEeec-CCCceEEeHHH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRR  280 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Kr  280 (343)
                          .....+|+.+.+.|+..+ ..+++.||+|+
T Consensus        47 ----~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k~   76 (76)
T cd04452          47 ----RKLVKVGRKEVVKVIRVDKEKGYIDLSKKR   76 (76)
T ss_pred             ----HHeeCCCCEEEEEEEEEECCCCEEEEEEcC
Confidence                122366778888888765 56889999764

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c

>PRK05807 hypothetical protein; Provisional

Probab=98.42  E-value=1.1e-06  Score=76.56  Aligned_cols=75  Identities=21%  Similarity=0.213  Sum_probs=59.7

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS  248 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i  248 (343)
                      ++++|++|+|+|+.|+++|+||++ .+.+|+||++|+++.+                       +..        +    
T Consensus         2 ~~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~-----------------------v~~--------~----   45 (136)
T PRK05807          2 TLKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTY-----------------------VKD--------I----   45 (136)
T ss_pred             CccCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhccccc-----------------------ccC--------c----
Confidence            367899999999999999999999 4679999999997431                       110        0    


Q ss_pred             CCCCCceeccceEEEEEEeecCCCceEEeHHHHH
Q 019315          249 GPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLF  282 (343)
Q Consensus       249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~  282 (343)
                         .....+|+.+.+.|+..+.+|+|.||+|++.
T Consensus        46 ---~~~~kvGd~V~VkV~~id~~gkI~LSlk~~~   76 (136)
T PRK05807         46 ---REHLKEQDKVKVKVISIDDNGKISLSIKQAM   76 (136)
T ss_pred             ---cccCCCCCEEEEEEEEECCCCcEEEEEEecc
Confidence               1224678888899988777899999998876

>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=98.41  E-value=1.4e-06  Score=66.00  Aligned_cols=68  Identities=16%  Similarity=0.152  Sum_probs=53.2

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR  252 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i  252 (343)
                      |++++|+|+++.++|++|+++.+.+|++|++++++.+...                               .       .
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~-------------------------------~-------~   42 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKH-------------------------------P-------E   42 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccC-------------------------------H-------H
Confidence            7999999999999999999988899999999997431000                               0       1


Q ss_pred             CceeccceEEEEEEeec-CCCceEEeH
Q 019315          253 PVVETGTVLFAEVLGRT-LSGRPLLST  278 (343)
Q Consensus       253 ~v~eiGd~v~~eVl~~d-e~G~I~LS~  278 (343)
                      ....+|+.+.+.|+..+ +++++.||+
T Consensus        43 ~~~~~Gd~i~~~V~~id~~~~~i~ls~   69 (69)
T cd05697          43 KKFKPGLKVKCRVLSVEPERKRLVLTL   69 (69)
T ss_pred             HcCCCCCEEEEEEEEEECCCCEEEEEC
Confidence            12467788888998876 568898883

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.

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

Probab=98.39  E-value=1.8e-06  Score=65.14  Aligned_cols=66  Identities=20%  Similarity=0.160  Sum_probs=50.9

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR  252 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i  252 (343)
                      |++|+|+|+++.++|++|++ .+.+||||.+++++....       +                        .        
T Consensus         1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~-------~------------------------~--------   40 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVE-------D------------------------L--------   40 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccC-------C------------------------h--------
Confidence            79999999999999999999 579999999999743100       0                        0        


Q ss_pred             CceeccceEEEEEEeec-CCCceEEeHH
Q 019315          253 PVVETGTVLFAEVLGRT-LSGRPLLSTR  279 (343)
Q Consensus       253 ~v~eiGd~v~~eVl~~d-e~G~I~LS~K  279 (343)
                       ...+|+.+.+.|+..+ +++++.||+|
T Consensus        41 -~~~vG~~i~~~i~~vd~~~~~i~lS~k   67 (67)
T cd04465          41 -DEYVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             -HHhCCCEEEEEEEEEeCCCCEEEEEcC
Confidence             0125677788888766 5789999974

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.

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

Probab=98.35  E-value=1.8e-06  Score=65.16  Aligned_cols=67  Identities=22%  Similarity=0.292  Sum_probs=52.0

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR  252 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i  252 (343)
                      |++|.|+|+++.++|+||+++.+.+|++|++++++.+.+                          .     .       .
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~--------------------------~-----~-------~   42 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLK--------------------------D-----W-------K   42 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhc--------------------------C-----H-------h
Confidence            799999999999999999999889999999999743100                          0     0       1


Q ss_pred             CceeccceEEEEEEeec-CCCceEEe
Q 019315          253 PVVETGTVLFAEVLGRT-LSGRPLLS  277 (343)
Q Consensus       253 ~v~eiGd~v~~eVl~~d-e~G~I~LS  277 (343)
                      ....+|+.+.+.|+..+ +.+++.||
T Consensus        43 ~~~~~Gd~v~~~v~~~d~~~~~i~ls   68 (68)
T cd05707          43 KRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             hccCCCCEEEEEEEEEeCCCCEEecC
Confidence            22366788888888765 46888886

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.

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

Probab=98.35  E-value=1.5e-06  Score=83.42  Aligned_cols=87  Identities=20%  Similarity=0.252  Sum_probs=66.5

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCC--CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNVGA--DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDIG~--KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      -+++|++|.|+|++|.++|+||++..  +.+|+||++|+++..                       +..        +  
T Consensus         5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~-----------------------i~~--------i--   51 (262)
T PRK03987          5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGW-----------------------VKN--------I--   51 (262)
T ss_pred             CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCccc-----------------------ccC--------H--
Confidence            36789999999999999999999964  699999999997431                       000        1  


Q ss_pred             CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQI  293 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa  293 (343)
                           .....+|+.+.+.|+..+ ..++|.||+|++.....|+.+.+.
T Consensus        52 -----~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~v~~~e~~~~~~~~   94 (262)
T PRK03987         52 -----RDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNEHQRREKIQEW   94 (262)
T ss_pred             -----HHhCCCCCEEEEEEEEEecccCeEEEEEEecccchHHHHHHHH
Confidence                 123467888889998876 568999999987766666655543

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

Probab=98.31  E-value=3.4e-06  Score=62.12  Aligned_cols=69  Identities=25%  Similarity=0.288  Sum_probs=52.5

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR  252 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i  252 (343)
                      |+++.|+|+++.++|+||+++.+.+|++|.+|+++.+..       +                        .       .
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~-------~------------------------~-------~   42 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVK-------D------------------------V-------K   42 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccC-------C------------------------H-------H
Confidence            799999999999999999999889999999999742100       0                        0       0


Q ss_pred             CceeccceEEEEEEeecCCCceEEeHH
Q 019315          253 PVVETGTVLFAEVLGRTLSGRPLLSTR  279 (343)
Q Consensus       253 ~v~eiGd~v~~eVl~~de~G~I~LS~K  279 (343)
                      ....+|+.+.+.++..+.++++.||.|
T Consensus        43 ~~~~~Gd~v~v~v~~~~~~~~i~ls~k   69 (69)
T cd05692          43 DVLKEGDKVKVKVLSIDARGRISLSIK   69 (69)
T ss_pred             HccCCCCEEEEEEEEECCCCcEEEEEC
Confidence            123567777788877655788999864

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.

>PRK08059 general stress protein 13; Validated

Probab=98.31  E-value=2e-06  Score=73.36  Aligned_cols=78  Identities=19%  Similarity=0.187  Sum_probs=61.1

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      .++++|++|.|+|+++.+.|++|+++.+.+|++|.+++++..                       +.   +     +   
T Consensus         3 ~~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~-----------------------~~---~-----~---   48 (123)
T PRK08059          3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGF-----------------------VK---D-----I---   48 (123)
T ss_pred             ccCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCccc-----------------------cc---C-----H---
Confidence            358899999999999999999999999999999999997421                       00   0     0   


Q ss_pred             CCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFR  283 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~  283 (343)
                          .....+|+.+.+.|+..+ +++++.||++++..
T Consensus        49 ----~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~   81 (123)
T PRK08059         49 ----HDFLSVGDEVKVKVLSVDEEKGKISLSIRATEE   81 (123)
T ss_pred             ----HHcCCCCCEEEEEEEEEECCCCeEEEEEEEccc
Confidence                112466788888888764 67899999888763

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

Probab=98.28  E-value=4.4e-06  Score=64.42  Aligned_cols=68  Identities=19%  Similarity=0.105  Sum_probs=52.9

Q ss_pred             CCEEE-EEEEEE-eCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCC
Q 019315          173 GDFVI-GVVVSG-NENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGP  250 (343)
Q Consensus       173 GdiVe-G~VVsI-~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg  250 (343)
                      |++++ |+|+++ .++|+||++..+.+|+||.+++++.+.                       ..               
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~-----------------------~~---------------   42 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKV-----------------------PS---------------   42 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchh-----------------------cC---------------
Confidence            78999 999999 699999999878999999999974210                       00               


Q ss_pred             CCCceeccceEEEEEEeec-CCCceEEeH
Q 019315          251 GRPVVETGTVLFAEVLGRT-LSGRPLLST  278 (343)
Q Consensus       251 ~i~v~eiGd~v~~eVl~~d-e~G~I~LS~  278 (343)
                      ......+|+.+.+.|+..+ .++++.||.
T Consensus        43 ~~~~~~vG~~v~~kV~~id~~~~~i~lS~   71 (71)
T cd05696          43 DTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             cccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            0123477888999999875 678999983

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=98.27  E-value=4e-06  Score=63.74  Aligned_cols=72  Identities=18%  Similarity=0.165  Sum_probs=55.3

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315          171 KPGDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG  249 (343)
Q Consensus       171 k~GdiVeG~VVsI~~~gv~VDIG~-KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie  249 (343)
                      ++|++++|+|++++++|+||++.. +.+|++|.+++++.+..       +                        .     
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~-------~------------------------~-----   44 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVA-------D------------------------A-----   44 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccC-------C------------------------H-----
Confidence            469999999999999999999974 79999999999743100       0                        0     


Q ss_pred             CCCCceeccceEEEEEEeec-CCCceEEeHHH
Q 019315          250 PGRPVVETGTVLFAEVLGRT-LSGRPLLSTRR  280 (343)
Q Consensus       250 g~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Kr  280 (343)
                        .....+|+.+.+.|+..+ +.+++.||+|+
T Consensus        45 --~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~   74 (77)
T cd05708          45 --SKLFRVGDKVRAKVLKIDAEKKRISLGLKA   74 (77)
T ss_pred             --hHeecCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence              123467788888888765 57899999765

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.

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

Probab=98.25  E-value=6.2e-06  Score=60.24  Aligned_cols=71  Identities=25%  Similarity=0.271  Sum_probs=54.0

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCC
Q 019315          171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGP  250 (343)
Q Consensus       171 k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg  250 (343)
                      ++|++++|+|+++++++++|+++.+..|++|.+++.+....+                               .      
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~-------------------------------~------   43 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKD-------------------------------P------   43 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCC-------------------------------H------
Confidence            369999999999999999999998899999999997431000                               0      


Q ss_pred             CCCceeccceEEEEEEeec-CCCceEEeHH
Q 019315          251 GRPVVETGTVLFAEVLGRT-LSGRPLLSTR  279 (343)
Q Consensus       251 ~i~v~eiGd~v~~eVl~~d-e~G~I~LS~K  279 (343)
                       .....+|+.+.+.|+..+ .++++.||.+
T Consensus        44 -~~~~~~G~~v~~~V~~~~~~~~~i~ls~~   72 (72)
T smart00316       44 -EEVLKVGDEVKVKVLSVDEEKGRIILSLK   72 (72)
T ss_pred             -HHeecCCCEEEEEEEEEeCCCCEEEEEeC
Confidence             112466777888888765 4488998863

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

Probab=98.22  E-value=7.7e-06  Score=62.29  Aligned_cols=65  Identities=20%  Similarity=0.086  Sum_probs=51.1

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR  252 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i  252 (343)
                      |++|+|+|+++.++|++|++....+|++|.++++....                           .             .
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~---------------------------~-------------~   40 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKS---------------------------S-------------K   40 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccC---------------------------c-------------c
Confidence            89999999999999999999667999999999863200                           0             1


Q ss_pred             CceeccceEEEEEEeec-CCCceEEe
Q 019315          253 PVVETGTVLFAEVLGRT-LSGRPLLS  277 (343)
Q Consensus       253 ~v~eiGd~v~~eVl~~d-e~G~I~LS  277 (343)
                      ....+|+++.+.|+..+ ++++|.||
T Consensus        41 ~~~~~G~~i~~kVi~id~~~~~i~LS   66 (66)
T cd05695          41 STYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             cCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            23467788889998765 56788887

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.

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

Probab=98.17  E-value=9.8e-06  Score=65.51  Aligned_cols=40  Identities=25%  Similarity=0.344  Sum_probs=36.8

Q ss_pred             CCCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEeccccCc
Q 019315          168 YEPKPGDFVIGVVVSGNEN--KLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~--gv~VDIG~KsEG~IPisEls~  207 (343)
                      .+++.|+++.|+|++|.+.  |+||+++.+.+||||++|+++
T Consensus         3 ~~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~   44 (88)
T cd04453           3 REPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILP   44 (88)
T ss_pred             CcCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCc
Confidence            4578999999999999996  999999988999999999975

RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.13  E-value=8.7e-06  Score=87.56  Aligned_cols=75  Identities=17%  Similarity=0.135  Sum_probs=58.5

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS  248 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i  248 (343)
                      .++.|++++|+|++|.++|+||+|+.+.+|++|++|+++..     |              ..+|..             
T Consensus       644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls-----~--------------~~rv~~-------------  691 (719)
T TIGR02696       644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLA-----G--------------GKRVEN-------------  691 (719)
T ss_pred             cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccc-----c--------------ccCcCC-------------
Confidence            47899999999999999999999988899999999996210     0              001111             


Q ss_pred             CCCCCceeccceEEEEEEeecCCCceEEe
Q 019315          249 GPGRPVVETGTVLFAEVLGRTLSGRPLLS  277 (343)
Q Consensus       249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS  277 (343)
                        ...++++|+++.++|++++++|++.||
T Consensus       692 --~~dv~kvGd~V~VKVl~ID~~gKI~L~  718 (719)
T TIGR02696       692 --VEDVLSVGQKIQVEIADIDDRGKLSLV  718 (719)
T ss_pred             --HHHcCCCCCEEEEEEEEECCCCCeeec
Confidence              123457889999999998888999986

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.

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

Probab=98.11  E-value=1.4e-05  Score=59.90  Aligned_cols=68  Identities=18%  Similarity=0.146  Sum_probs=51.5

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR  252 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i  252 (343)
                      |+++.|+|+++.++|+||++..+.+|++|.+++++..  ..                       ..     .       .
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~--~~-----------------------~~-----~-------~   43 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQ--RV-----------------------RH-----P-------S   43 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCcc--cc-----------------------CC-----h-------h
Confidence            7899999999999999999988999999999997320  00                       00     0       1


Q ss_pred             CceeccceEEEEEEeec-CCCceEEe
Q 019315          253 PVVETGTVLFAEVLGRT-LSGRPLLS  277 (343)
Q Consensus       253 ~v~eiGd~v~~eVl~~d-e~G~I~LS  277 (343)
                      ....+|+.+.+.|+..+ +.+++.||
T Consensus        44 ~~~~~G~~v~v~v~~id~~~~~i~l~   69 (69)
T cd05690          44 EIYKKGQEVEAVVLNIDVERERISLG   69 (69)
T ss_pred             hEECCCCEEEEEEEEEECCcCEEeCC
Confidence            23467788888888765 55778775

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.

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

Probab=98.11  E-value=1.7e-05  Score=58.61  Aligned_cols=67  Identities=25%  Similarity=0.166  Sum_probs=50.6

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCC
Q 019315          172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPG  251 (343)
Q Consensus       172 ~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~  251 (343)
                      +|++++|+|+++++++++|+++ ..+|++|.+|+++.+..                          .     .       
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~~~~--------------------------~-----~-------   41 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVK--------------------------H-----P-------   41 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCcccc--------------------------C-----H-------
Confidence            4899999999999999999998 69999999999732100                          0     0       


Q ss_pred             CCceeccceEEEEEEeec-CCCceEEe
Q 019315          252 RPVVETGTVLFAEVLGRT-LSGRPLLS  277 (343)
Q Consensus       252 i~v~eiGd~v~~eVl~~d-e~G~I~LS  277 (343)
                      ....++|+.+.+.++..+ .++++.||
T Consensus        42 ~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05688          42 SEVVNVGDEVEVKVLKIDKERKRISLG   68 (68)
T ss_pred             hHEECCCCEEEEEEEEEECCCCEEecC
Confidence            122467778888888765 56788876

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.

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

Probab=98.10  E-value=1.1e-05  Score=62.78  Aligned_cols=72  Identities=19%  Similarity=0.116  Sum_probs=55.7

Q ss_pred             CCEEEEEEEEEeCCeEEEEeC---CCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315          173 GDFVIGVVVSGNENKLDVNVG---ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG  249 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG---~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie  249 (343)
                      |++++|+|+++.++|+||+++   .+.+|++|.+++.+..                       .  +..     .     
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~-----------------------~--~~~-----~-----   45 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEG-----------------------R--VAN-----P-----   45 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCC-----------------------C--cCC-----h-----
Confidence            789999999999999999997   3689999999997431                       0  000     0     


Q ss_pred             CCCCceeccceEEEEEEeecCCCceEEeHHHHH
Q 019315          250 PGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLF  282 (343)
Q Consensus       250 g~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~  282 (343)
                        .....+|+.+.+.++..+ .+++.||+|+++
T Consensus        46 --~~~~~~Gd~v~v~v~~vd-~~~i~~s~k~~~   75 (79)
T cd05684          46 --SDVVKRGQKVKVKVISIQ-NGKISLSMKDVD   75 (79)
T ss_pred             --hheeCCCCEEEEEEEEEe-CCEEEEEEEecc
Confidence              123467788888888877 899999988765

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

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

Probab=98.08  E-value=2.1e-05  Score=58.29  Aligned_cols=68  Identities=21%  Similarity=0.138  Sum_probs=52.3

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR  252 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i  252 (343)
                      |+++.|+|+++.++|+||+++.+.+|++|.+++.+..                       +..        .       .
T Consensus         1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~-----------------------~~~--------~-------~   42 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDER-----------------------VEK--------V-------E   42 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCcc-----------------------ccC--------H-------H
Confidence            7899999999999999999998899999999997421                       000        0       0


Q ss_pred             CceeccceEEEEEEeecCCCceEEeH
Q 019315          253 PVVETGTVLFAEVLGRTLSGRPLLST  278 (343)
Q Consensus       253 ~v~eiGd~v~~eVl~~de~G~I~LS~  278 (343)
                      ....+|+.+.+.|+..+.++++.||+
T Consensus        43 ~~~~~Gd~v~v~v~~~d~~~~i~ls~   68 (68)
T cd04472          43 DVLKVGDEVKVKVIEVDDRGRISLSR   68 (68)
T ss_pred             HccCCCCEEEEEEEEECCCCcEEeeC
Confidence            12366777888888766678898884

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.

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

Probab=98.07  E-value=1.8e-05  Score=58.21  Aligned_cols=35  Identities=20%  Similarity=0.228  Sum_probs=33.1

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      |+++.|+|+++.++|+||+++.+.+|++|.+++.+
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~   35 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMAD   35 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCC
Confidence            78999999999999999999999999999999973

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

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

Probab=98.05  E-value=1e-05  Score=66.98  Aligned_cols=92  Identities=15%  Similarity=0.121  Sum_probs=59.8

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG  249 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie  249 (343)
                      +++|++|.|+|.+|.+.+++|++..+.+|++|++|+++.+.....   ..+.+.  ++   ++.     + .     ...
T Consensus         1 L~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~---~~~~~~--~~---~~~-----~-~-----~~~   61 (100)
T cd05693           1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLE---ELDEES--EE---EDD-----E-E-----ELP   61 (100)
T ss_pred             CCCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHH---Hhhhhc--cc---ccc-----c-c-----ccC
Confidence            468999999999999999999998899999999999843100000   000000  00   000     0 0     000


Q ss_pred             CCCCceeccceEEEEEEeecC----CCceEEeHHH
Q 019315          250 PGRPVVETGTVLFAEVLGRTL----SGRPLLSTRR  280 (343)
Q Consensus       250 g~i~v~eiGd~v~~eVl~~de----~G~I~LS~Kr  280 (343)
                      .....+.+|+.+.+.|+..+.    +++|.||+|-
T Consensus        62 ~~~~~f~vGd~V~~kVi~~d~~~~~~~~i~LSlr~   96 (100)
T cd05693          62 DLEDLFSVGQLVRCKVVSLDKSKSGKKRIELSLEP   96 (100)
T ss_pred             CHHHhccCCCEEEEEEEEccCCcCCCcEEEEEecH
Confidence            112345788899999997654    5799999864

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.

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

Probab=98.03  E-value=1e-05  Score=77.74  Aligned_cols=87  Identities=23%  Similarity=0.315  Sum_probs=64.3

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEe-CC-CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNV-GA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDI-G~-KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      -++.|++|-|+|.+|.+.|+||.+ .| +.+||||++|++.                       |.|.+|+         
T Consensus         8 ~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas-----------------------~wVknIr---------   55 (269)
T COG1093           8 YPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVAS-----------------------GWVKNIR---------   55 (269)
T ss_pred             CCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHH-----------------------HHHHHHH---------
Confidence            367899999999999999999999 33 4899999999972                       3333332         


Q ss_pred             CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHH------HHHHHHHHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFR------KMAWHRVRQI  293 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~------~~aWe~l~qa  293 (343)
                            ..++.|..+.++||..| +.|.|-||+||...      ...|.+-..+
T Consensus        56 ------d~vkegqkvV~kVlrVd~~rg~IDLSlkrV~~~q~~~k~~~wk~~qka  103 (269)
T COG1093          56 ------DYVKEGQKVVAKVLRVDPKRGHIDLSLKRVTEHQRRKKIQEWKKEQKA  103 (269)
T ss_pred             ------HHhhcCCeEEEEEEEEcCCCCeEeeehhhCCHHHHHHHHHHHHHHHHH
Confidence                  23456677888999865 66999999988542      2346555444

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

Probab=98.01  E-value=4.6e-05  Score=57.87  Aligned_cols=38  Identities=16%  Similarity=0.065  Sum_probs=35.1

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      +.+|++++|+|++|.+.|+||.+....+|++|.+++.+
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~   38 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDW   38 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccC
Confidence            46899999999999999999999888999999999963

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.94  E-value=2.9e-05  Score=83.44  Aligned_cols=76  Identities=22%  Similarity=0.193  Sum_probs=61.7

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      ..+++|++++|+|++|.++|+||+|+.+.+|++|++++++.+                       +..        +   
T Consensus       617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~-----------------------v~~--------~---  662 (693)
T PRK11824        617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADER-----------------------VEK--------V---  662 (693)
T ss_pred             ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCcc-----------------------ccC--------c---
Confidence            467899999999999999999999988899999999997431                       100        0   


Q ss_pred             CCCCCCceeccceEEEEEEeecCCCceEEeHHHH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl  281 (343)
                          ..++++|+.+.++|+..+.+|++.||+|.+
T Consensus       663 ----~~v~kvGD~V~VkV~~iD~~grI~LS~k~~  692 (693)
T PRK11824        663 ----EDVLKEGDEVKVKVLEIDKRGRIRLSRKAV  692 (693)
T ss_pred             ----cceeCCCCEEEEEEEEECCCCcEEEEEEec
Confidence                134578888999999887569999998764

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=97.92  E-value=3.5e-05  Score=72.63  Aligned_cols=79  Identities=23%  Similarity=0.271  Sum_probs=59.8

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      |.+++||+|.|+|+++.+++++|||+...+|+||++++++.+.   +   .|.                           
T Consensus        59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~---~---~d~---------------------------  105 (235)
T PRK04163         59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPV---N---VEG---------------------------  105 (235)
T ss_pred             ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCcc---c---cch---------------------------
Confidence            6678999999999999999999999989999999999985310   0   000                           


Q ss_pred             CCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr  280 (343)
                       .-..+.+++||.+.++|+..+.++.+.||.+.
T Consensus       106 -~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~  137 (235)
T PRK04163        106 -TDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKG  137 (235)
T ss_pred             -hhhHhhCCCCCEEEEEEEEECCCCcEEEEEcC
Confidence             00123457788888888877666678888753

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

Probab=97.89  E-value=0.00011  Score=57.37  Aligned_cols=39  Identities=15%  Similarity=0.189  Sum_probs=36.1

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      ..++.|++++|+|.++++.|+||++..+.+|++|.+|+.
T Consensus        12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~   50 (77)
T cd04473          12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL   50 (77)
T ss_pred             hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc
Confidence            458899999999999999999999988899999999974

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=97.89  E-value=3.2e-05  Score=70.27  Aligned_cols=74  Identities=26%  Similarity=0.218  Sum_probs=57.4

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCC----------CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeee
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGA----------DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV  236 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~----------KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i  236 (343)
                      .+.+++||+|.|+|++|.+++++|+|+.          ..+|++|.+++++....       +                 
T Consensus        59 ~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~-------~-----------------  114 (189)
T PRK09521         59 PPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVE-------S-----------------  114 (189)
T ss_pred             CCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhh-------h-----------------
Confidence            3567899999999999999999999963          57899999999742100       0                 


Q ss_pred             cCCcceeccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315          237 KDDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (343)
Q Consensus       237 ~~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr  280 (343)
                                    ..+.+.+||.+.+.|+..+  +++.||.|+
T Consensus       115 --------------~~~~~~~GD~V~akV~~i~--~~i~LS~k~  142 (189)
T PRK09521        115 --------------LTDAFKIGDIVRAKVISYT--DPLQLSTKG  142 (189)
T ss_pred             --------------HHhccCCCCEEEEEEEecC--CcEEEEEec
Confidence                          0233577888999998776  789999864

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=97.88  E-value=2.7e-05  Score=80.44  Aligned_cols=74  Identities=20%  Similarity=0.231  Sum_probs=56.6

Q ss_pred             eccceEEEEEEeecCCCceEEeHHHHHHHHHHH-----HHHHHhh--CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcc
Q 019315          256 ETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWH-----RVRQIKQ--LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL  328 (343)
Q Consensus       256 eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe-----~l~qa~e--~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl  328 (343)
                      ++|+.+.+.+...+ -|++.++..|......|.     .+.+.|+  .|++|+|+|+++.++|++|+++|++||||+|++
T Consensus        88 ~vGD~ie~~I~~~~-fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~G~V~ri~~~giiVDLggvea~LP~sE~  166 (470)
T PRK09202         88 EVGDYIEEEIESVD-FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGRAEAILPRKEQ  166 (470)
T ss_pred             cCCCeEEEEEcccc-CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCEEEEECCeEEEecHHHc
Confidence            55666666554333 566666665544344555     7777887  999999999999999999999999999999998


Q ss_pred             cc
Q 019315          329 LS  330 (343)
Q Consensus       329 ~~  330 (343)
                      ..
T Consensus       167 ip  168 (470)
T PRK09202        167 IP  168 (470)
T ss_pred             CC
Confidence            63

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

Probab=97.88  E-value=2.4e-05  Score=59.46  Aligned_cols=38  Identities=24%  Similarity=0.388  Sum_probs=35.5

Q ss_pred             hhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR  331 (343)
Q Consensus       294 ~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r  331 (343)
                      ++.|++++|+|++++++|++|+++ |++||||.++++..
T Consensus         2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~   40 (74)
T PF00575_consen    2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDD   40 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSS
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCc
Confidence            578999999999999999999997 99999999999864

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 ....

>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=97.79  E-value=0.00011  Score=56.05  Aligned_cols=35  Identities=29%  Similarity=0.440  Sum_probs=33.5

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          173 GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      |++|.|+|+++.+++++|+++.+.+|++|++|+++
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~   35 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFD   35 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhcc
Confidence            89999999999999999999999999999999974

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.

>PHA02945 interferon resistance protein; Provisional

Probab=97.77  E-value=7.9e-05  Score=61.08  Aligned_cols=74  Identities=15%  Similarity=0.178  Sum_probs=55.8

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEe-CC-CeeEEEecccc--CcccccchhhhhhhhhhhhhHhhhcceeeeecCCccee
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNV-GA-DLLGTMLTKEV--LPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA  243 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDI-G~-KsEG~IPisEl--s~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~  243 (343)
                      .-+.+|++|.|+|.. .++|+||++ .| +.+|+||++|+  +.                       |-+.+ +      
T Consensus         7 ~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~-----------------------~wvK~-r------   55 (88)
T PHA02945          7 SLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMN-----------------------RYFKY-R------   55 (88)
T ss_pred             cCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhcc-----------------------ceEee-e------
Confidence            346899999999999 999999999 55 69999999966  52                       22222 1      


Q ss_pred             ccCCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHH
Q 019315          244 MSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLF  282 (343)
Q Consensus       244 Ig~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~  282 (343)
                               +.. .|.++.++|+..| ..|.|=||+|+..
T Consensus        56 ---------d~l-~GqkvV~KVirVd~~kg~IDlSlK~V~   85 (88)
T PHA02945         56 ---------DKL-VGKTVKVKVIRVDYTKGYIDVNYKRMC   85 (88)
T ss_pred             ---------eEe-cCCEEEEEEEEECCCCCEEEeEeeEcc
Confidence                     223 4566778888765 6699999998764

>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=97.71  E-value=5e-05  Score=59.31  Aligned_cols=43  Identities=7%  Similarity=0.059  Sum_probs=37.8

Q ss_pred             hhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChh
Q 019315          294 KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFT  336 (343)
Q Consensus       294 ~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nle  336 (343)
                      ++.|++|+|+|+++..+|++|++ .|++||+|.|+++.+ +.+++
T Consensus         1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~   45 (74)
T cd05705           1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPS   45 (74)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChh
Confidence            36799999999999999999999 589999999999876 45554

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.

>TIGR01953 NusA transcription termination factor NusA

Probab=97.69  E-value=0.00014  Score=72.31  Aligned_cols=36  Identities=33%  Similarity=0.511  Sum_probs=32.9

Q ss_pred             CCCCEEEEEEEEEeCCe-EEEEeCCCeeEEEeccccCc
Q 019315          171 KPGDFVIGVVVSGNENK-LDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       171 k~GdiVeG~VVsI~~~g-v~VDIG~KsEG~IPisEls~  207 (343)
                      +.|++|+|+|.++++++ ++||+| +.+|+||.+|..+
T Consensus       130 k~GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP~~E~ip  166 (341)
T TIGR01953       130 KEGEIISGTVKRVNRRGNLYVELG-KTEGILPKKEQIP  166 (341)
T ss_pred             hcCCEEEEEEEEEecCCcEEEEEC-CeEEEecHHHcCC
Confidence            58999999999999977 799997 8999999999874

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=97.68  E-value=0.00011  Score=76.00  Aligned_cols=39  Identities=28%  Similarity=0.405  Sum_probs=34.9

Q ss_pred             CCCC--CCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          168 YEPK--PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       168 ~~~k--~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      ..|+  .|++|+|+|.++++++++||+| +.+|+||.+|+.+
T Consensus       128 ~eyk~~~GeIV~G~V~ri~~~giiVDLg-gvea~LP~sE~ip  168 (470)
T PRK09202        128 EEYKDRVGEIITGVVKRVERGNIIVDLG-RAEAILPRKEQIP  168 (470)
T ss_pred             HHHHhhcCCEEEEEEEEEecCCEEEEEC-CeEEEecHHHcCC
Confidence            3454  8999999999999999999996 7999999999974

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

Probab=97.52  E-value=0.00078  Score=51.88  Aligned_cols=36  Identities=17%  Similarity=0.111  Sum_probs=33.1

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCC-CeeEEEeccccCc
Q 019315          172 PGDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVLP  207 (343)
Q Consensus       172 ~GdiVeG~VVsI~~~gv~VDIG~-KsEG~IPisEls~  207 (343)
                      .|++++|+|+++.+.|+||+++. +.+|++|.+++.+
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~   37 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGD   37 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCC
Confidence            38999999999999999999986 7999999999873

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.

>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=97.48  E-value=0.00017  Score=54.45  Aligned_cols=35  Identities=9%  Similarity=0.377  Sum_probs=32.3

Q ss_pred             CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      |++++|+|+++.+.|++|++ +|++||+|.|+++..
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~   36 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADV   36 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCc
Confidence            68899999999999999999 589999999999754

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.47  E-value=0.00036  Score=75.07  Aligned_cols=71  Identities=23%  Similarity=0.170  Sum_probs=55.7

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      ..+++|++++|+|++|.++|+||++..+.+|++|++|+++.+                       +..        +   
T Consensus       614 ~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~-----------------------v~~--------~---  659 (684)
T TIGR03591       614 AEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANER-----------------------VEK--------V---  659 (684)
T ss_pred             cccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCc-----------------------ccC--------h---
Confidence            457899999999999999999999988899999999997431                       000        1   


Q ss_pred             CCCCCCceeccceEEEEEEeecCCCceEE
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLL  276 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de~G~I~L  276 (343)
                          ..++++|+.+.++|++.+..|++.|
T Consensus       660 ----~~~~kvGD~V~VkVi~id~~gki~L  684 (684)
T TIGR03591       660 ----EDVLKEGDEVKVKVLEIDKQGRIKL  684 (684)
T ss_pred             ----hhccCCCCEEEEEEEEECCCCCccC
Confidence                1234778888999988776677654

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).

>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=97.46  E-value=0.00018  Score=54.25  Aligned_cols=41  Identities=20%  Similarity=0.353  Sum_probs=34.6

Q ss_pred             CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTE  337 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nlee  337 (343)
                      |++++|+|+++.++|++|++ ++++||+|.|+++.. ..++.+
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~   43 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEE   43 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHH
Confidence            67899999999999999999 479999999999754 444443

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.

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

Probab=97.46  E-value=0.00052  Score=49.10  Aligned_cols=32  Identities=25%  Similarity=0.192  Sum_probs=29.6

Q ss_pred             EEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          176 VIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       176 VeG~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      +.|+|+++.+++++|+++.+.+|++|.+++.+
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~   32 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSD   32 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCC
Confidence            57999999999999999988999999999874

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.

>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=97.45  E-value=0.00018  Score=56.44  Aligned_cols=49  Identities=12%  Similarity=0.142  Sum_probs=39.7

Q ss_pred             HHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChh
Q 019315          287 WHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFT  336 (343)
Q Consensus       287 We~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nle  336 (343)
                      |..+.+ ++.|+++.|+|+++.+.|++|++ +|++||+|.++++.+ ..++.
T Consensus         6 ~~~~~~-~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~   56 (83)
T cd04461           6 PTNFSD-LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPS   56 (83)
T ss_pred             hhhHHh-CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHH
Confidence            344433 67999999999999999999999 589999999999765 34443

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=97.44  E-value=0.00018  Score=56.30  Aligned_cols=37  Identities=19%  Similarity=0.198  Sum_probs=33.9

Q ss_pred             hhCCCcEEEEEEEEecCeeEEEEC--CeEEEEeCCcccc
Q 019315          294 KQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS  330 (343)
Q Consensus       294 ~e~g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~  330 (343)
                      ++.|.+|.|+|+++...|++|+++  |++||||+++++.
T Consensus         2 l~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~   40 (74)
T cd05694           2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGN   40 (74)
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCc
Confidence            357999999999999999999995  8999999999975

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.

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=97.42  E-value=0.00018  Score=77.86  Aligned_cols=78  Identities=22%  Similarity=0.204  Sum_probs=61.8

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      ...+++|.+++|+|.++.++|+|||||-+.+|+||+++++...   +    .++                          
T Consensus       653 i~dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~f---v----~~P--------------------------  699 (780)
T COG2183         653 ITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKF---V----KDP--------------------------  699 (780)
T ss_pred             HhhccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhh---c----CCh--------------------------
Confidence            3579999999999999999999999999999999999998320   0    000                          


Q ss_pred             CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLF  282 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~  282 (343)
                           ..++++|+.+.+.|++.+ ..++|.||.+.-+
T Consensus       700 -----~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~  731 (780)
T COG2183         700 -----NEVVKVGDIVKVKVIEVDTARKRIALSMRLDE  731 (780)
T ss_pred             -----HHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence                 234577788888888765 6689999986644

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=97.41  E-value=0.00035  Score=70.16  Aligned_cols=36  Identities=31%  Similarity=0.515  Sum_probs=33.5

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       171 k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      +.|++|+|+|.++++++++||+|. .+|+||.+|..+
T Consensus       133 k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~ip  168 (362)
T PRK12327        133 REGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQIP  168 (362)
T ss_pred             hcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcCC
Confidence            899999999999999999999975 999999999864

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

Probab=97.36  E-value=0.00075  Score=55.05  Aligned_cols=77  Identities=21%  Similarity=0.251  Sum_probs=56.6

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEe--------CCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNV--------GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD  239 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDI--------G~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~d  239 (343)
                      +-+++||+|.|+|+++....+.|||        .....|++|.+++......+.                          
T Consensus         2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~--------------------------   55 (92)
T cd05791           2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKV--------------------------   55 (92)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchH--------------------------
Confidence            3468999999999999999999999        878899999999874311000                          


Q ss_pred             cceeccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315          240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (343)
Q Consensus       240 gaV~Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr  280 (343)
                         .+       ...+.+||.+.++|+..++...+.||.+.
T Consensus        56 ---~~-------~~~f~~GDiV~AkVis~~~~~~~~Lst~~   86 (92)
T cd05791          56 ---EM-------YKCFRPGDIVRAKVISLGDASSYYLSTAE   86 (92)
T ss_pred             ---HH-------HhhcCCCCEEEEEEEEcCCCCCcEEEecC
Confidence               01       12346778888888876555668888643

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".

>TIGR01953 NusA transcription termination factor NusA

Probab=97.32  E-value=0.00056  Score=68.14  Aligned_cols=74  Identities=23%  Similarity=0.223  Sum_probs=56.7

Q ss_pred             eccceEEEEEEeecCCCceEEeHHHH-----HHHHHHHHHHHHhh--CCCcEEEEEEEEecCe-eEEEECCeEEEEeCCc
Q 019315          256 ETGTVLFAEVLGRTLSGRPLLSTRRL-----FRKMAWHRVRQIKQ--LNEPIEVKFTEWNTGG-LLTRIEGLRAFLPKAE  327 (343)
Q Consensus       256 eiGd~v~~eVl~~de~G~I~LS~Krl-----~~~~aWe~l~qa~e--~g~~VeGkVve~nKGG-liVeIeGlrgFIP~SQ  327 (343)
                      ++|+.+...+.. .+-|++.++..+.     .+...|+.+.+.|.  .|++|+|+|.++.++| ++|+++|++||||.++
T Consensus        85 ~vGD~I~~~I~~-~~fgR~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP~~E  163 (341)
T TIGR01953        85 QIGDEVKKEIPP-ENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGILPKKE  163 (341)
T ss_pred             ccCCEEEEEecc-cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEEEEEEecCCcEEEEECCeEEEecHHH
Confidence            556666555432 3446666665554     34677899999885  9999999999999988 5999999999999999


Q ss_pred             ccc
Q 019315          328 LLS  330 (343)
Q Consensus       328 l~~  330 (343)
                      ...
T Consensus       164 ~ip  166 (341)
T TIGR01953       164 QIP  166 (341)
T ss_pred             cCC
Confidence            864

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.

>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=97.30  E-value=0.0003  Score=53.51  Aligned_cols=34  Identities=9%  Similarity=0.115  Sum_probs=31.4

Q ss_pred             CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS  330 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~  330 (343)
                      |++|+|+|+++...|++|++ +|++||+|.||+..
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~   35 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDP   35 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCC
Confidence            68899999999999999999 68999999999963

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.

>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=97.30  E-value=0.00034  Score=54.31  Aligned_cols=34  Identities=9%  Similarity=0.091  Sum_probs=31.8

Q ss_pred             CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS  330 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~  330 (343)
                      |++|+|+|+++...|++|++ +|++||||.|+++.
T Consensus         1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~   35 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSD   35 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCC
Confidence            68899999999999999999 58999999999974

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.

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

Probab=97.29  E-value=0.00047  Score=73.71  Aligned_cols=79  Identities=18%  Similarity=0.117  Sum_probs=64.7

Q ss_pred             ccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceecc
Q 019315          166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS  245 (343)
Q Consensus       166 ~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig  245 (343)
                      ....+++|++.+|+|++|.++|+||.+-.+.+|++|++++....                       |.+        + 
T Consensus       613 i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~r-----------------------v~k--------v-  660 (692)
T COG1185         613 ITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKER-----------------------VEK--------V-  660 (692)
T ss_pred             HHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhh-----------------------hhc--------c-
Confidence            34679999999999999999999999988889999999997321                       111        1 


Q ss_pred             CCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHH
Q 019315          246 GGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLF  282 (343)
Q Consensus       246 ~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~  282 (343)
                            -+++++|+.+.++++..++.|++.||++.+.
T Consensus       661 ------~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~~~  691 (692)
T COG1185         661 ------EDVLKEGDEVKVKVIEIDKQGRIRLSIKAVL  691 (692)
T ss_pred             ------cceeecCceEEEEEeeecccCCccceehhcc
Confidence                  2456788899999999999999999987653

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

Probab=97.27  E-value=0.0014  Score=62.61  Aligned_cols=78  Identities=22%  Similarity=0.393  Sum_probs=62.6

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      .|.++.||+|-|+|+.+...+..||||++..+++|++++..+.   ++                               .
T Consensus        59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~---~~-------------------------------~  104 (239)
T COG1097          59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRK---FE-------------------------------N  104 (239)
T ss_pred             cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhccc---cc-------------------------------c
Confidence            5788999999999999999999999999999999999995321   00                               0


Q ss_pred             CCCCCCCceeccceEEEEEEeecCCCceEEeH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLST  278 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~  278 (343)
                      .-..+.+..++||-+.++|...+.++.+.|+.
T Consensus       105 ~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~  136 (239)
T COG1097         105 AEKDLRPFLNVGDLVYAKVVDVDRDGEVELTL  136 (239)
T ss_pred             cccccccccccCCEEEEEEEEccCCCceEEEe
Confidence            00122566788999999998888888888886

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

Probab=97.26  E-value=0.00032  Score=53.36  Aligned_cols=35  Identities=20%  Similarity=0.322  Sum_probs=32.8

Q ss_pred             CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      .|++|+|+|++++++|++|++++++||||.+++..
T Consensus         3 ~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~   37 (67)
T cd04455           3 EGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIP   37 (67)
T ss_pred             CCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCC
Confidence            68999999999999999999988999999999963

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.

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

Probab=97.24  E-value=0.00072  Score=52.09  Aligned_cols=43  Identities=19%  Similarity=0.262  Sum_probs=36.7

Q ss_pred             hCCCcEEEEEEEEecCeeEEEECC--eEEEEeCCccccC-CCChhh
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIEG--LRAFLPKAELLSR-VNNFTE  337 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIeG--lrgFIP~SQl~~r-v~nlee  337 (343)
                      +.|++++|+|+++.+.|++|+++|  ++||+|.|++..+ +.++.+
T Consensus         2 ~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~   47 (73)
T cd05686           2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSE   47 (73)
T ss_pred             cCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhh
Confidence            469999999999999999999977  5999999999765 555444

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

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

Probab=97.20  E-value=0.00067  Score=51.17  Aligned_cols=41  Identities=12%  Similarity=0.217  Sum_probs=35.1

Q ss_pred             CCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC-CCChhh
Q 019315          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR-VNNFTE  337 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r-v~nlee  337 (343)
                      |++|+|+|+++...|++|++. +.+||||.+++... ..++.+
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~   43 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGED   43 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhH
Confidence            688999999999999999994 79999999999754 455544

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.

>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=97.20  E-value=0.00059  Score=51.39  Aligned_cols=35  Identities=14%  Similarity=0.239  Sum_probs=32.1

Q ss_pred             CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      |+++.|+|+++.+.|++|++ +++.||+|.|+++.+
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~   36 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDS   36 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCch
Confidence            67899999999999999999 589999999999754

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.

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

Probab=97.20  E-value=0.0026  Score=51.90  Aligned_cols=39  Identities=28%  Similarity=0.472  Sum_probs=36.0

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      |.+++||+|-|+|+.+..+...|||+....|++|..+|.
T Consensus         2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~   40 (86)
T cd05790           2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFE   40 (86)
T ss_pred             CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcc
Confidence            568899999999999999999999999999999997774

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".

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

Probab=97.14  E-value=0.00088  Score=50.38  Aligned_cols=40  Identities=30%  Similarity=0.431  Sum_probs=34.3

Q ss_pred             CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChh
Q 019315          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFT  336 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nle  336 (343)
                      |++|.|+|+++...|++|++ ++++||+|.|+++.+ ..++.
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~   42 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDAT   42 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHH
Confidence            67899999999999999999 689999999999764 44433

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.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=97.10  E-value=0.00066  Score=67.20  Aligned_cols=48  Identities=17%  Similarity=0.250  Sum_probs=42.8

Q ss_pred             HHhh-CCCcEEEEEEEEecCeeEEEE---CCeEEEEeCCccccC-CCChhhhc
Q 019315          292 QIKQ-LNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAELLSR-VNNFTELK  339 (343)
Q Consensus       292 qa~e-~g~~VeGkVve~nKGGliVeI---eGlrgFIP~SQl~~r-v~nleel~  339 (343)
                      +.|+ .|++|.|+|+++...|++|++   +|++||||.|+++++ ++++.+++
T Consensus        12 ~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~v   64 (319)
T PTZ00248         12 QKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLI   64 (319)
T ss_pred             hhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhc
Confidence            4676 699999999999999999999   489999999999986 78888764

>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=97.09  E-value=0.00067  Score=52.23  Aligned_cols=34  Identities=24%  Similarity=0.356  Sum_probs=30.5

Q ss_pred             CCcEE-EEEEEE-ecCeeEEEE-CCeEEEEeCCcccc
Q 019315          297 NEPIE-VKFTEW-NTGGLLTRI-EGLRAFLPKAELLS  330 (343)
Q Consensus       297 g~~Ve-GkVve~-nKGGliVeI-eGlrgFIP~SQl~~  330 (343)
                      |++++ |+|+++ .+.|++|++ +|++||||.||++.
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~   37 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSD   37 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCc
Confidence            67888 999998 599999999 68999999999974

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.

>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=97.08  E-value=0.0013  Score=50.02  Aligned_cols=37  Identities=11%  Similarity=0.095  Sum_probs=33.9

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR  331 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r  331 (343)
                      +.|++++|+|+++...|++|+++ +++||+|.|++..+
T Consensus         2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~   39 (73)
T cd05706           2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDD   39 (73)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCc
Confidence            47999999999999999999994 89999999999754

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.

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

Probab=97.04  E-value=0.001  Score=53.80  Aligned_cols=38  Identities=16%  Similarity=0.209  Sum_probs=34.5

Q ss_pred             HhhCCCcEEEEEEEEecC--eeEEEEC-CeEEEEeCCcccc
Q 019315          293 IKQLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELLS  330 (343)
Q Consensus       293 a~e~g~~VeGkVve~nKG--GliVeIe-GlrgFIP~SQl~~  330 (343)
                      .++.|+++.|+|+++.++  |++|+++ |.+||||.|++++
T Consensus         4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~   44 (88)
T cd04453           4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILP   44 (88)
T ss_pred             cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCc
Confidence            356899999999999997  9999995 8999999999975

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

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

Probab=96.99  E-value=0.0017  Score=47.54  Aligned_cols=35  Identities=11%  Similarity=0.262  Sum_probs=32.0

Q ss_pred             CCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315          297 NEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR  331 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r  331 (343)
                      |++++|+|+++.+.|++|+++ +++||||.+++..+
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~   36 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHK   36 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCc
Confidence            678999999999999999995 89999999999754

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.

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

Probab=96.98  E-value=0.0028  Score=72.21  Aligned_cols=134  Identities=16%  Similarity=0.112  Sum_probs=88.5

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      ...++.|++|.|.|..+.+.|+||-++++.+|++|++++.+...+        .|+.   +                   
T Consensus      1157 ~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k--------~w~k---~------------------- 1206 (1710)
T KOG1070|consen 1157 IEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEK--------EWEK---H------------------- 1206 (1710)
T ss_pred             hhhcccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhh--------hhhc---c-------------------
Confidence            356889999999999999999999999999999999998743110        1110   0                   


Q ss_pred             CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHH--HHHHHhhCCCcEEEEEEEEecCeeEEEEC-C--eE
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWH--RVRQIKQLNEPIEVKFTEWNTGGLLTRIE-G--LR  320 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe--~l~qa~e~g~~VeGkVve~nKGGliVeIe-G--lr  320 (343)
                              ..+|..+...|+..+ ..+++.||.|.-+...+-.  ........|+...|.|...-++|++++++ +  +-
T Consensus      1207 --------~~~gklv~~rv~~ve~~s~riel~Lk~s~~~d~~~~~~~~~~l~~gd~~~g~v~~~~~~G~fi~l~~tv~~~ 1278 (1710)
T KOG1070|consen 1207 --------LPVGKLVTGRVLSVEEDSKRIELSLKNSDIKDTVKLLKDSKDLKKGDREDGTVEVVDPFGLFIKLDVTVNMV 1278 (1710)
T ss_pred             --------CCccceeeeEEEEeeccCceEEEEEeccccCCchhhhhhhhhhhccccccceEEEecCCceEEEecCcceec
Confidence                    011111222333322 3356666665533211111  11123468999999999999999999995 3  58


Q ss_pred             EEEeCCccccC-CCChhhh
Q 019315          321 AFLPKAELLSR-VNNFTEL  338 (343)
Q Consensus       321 gFIP~SQl~~r-v~nleel  338 (343)
                      |.+|.++.... ..+...+
T Consensus      1279 g~~~~~e~~d~~~e~it~~ 1297 (1710)
T KOG1070|consen 1279 GLCHISEEADDRGENITAL 1297 (1710)
T ss_pred             ccccceeecchhhhhcccc
Confidence            99999998753 5555544

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

Probab=96.97  E-value=0.0012  Score=47.97  Aligned_cols=36  Identities=22%  Similarity=0.417  Sum_probs=33.3

Q ss_pred             CCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR  331 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r  331 (343)
                      .|++++|+|+++++.|++|+++ ++.||+|.+++..+
T Consensus         2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~   38 (72)
T smart00316        2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDK   38 (72)
T ss_pred             CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcc
Confidence            5899999999999999999996 89999999999754

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

Probab=96.97  E-value=0.0019  Score=49.08  Aligned_cols=43  Identities=14%  Similarity=0.210  Sum_probs=36.1

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC---CeEEEEeCCccccC-CCChhh
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAELLSR-VNNFTE  337 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe---GlrgFIP~SQl~~r-v~nlee  337 (343)
                      +.|+.+.|+|+++.+.|++|++.   |+.||||.|+++.+ ..++.+
T Consensus         2 ~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~   48 (76)
T cd04452           2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRK   48 (76)
T ss_pred             CCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHH
Confidence            36899999999999999999994   59999999999865 444443

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

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

Probab=96.95  E-value=0.0045  Score=60.19  Aligned_cols=120  Identities=16%  Similarity=0.092  Sum_probs=81.7

Q ss_pred             CCCCCCCEEEEEEEEEe-CCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          168 YEPKPGDFVIGVVVSGN-ENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~-~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      ....+|+---++|+.++ +-|||||.|-..+-++|.+|+...         .+.|                         
T Consensus        69 p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~---------~~~w-------------------------  114 (287)
T COG2996          69 PKATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTL---------KSLW-------------------------  114 (287)
T ss_pred             ceEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccc---------cccC-------------------------
Confidence            34567999999999999 679999999999999999998632         0111                         


Q ss_pred             CCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhh--CCCcEEEEEEEEecCeeEEEE-CCeEEEE
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQ--LNEPIEVKFTEWNTGGLLTRI-EGLRAFL  323 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e--~g~~VeGkVve~nKGGliVeI-eGlrgFI  323 (343)
                              .++|+...+.+ ..+..+||.-..+  ..+.-|.-...++.  .++.|.|+|.+...-|.+|-+ ++..|||
T Consensus       115 --------pq~Gd~l~v~l-~~Dkk~Ri~g~~a--~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfI  183 (287)
T COG2996         115 --------PQKGDKLLVYL-YVDKKGRIWGTLA--IEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFI  183 (287)
T ss_pred             --------CCCCCEEEEEE-EEccCCcEEEEec--chhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEE
Confidence                    12334443333 3355566554321  11112222222333  489999999999999999988 5899999


Q ss_pred             eCCccccCC
Q 019315          324 PKAELLSRV  332 (343)
Q Consensus       324 P~SQl~~rv  332 (343)
                      |.|+.-..+
T Consensus       184 h~sEr~~~p  192 (287)
T COG2996         184 HKSERFAEP  192 (287)
T ss_pred             cchhhcccc
Confidence            999975443

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

Probab=96.92  E-value=0.0014  Score=49.68  Aligned_cols=37  Identities=16%  Similarity=0.153  Sum_probs=34.0

Q ss_pred             hhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315          294 KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS  330 (343)
Q Consensus       294 ~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~  330 (343)
                      |+.|++++|+|+++.+.|++|++ +|+.||+|.+++.+
T Consensus         1 ~~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~   38 (72)
T cd05689           1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDW   38 (72)
T ss_pred             CcCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccC
Confidence            56899999999999999999999 58999999999974

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.

>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=96.92  E-value=0.0014  Score=50.54  Aligned_cols=43  Identities=16%  Similarity=0.067  Sum_probs=37.0

Q ss_pred             hCCCcEEEEEEEEec-CeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315          295 QLNEPIEVKFTEWNT-GGLLTRI-EGLRAFLPKAELLSR-VNNFTE  337 (343)
Q Consensus       295 e~g~~VeGkVve~nK-GGliVeI-eGlrgFIP~SQl~~r-v~nlee  337 (343)
                      +.|+++.|+|+++.+ .|++|++ .|.+||+|.|+++.+ ..++.+
T Consensus         2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~   47 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLE   47 (72)
T ss_pred             CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHH
Confidence            479999999999986 8999999 599999999999875 566544

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

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

Probab=96.83  E-value=0.0035  Score=50.97  Aligned_cols=90  Identities=18%  Similarity=0.237  Sum_probs=57.5

Q ss_pred             CEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCCC
Q 019315          174 DFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGRP  253 (343)
Q Consensus       174 diVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i~  253 (343)
                      +++.|+|+++.+.|+||+++ ..+|++|++++.+.+   +.+   +.          ... .+       ++..   -..
T Consensus         1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~---~~~---~~----------~~~-~~-------~~~~---~~~   52 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDY---ISY---DP----------KNK-RL-------IGEE---TKR   52 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCc---eEe---ch----------hhe-ee-------cccC---cCC
Confidence            47999999999999999997 499999999997431   100   00          000 00       0000   012


Q ss_pred             ceeccceEEEEEEeecC------CCceEEeHHHHHHHHHHHHHHH
Q 019315          254 VVETGTVLFAEVLGRTL------SGRPLLSTRRLFRKMAWHRVRQ  292 (343)
Q Consensus       254 v~eiGd~v~~eVl~~de------~G~I~LS~Krl~~~~aWe~l~q  292 (343)
                      +..+|+.+.+.|...+.      .+++.||++.-.. -+|+-+++
T Consensus        53 ~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ls~k~~~~-g~~~~~~~   96 (99)
T cd04460          53 VLKVGDVVRARIVAVSLKERRPRESKIGLTMRQPGL-GKLEWIEE   96 (99)
T ss_pred             EECCCCEEEEEEEEEeHHHCcCCCceEEEEEecCCC-CcHHHhhh
Confidence            34778888888876542      2689999988553 55554443

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.

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

Probab=96.80  E-value=0.0027  Score=46.71  Aligned_cols=36  Identities=11%  Similarity=0.156  Sum_probs=32.8

Q ss_pred             CCCcEEEEEEEEecCeeEEEECCeEEEEeCCccccC
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR  331 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~r  331 (343)
                      .|++++|+|+++.+.|++|+++++.||||.+++..+
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~~~~g~l~~~e~~~~   36 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWG   36 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCc
Confidence            378999999999999999999889999999998743

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.

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

Probab=96.75  E-value=0.0012  Score=57.51  Aligned_cols=46  Identities=15%  Similarity=0.252  Sum_probs=40.6

Q ss_pred             hhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC-CCChhhhc
Q 019315          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR-VNNFTELK  339 (343)
Q Consensus       294 ~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r-v~nleel~  339 (343)
                      ++.|..++|+|+++.+.|++|+++ |-+|+++.|++... ++|+.++.
T Consensus         3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L   50 (129)
T COG1098           3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHL   50 (129)
T ss_pred             ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHh
Confidence            568999999999999999999995 79999999999876 77777663

>PRK08582 hypothetical protein; Provisional

Probab=96.70  E-value=0.0031  Score=55.27  Aligned_cols=38  Identities=16%  Similarity=0.241  Sum_probs=34.8

Q ss_pred             hhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          294 KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       294 ~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      ++.|++|+|+|+++.+.|++|++ +++.||||.|++...
T Consensus         3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~   41 (139)
T PRK08582          3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADN   41 (139)
T ss_pred             CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcc
Confidence            56899999999999999999999 589999999999754

>PRK05807 hypothetical protein; Provisional

Probab=96.68  E-value=0.0037  Score=54.54  Aligned_cols=43  Identities=14%  Similarity=0.212  Sum_probs=37.3

Q ss_pred             hhCCCcEEEEEEEEecCeeEEEECCeEEEEeCCccccC-CCChh
Q 019315          294 KQLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR-VNNFT  336 (343)
Q Consensus       294 ~e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~r-v~nle  336 (343)
                      ++.|++|+|+|+++.+.|++|+++|..||||.|++... +.+..
T Consensus         3 ~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~~   46 (136)
T PRK05807          3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIR   46 (136)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCcc
Confidence            56799999999999999999999999999999999754 44433

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

Probab=96.65  E-value=0.0034  Score=49.09  Aligned_cols=37  Identities=16%  Similarity=0.014  Sum_probs=33.9

Q ss_pred             hCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      +.|++|.|+|+++...|++|++ .+..||||.|++...
T Consensus         5 ~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~   42 (82)
T cd04454           5 DVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK   42 (82)
T ss_pred             CCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCc
Confidence            5799999999999999999999 579999999999754

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".

>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=96.62  E-value=0.0046  Score=47.04  Aligned_cols=35  Identities=9%  Similarity=0.216  Sum_probs=32.1

Q ss_pred             CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      |++|.|+|+++...|++|++ .|++|++|.+++..+
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~   36 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDE   36 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccc
Confidence            68899999999999999999 599999999999754

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.

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

Probab=96.59  E-value=0.012  Score=67.32  Aligned_cols=163  Identities=17%  Similarity=0.116  Sum_probs=107.7

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc-cc-----------ccchhhhhhhhh--------------
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP-LY-----------DKEMDFLLCDLK--------------  221 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~-~~-----------~ke~e~l~~d~~--------------  221 (343)
                      .+|+.||.|+|-|..++.+.++|-|-.-..|.||+-.++. .+           ++-+..+.....              
T Consensus       983 ~q~~~gq~vtGfV~nv~ke~~w~~isp~v~~RIplld~s~~~~~le~~e~~F~~g~al~~~V~~~~~~~tv~~iG~~~~~ 1062 (1710)
T KOG1070|consen  983 KQFKAGQEVTGFVNNVSKEWLWVRISPFVDGRIPLLDTSLDLHVLELPESLFPLGKALDEYVVRNDKSKTVRAIGFSKSD 1062 (1710)
T ss_pred             hhhhcCCeEEEEEEccccceeEEEccccccceeeeeeccchhhhhhCchhhcccccceeeEEecccceeEEEecccccCC
Confidence            5789999999999999999999999999999999998871 11           000000000000              


Q ss_pred             -hhhhHhhhcceeeeecCCcc-eeccCCCCC-CCCceecc--------------ceEEEEEEeec-CCCceEEeHH----
Q 019315          222 -KDAEEFMVRGKMGIVKDDDA-IAMSGGSGP-GRPVVETG--------------TVLFAEVLGRT-LSGRPLLSTR----  279 (343)
Q Consensus       222 -k~~ee~~VeGkV~~i~~dga-V~Ig~~ieg-~i~v~eiG--------------d~v~~eVl~~d-e~G~I~LS~K----  279 (343)
                       ...++...-|+|..+....+ +..+...-| ..-+.++.              ..+...++..+ .++.+-||.|    
T Consensus      1063 k~~s~G~~l~Grv~kv~~~~~~l~~~~~~~G~~~~i~~~~d~~~~~P~~~f~~~~~v~~~~L~vs~~n~~leLslr~sr~ 1142 (1710)
T KOG1070|consen 1063 KNPSPGDILFGRVSKVLPGYLILQLPFKVFGRVSFIEDMSDSYSMTPVEHFTKIQIVYVCVLSVSALNKGLELSLRESRT 1142 (1710)
T ss_pred             CCCCcchhhcceeeeeccceeEEecCCccccceEEeeehhccccCChHHhcccccEEEEEEEEEecccccceeecccccc
Confidence             00134566688888766553 444333322 11111111              12333445443 4445999998    


Q ss_pred             ---HHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315          280 ---RLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS  330 (343)
Q Consensus       280 ---rl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~  330 (343)
                         .++....=-+..+.++.|+++.|.|..+.+.|+++.+ -++.||+|.|++..
T Consensus      1143 ~~t~~~~kd~~iks~eDlk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~d 1197 (1710)
T KOG1070|consen 1143 KITPVDSKDGSIKSIEDLKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSD 1197 (1710)
T ss_pred             cCccccccCCcccchhhcccCceeEEEEEEecCCcEEEEEccceEEEEEcccccc
Confidence               5554444444567788999999999999999999998 58999999998864

>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=96.56  E-value=0.0053  Score=46.47  Aligned_cols=36  Identities=14%  Similarity=0.269  Sum_probs=32.8

Q ss_pred             CCCcEEEEEEEEecCeeEEEEC--CeEEEEeCCccccC
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLSR  331 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~r  331 (343)
                      .|++++|+|+++.+.|++|++.  ++.||+|.+++...
T Consensus         2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~   39 (77)
T cd05708           2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDN   39 (77)
T ss_pred             CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCC
Confidence            5899999999999999999996  69999999999754

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.

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

Probab=96.56  E-value=0.0035  Score=49.27  Aligned_cols=36  Identities=19%  Similarity=0.165  Sum_probs=33.4

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCcccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLS  330 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~  330 (343)
                      +.|++|+|+|+++...|++|++. ++.||||.|++..
T Consensus         5 ~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~   41 (86)
T cd05789           5 EVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNL   41 (86)
T ss_pred             CCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccC
Confidence            58999999999999999999994 8999999999974

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".

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=96.48  E-value=0.0084  Score=65.10  Aligned_cols=72  Identities=14%  Similarity=0.148  Sum_probs=52.6

Q ss_pred             eecCCCceEEeHHHHH-HHHHHHHHHHH-----hhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccc-----cCCCC
Q 019315          267 GRTLSGRPLLSTRRLF-RKMAWHRVRQI-----KQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELL-----SRVNN  334 (343)
Q Consensus       267 ~~de~G~I~LS~Krl~-~~~aWe~l~qa-----~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~-----~rv~n  334 (343)
                      .++++|.+.++-.... ..++-+.+...     .+.|++++|+|+++..+|++|++ .|++||||.||++     .++.+
T Consensus       612 di~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~  691 (719)
T TIGR02696       612 SIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVEN  691 (719)
T ss_pred             EEecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCC
Confidence            3457898887653222 22344444432     46999999999999999999999 5999999999995     24677


Q ss_pred             hhhh
Q 019315          335 FTEL  338 (343)
Q Consensus       335 leel  338 (343)
                      +.++
T Consensus       692 ~~dv  695 (719)
T TIGR02696       692 VEDV  695 (719)
T ss_pred             HHHc
Confidence            7764

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.

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

Probab=96.36  E-value=0.023  Score=51.36  Aligned_cols=40  Identities=25%  Similarity=0.313  Sum_probs=35.9

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcc
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPL  208 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~  208 (343)
                      .++.+|++++|+|+++++.|+||++|. .+|+++.+++.+.
T Consensus        77 f~p~~gEvv~G~V~~v~~~GifV~lg~-~~gi~~~~~l~~~  116 (179)
T TIGR00448        77 FKPELGEIVEGEVIEIVEFGAFVSLGP-FDGLFHVSQVTDD  116 (179)
T ss_pred             EeccCCCEEEEEEEEEEeeEEEEEeCC-ceEEEEcHHhCCC
Confidence            567789999999999999999999975 9999999999743

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

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.35  E-value=0.0084  Score=60.39  Aligned_cols=43  Identities=12%  Similarity=0.095  Sum_probs=36.1

Q ss_pred             HHHHHHHh--hCCCcEEEEEEEEecCeeEEEECCeEEEEeCCccc
Q 019315          287 WHRVRQIK--QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL  329 (343)
Q Consensus       287 We~l~qa~--e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~  329 (343)
                      .+.+.+.|  +.|++|+|+|+++.++|++|+++|++||||.+++.
T Consensus       123 re~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP~~E~i  167 (362)
T PRK12327        123 REIIYNEFSEREGDIVTGVVQRRDNRFVYVNLGKIEAVLPPAEQI  167 (362)
T ss_pred             HHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeCCeEEEecHHHcC
Confidence            44455555  79999999999999999999999999999966553

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

Probab=96.30  E-value=0.0053  Score=45.81  Aligned_cols=34  Identities=9%  Similarity=0.201  Sum_probs=31.4

Q ss_pred             CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS  330 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~  330 (343)
                      |+++.|+|+++.+.|++|++ .|++||+|.|++.+
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~   35 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISW   35 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCC
Confidence            67899999999999999999 58999999999974

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.

>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=96.25  E-value=0.0091  Score=47.44  Aligned_cols=35  Identities=26%  Similarity=0.410  Sum_probs=32.1

Q ss_pred             CCcEEEEEEEEecCeeEEEEC--CeEEEEeCCccccC
Q 019315          297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLSR  331 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~r  331 (343)
                      |..|+|+|.++.+.+++|+++  |++||||.-|++..
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~   37 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDH   37 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCc
Confidence            578999999999999999993  89999999999764

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.

>PRK08059 general stress protein 13; Validated

Probab=96.16  E-value=0.0093  Score=50.87  Aligned_cols=38  Identities=11%  Similarity=0.157  Sum_probs=34.6

Q ss_pred             hhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR  331 (343)
Q Consensus       294 ~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r  331 (343)
                      ++.|+++.|+|+++.+.|++|+++ +++||+|.|+++.+
T Consensus         5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~   43 (123)
T PRK08059          5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHG   43 (123)
T ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcc
Confidence            678999999999999999999994 89999999999654

>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=96.10  E-value=0.0097  Score=43.50  Aligned_cols=35  Identities=14%  Similarity=0.113  Sum_probs=31.4

Q ss_pred             CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      |+.+.|+|+++...|++|++ .++.||+|.+++...
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~   36 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADR   36 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCc
Confidence            57899999999999999999 479999999999653

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.

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

Probab=96.07  E-value=0.019  Score=48.56  Aligned_cols=50  Identities=14%  Similarity=0.132  Sum_probs=41.6

Q ss_pred             hhHHHHhhccc---CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          157 KVGEDKVSVEY---YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       157 ~dFa~lLe~~~---~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      +.|+.||..+-   -.-..|.+|.|+|..|.++.+|||+|.|..++++..+..
T Consensus         5 ~sFaslLR~S~fi~lG~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~   57 (104)
T PF10246_consen    5 ESFASLLRNSPFIQLGDPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVN   57 (104)
T ss_pred             ccHHHHhcCChhhhcCCccCCEEEEEEEEEecCceEEEeCCceeEEEeccccc
Confidence            78999996542   112369999999999999999999999999999987653

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 [].

>TIGR02063 RNase_R ribonuclease R

Probab=96.01  E-value=0.045  Score=59.15  Aligned_cols=85  Identities=18%  Similarity=0.173  Sum_probs=56.7

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceecc
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS  245 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~-KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig  245 (343)
                      +.+.+.|++++|+|++|+++|+||.+.. ..+|++|++++....   +.   .|.         .+..        + .+
T Consensus       622 yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~---~~---~d~---------~~~~--------l-~g  677 (709)
T TIGR02063       622 YMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDY---YV---FDE---------KGLA--------L-VG  677 (709)
T ss_pred             hhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCc---EE---Ecc---------cceE--------E-Ee
Confidence            3455789999999999999999999965 799999999997321   10   010         0000        0 01


Q ss_pred             CCCCCCCCceeccceEEEEEEeec-CCCceEEeH
Q 019315          246 GGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLST  278 (343)
Q Consensus       246 ~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~  278 (343)
                      ..   ......+|+.+.++|...+ ..++|.++.
T Consensus       678 ~~---~~~~~~lGd~V~Vkv~~vd~~~~~I~~~l  708 (709)
T TIGR02063       678 ER---TGKVFRLGDRVKVRVVKADLDTGKIDFEL  708 (709)
T ss_pred             cc---CCcEECCCCEEEEEEEEEecccCeEEEEE
Confidence            00   0134577888888888766 568888773

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.

>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=95.97  E-value=0.012  Score=45.55  Aligned_cols=35  Identities=14%  Similarity=0.085  Sum_probs=32.0

Q ss_pred             CCcEEEEEEEEecCeeEEEEC----CeEEEEeCCccccC
Q 019315          297 NEPIEVKFTEWNTGGLLTRIE----GLRAFLPKAELLSR  331 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeIe----GlrgFIP~SQl~~r  331 (343)
                      |++++|+|+++..+|++|+++    |+.||+|.|++..+
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~   39 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFE   39 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCC
Confidence            578999999999999999997    68999999999765

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.

>PRK07252 hypothetical protein; Provisional

Probab=95.96  E-value=0.013  Score=50.21  Aligned_cols=37  Identities=11%  Similarity=0.263  Sum_probs=33.4

Q ss_pred             hCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      +.|+++.|+|+++...|++|++ .++.||+|.|++...
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~   39 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTG   39 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCc
Confidence            3689999999999999999999 579999999999754

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.94  E-value=0.018  Score=58.35  Aligned_cols=39  Identities=21%  Similarity=0.398  Sum_probs=34.2

Q ss_pred             CCCCCCCEEEEEEEEEeC-CeEEEEeCCCeeEEEeccccCc
Q 019315          168 YEPKPGDFVIGVVVSGNE-NKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~-~gv~VDIG~KsEG~IPisEls~  207 (343)
                      |.-+.|++|+|+|.+++. +.++||+| +++|+||.+|..+
T Consensus       134 y~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eqip  173 (374)
T PRK12328        134 YKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNRIK  173 (374)
T ss_pred             HHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHcCC
Confidence            456789999999999996 56999998 7999999999874

>PHA02945 interferon resistance protein; Provisional

Probab=95.88  E-value=0.012  Score=48.52  Aligned_cols=42  Identities=17%  Similarity=0.207  Sum_probs=35.5

Q ss_pred             hCCCcEEEEEEEEecCeeEEEE---CCeEEEEeCCcc--ccC-CCChhhh
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAEL--LSR-VNNFTEL  338 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeI---eGlrgFIP~SQl--~~r-v~nleel  338 (343)
                      +.|+.|-|+|++ ...|++|.+   +|++||||.|++  +.+ ++| .++
T Consensus        10 ~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~   57 (88)
T PHA02945         10 NVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDK   57 (88)
T ss_pred             CCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeE
Confidence            589999999999 999999988   499999999966  766 666 443

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

Probab=95.81  E-value=0.0046  Score=59.99  Aligned_cols=90  Identities=19%  Similarity=0.117  Sum_probs=61.0

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEe-CC-CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNV-GA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDI-G~-KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      -++.+++|-+.|.+|.+-|+||.+ .| ..||+|.++|++.++   +.    .+.                         
T Consensus        13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRR---IR----SI~-------------------------   60 (304)
T KOG2916|consen   13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRR---IR----SIQ-------------------------   60 (304)
T ss_pred             CCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHH---HH----HHH-------------------------
Confidence            467899999999999999999999 33 499999999999542   00    000                         


Q ss_pred             CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCC
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLN  297 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g  297 (343)
                            .+..+|-...+.|+..+ +.|+|-||+||... ..-.+.++.|++.
T Consensus        61 ------klirVGr~E~vvVlrVDkekGYIDLSkrrVs~-ed~~kC~Er~~ks  105 (304)
T KOG2916|consen   61 ------KLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP-EDKEKCEERFAKS  105 (304)
T ss_pred             ------HHHhcCCcceEEEEEEcCCCCceechhccCCH-HHHHHHHHHHHHh
Confidence                  01123333345566544 77999999999774 4444555555443

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

Probab=95.80  E-value=0.017  Score=44.44  Aligned_cols=34  Identities=12%  Similarity=0.201  Sum_probs=31.4

Q ss_pred             CCcEEEEEEEEecCeeEEEEC--CeEEEEeCCcccc
Q 019315          297 NEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS  330 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~  330 (343)
                      |++++|+|+++++.|++|+++  |++||+|.|++..
T Consensus         2 g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~   37 (83)
T cd04471           2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGD   37 (83)
T ss_pred             CCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCC
Confidence            789999999999999999996  7999999999863

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.

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

Probab=95.75  E-value=0.018  Score=42.43  Aligned_cols=35  Identities=20%  Similarity=0.202  Sum_probs=31.6

Q ss_pred             CCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          297 NEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      |+++.|+|+++.+.|++|++ .+..||+|.+++..+
T Consensus         1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~   36 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDE   36 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCc
Confidence            57899999999999999999 479999999999764

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.

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=95.69  E-value=0.0065  Score=55.28  Aligned_cols=47  Identities=9%  Similarity=0.163  Sum_probs=40.6

Q ss_pred             HHHHHHHHHhhCCCcEEEEEEEEecCeeEEEEC-----------CeEEEEeCCccccC
Q 019315          285 MAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-----------GLRAFLPKAELLSR  331 (343)
Q Consensus       285 ~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIe-----------GlrgFIP~SQl~~r  331 (343)
                      .||......++.|++|.|+|+++...|++|+|.           ++.||||.|++...
T Consensus        53 ~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~  110 (189)
T PRK09521         53 IPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDG  110 (189)
T ss_pred             ecCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChh
Confidence            478876667789999999999999999999984           57899999999754

>PRK11642 exoribonuclease R; Provisional

Probab=95.65  E-value=0.048  Score=60.17  Aligned_cols=86  Identities=12%  Similarity=0.024  Sum_probs=57.2

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCC-eeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceecc
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGAD-LLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS  245 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~K-sEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig  245 (343)
                      +.+-+.|++++|+|++|+++|+||.+... .+|+||++++.+.      |+..|..    ...             + ++
T Consensus       638 ~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d------~y~~d~~----~~~-------------L-~g  693 (813)
T PRK11642        638 FMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDND------YYRFDQV----GQR-------------L-IG  693 (813)
T ss_pred             hhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCc------ceEecch----heE-------------E-ec
Confidence            33447899999999999999999999654 9999999998632      1111110    000             0 11


Q ss_pred             CCCCCCCCceeccceEEEEEEeec-CCCceEEeHH
Q 019315          246 GGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTR  279 (343)
Q Consensus       246 ~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~K  279 (343)
                      ..   -.....+|+.+.+.|+..+ ..++|.+++-
T Consensus       694 ~~---~~~~~~lGD~V~VkV~~vD~~~rkI~f~l~  725 (813)
T PRK11642        694 ES---SGQTYRLGDRVEVRVEAVNMDERKIDFSLI  725 (813)
T ss_pred             cc---CCcEECCCCEEEEEEEEeecCCCeEEEEEe
Confidence            00   0134577888888887654 5688888874

>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=95.63  E-value=0.043  Score=43.64  Aligned_cols=35  Identities=20%  Similarity=0.223  Sum_probs=32.5

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCC-CeeEEEeccccCc
Q 019315          173 GDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVLP  207 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~-KsEG~IPisEls~  207 (343)
                      |++|+|+|+..+++++.|+++. ...|++|...+++
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD   36 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD   36 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC
Confidence            7899999999999999999955 8999999999985

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

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=95.62  E-value=0.027  Score=46.17  Aligned_cols=39  Identities=15%  Similarity=0.089  Sum_probs=34.6

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEe-CCCeeEEEe-ccccCc
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNV-GADLLGTML-TKEVLP  207 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDI-G~KsEG~IP-isEls~  207 (343)
                      --+++||++. .|+.+.+.++||.+ +|+.||+|. .+|++.
T Consensus        12 ~~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr   52 (86)
T PHA02858         12 VFPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNA   52 (86)
T ss_pred             ecCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhH
Confidence            3467899999 88899999999998 888999999 999973

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=95.57  E-value=0.038  Score=59.77  Aligned_cols=70  Identities=11%  Similarity=0.109  Sum_probs=49.3

Q ss_pred             ecCCCceEEeH---HHHHHHHH-HHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315          268 RTLSGRPLLST---RRLFRKMA-WHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTE  337 (343)
Q Consensus       268 ~de~G~I~LS~---Krl~~~~a-We~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nlee  337 (343)
                      ++++|.+.++.   ..++.... .+.+....+.|++++|+|+++...|++|++ .|++||||.|+++.+ +.+..+
T Consensus       586 i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~  661 (684)
T TIGR03591       586 IEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVED  661 (684)
T ss_pred             EecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhh
Confidence            35578777753   22222111 122233357899999999999999999999 689999999999765 555554

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).

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

Probab=95.48  E-value=0.13  Score=46.52  Aligned_cols=39  Identities=23%  Similarity=0.337  Sum_probs=35.5

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      .++.+|+++.|+|+++++.|++|++|. .+|+++.+++.+
T Consensus        77 f~P~~GEVv~g~V~~v~~~Gi~V~lg~-~~g~v~~~~l~~  115 (187)
T PRK08563         77 FKPELQEVVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMD  115 (187)
T ss_pred             EeccCCCEEEEEEEEEEccEEEEEEeC-ceEEEEcHHcCC
Confidence            467789999999999999999999984 899999999864

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

Probab=95.48  E-value=0.028  Score=43.82  Aligned_cols=38  Identities=13%  Similarity=0.229  Sum_probs=34.0

Q ss_pred             HhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCcccc
Q 019315          293 IKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLS  330 (343)
Q Consensus       293 a~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~  330 (343)
                      .++.|+.++|+|+++.+.|++|+++ ++.||+|.|++..
T Consensus        13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~~   51 (77)
T cd04473          13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLR   51 (77)
T ss_pred             hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhccC
Confidence            3668999999999999999999994 6999999998753

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.

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

Probab=95.45  E-value=0.017  Score=41.11  Aligned_cols=32  Identities=19%  Similarity=0.352  Sum_probs=28.8

Q ss_pred             EEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315          300 IEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR  331 (343)
Q Consensus       300 VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r  331 (343)
                      ++|+|+++.+.|++|+++ |++||+|.+++..+
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~   33 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDK   33 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCc
Confidence            479999999999999995 89999999999754

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.43  E-value=0.051  Score=58.91  Aligned_cols=70  Identities=16%  Similarity=0.129  Sum_probs=49.6

Q ss_pred             ecCCCceEEeHHHHH-HHHHHHHHH---HHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315          268 RTLSGRPLLSTRRLF-RKMAWHRVR---QIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTE  337 (343)
Q Consensus       268 ~de~G~I~LS~Krl~-~~~aWe~l~---qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nlee  337 (343)
                      .+++|.+.++..-.. ...+-+.+.   ...+.|++++|+|+++.+.|++|++ .|.+||+|.|+++.+ +++..+
T Consensus       589 i~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~  664 (693)
T PRK11824        589 IEDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVED  664 (693)
T ss_pred             cCCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccc
Confidence            356788887653221 112222222   2357899999999999999999999 589999999999864 555444

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.39  E-value=0.05  Score=56.29  Aligned_cols=40  Identities=15%  Similarity=0.281  Sum_probs=34.8

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEe----CC-CeeEEEeccccCc
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNV----GA-DLLGTMLTKEVLP  207 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDI----G~-KsEG~IPisEls~  207 (343)
                      +.-+.|++|+|+|.+++.+.++||+    |. +++|+||.+|..+
T Consensus       148 f~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip  192 (449)
T PRK12329        148 FQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLP  192 (449)
T ss_pred             HHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCC
Confidence            4556899999999999999999999    43 4999999999874

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=95.35  E-value=0.095  Score=39.61  Aligned_cols=35  Identities=23%  Similarity=0.056  Sum_probs=22.1

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       172 ~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      .|++.+.+|+.+++.|+|++.|...+-+||.+|+.
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~   35 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP   35 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG--
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC
Confidence            48999999999999999999988789999999974

>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=95.32  E-value=0.016  Score=47.93  Aligned_cols=36  Identities=14%  Similarity=0.233  Sum_probs=33.3

Q ss_pred             hCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS  330 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~  330 (343)
                      +.|++|.|+|+++...|++|.+ +|++||+|.+++..
T Consensus         2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~   38 (100)
T cd05693           2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISD   38 (100)
T ss_pred             CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhH
Confidence            4799999999999999999999 58999999999974

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.

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

Probab=95.27  E-value=0.033  Score=45.15  Aligned_cols=35  Identities=20%  Similarity=0.327  Sum_probs=32.4

Q ss_pred             CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      .|++|+|+|+++++-|++|.++.+++|++.+|+..
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~   35 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPS   35 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCc
Confidence            48999999999999999999988999999999953

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=95.24  E-value=0.043  Score=61.03  Aligned_cols=71  Identities=10%  Similarity=0.096  Sum_probs=50.0

Q ss_pred             ecCCCceEEeHHH-HHHHHHHHHHHHH---hhCCCcEE-EEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhhh
Q 019315          268 RTLSGRPLLSTRR-LFRKMAWHRVRQI---KQLNEPIE-VKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTEL  338 (343)
Q Consensus       268 ~de~G~I~LS~Kr-l~~~~aWe~l~qa---~e~g~~Ve-GkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nleel  338 (343)
                      ++++|.+.+...- .....+-+.+.++   .+.|++++ |+|+++..+|++|++ .|++||||.|+++++ +.+.++.
T Consensus       721 i~ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv  798 (891)
T PLN00207        721 TQDDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDA  798 (891)
T ss_pred             cCCCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHh
Confidence            3456666654322 2222344445554   36999995 699999999999999 599999999999875 6666553

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

Probab=94.68  E-value=0.22  Score=53.58  Aligned_cols=39  Identities=15%  Similarity=0.072  Sum_probs=35.0

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeC-CCeeEEEeccccCc
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNVG-ADLLGTMLTKEVLP  207 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDIG-~KsEG~IPisEls~  207 (343)
                      +-+.|+.++|+|+.|++.|+||.+. ...+|++|++++.+
T Consensus       569 ~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~  608 (654)
T TIGR00358       569 LDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHN  608 (654)
T ss_pred             hhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCC
Confidence            3467999999999999999999996 77999999999863

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.

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

Probab=94.59  E-value=0.032  Score=51.50  Aligned_cols=39  Identities=28%  Similarity=0.381  Sum_probs=35.7

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      ..+..|++|+|+|+++++.|+||.|| -.+|++|.+++.+
T Consensus        77 fkP~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~d  115 (183)
T COG1095          77 FKPFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMD  115 (183)
T ss_pred             EEeccccEEEEEEEEEeecceEEEec-cccccccHhhccC
Confidence            56778999999999999999999999 5799999999974

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

Probab=94.59  E-value=0.059  Score=43.77  Aligned_cols=33  Identities=21%  Similarity=0.279  Sum_probs=30.3

Q ss_pred             CcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          298 EPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       298 ~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      ++++|+|+++++.|++|++.++.||+|.+++..
T Consensus         1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~   33 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMD   33 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccC
Confidence            468999999999999999988999999999864

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.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=94.53  E-value=0.05  Score=55.69  Aligned_cols=40  Identities=18%  Similarity=0.198  Sum_probs=36.3

Q ss_pred             CCCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEeccccCc
Q 019315          168 YEPKPGDFVIGVVVSGNEN--KLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~--gv~VDIG~KsEG~IPisEls~  207 (343)
                      ....+|++..|+|.++.+.  +||||||.+..||+|++|+.+
T Consensus        21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~   62 (414)
T TIGR00757        21 SRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGP   62 (414)
T ss_pred             CcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCc
Confidence            4456899999999999998  999999999999999999864

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.

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

Probab=93.94  E-value=0.086  Score=56.11  Aligned_cols=78  Identities=15%  Similarity=0.185  Sum_probs=61.6

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      ..+..|-+-+++|.++.+.|+||.+-....|++|.+|++...                       +.  ++         
T Consensus       664 ~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~-----------------------ia--kp---------  709 (760)
T KOG1067|consen  664 QDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEK-----------------------IA--KP---------  709 (760)
T ss_pred             cceEeeeEEEEEEeeecccceEEEecCCchhhccchhccccc-----------------------cc--Ch---------
Confidence            356678888999999999999999988999999999997321                       00  01         


Q ss_pred             CCCCCCceeccceEEEEEEeecCCCceEEeHHHHHH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFR  283 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~  283 (343)
                          ..+.++|+++.+++++.|..|.+.||.|++..
T Consensus       710 ----sd~levGq~I~vk~ie~d~~g~~~ls~ralLp  741 (760)
T KOG1067|consen  710 ----SDLLEVGQEIQVKYIERDPRGGIMLSSRALLP  741 (760)
T ss_pred             ----HHHHhhcceeEEEEEeecCccceeehhhhhcC
Confidence                12247788899999999888888998888775

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

Probab=93.74  E-value=0.057  Score=49.86  Aligned_cols=35  Identities=20%  Similarity=0.249  Sum_probs=33.0

Q ss_pred             CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      .|++|+|.|++.++.|++|.+.=+.||+|.||+..
T Consensus        81 ~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~d  115 (183)
T COG1095          81 RGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMD  115 (183)
T ss_pred             cccEEEEEEEEEeecceEEEeccccccccHhhccC
Confidence            68999999999999999999977999999999964

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

Probab=93.43  E-value=0.1  Score=47.60  Aligned_cols=35  Identities=20%  Similarity=0.383  Sum_probs=32.6

Q ss_pred             CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      .|++|+|+|+++++.|++|.++=+++|+|.+||..
T Consensus        81 ~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~  115 (176)
T PTZ00162         81 KDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPP  115 (176)
T ss_pred             CCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCC
Confidence            69999999999999999999966899999999963

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

Probab=93.11  E-value=0.2  Score=40.62  Aligned_cols=34  Identities=24%  Similarity=0.203  Sum_probs=30.4

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       172 ~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      +|++|+|+|+++++.|+||.+| ..++|++...+-
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip   34 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIP   34 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecC
Confidence            5899999999999999999997 478999988774

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.

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=91.58  E-value=0.28  Score=46.37  Aligned_cols=37  Identities=27%  Similarity=0.430  Sum_probs=34.3

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR  331 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r  331 (343)
                      +.|++|.|+|+++...|+.|+++ ++.||||.|++..+
T Consensus        62 ~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~   99 (235)
T PRK04163         62 KVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGR   99 (235)
T ss_pred             CCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCC
Confidence            68999999999999999999996 79999999999764

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

Probab=91.48  E-value=0.28  Score=44.68  Aligned_cols=38  Identities=13%  Similarity=0.192  Sum_probs=34.3

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      .++-+|++|+|+|+++++.|++|++|. .+++||.+.+.
T Consensus        77 FrPf~gEVv~g~V~~v~~~G~~v~~Gp-~~ifI~~~~l~  114 (176)
T PTZ00162         77 FKPFKDEVLDAIVTDVNKLGFFAQAGP-LKAFVSRSAIP  114 (176)
T ss_pred             EecCCCCEEEEEEEEEecceEEEEeeC-eEEEEcHHHCC
Confidence            567789999999999999999999985 56999999984

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

Probab=91.06  E-value=0.37  Score=43.57  Aligned_cols=36  Identities=22%  Similarity=0.296  Sum_probs=33.2

Q ss_pred             CCCcEEEEEEEEecCeeEEEECCeEEEEeCCccccC
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLSR  331 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~r  331 (343)
                      .|++++|+|+++++.|++|+++.+.||++.+++..+
T Consensus        81 ~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~  116 (187)
T PRK08563         81 LQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDD  116 (187)
T ss_pred             CCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCC
Confidence            699999999999999999999779999999998643

>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=90.99  E-value=0.43  Score=45.38  Aligned_cols=87  Identities=20%  Similarity=0.299  Sum_probs=58.2

Q ss_pred             CCCCC--CCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeee-cCCcceec
Q 019315          168 YEPKP--GDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIV-KDDDAIAM  244 (343)
Q Consensus       168 ~~~k~--GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i-~~dgaV~I  244 (343)
                      ++++.  |++..|++.+..++|+.||++ +...-+|.+|+.+++.                    |.+..+ .-+|.|  
T Consensus        68 ~~le~v~Ge~y~G~l~s~~~~G~~~~v~-G~~~~ip~d~L~~Lg~--------------------g~~~Qi~~rFG~V--  124 (225)
T PF09883_consen   68 YSLEPVKGETYVGTLISWDEDGYGVDVD-GIFVPIPKDELKPLGP--------------------GSPRQIRRRFGLV--  124 (225)
T ss_pred             chhcccCCceEEEEEEeecccceEEEee-cccccCcHHHhcccCC--------------------CCHHHHHHHhCcc--
Confidence            44455  999999999999999999998 7788999999976642                    111111 112221  


Q ss_pred             cCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHH
Q 019315          245 SGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHR  289 (343)
Q Consensus       245 g~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~  289 (343)
                              +-    ..++..++..++....+||.++.++...|.+
T Consensus       125 --------~h----lPvev~~v~~~~~~~~rltd~q~d~l~~W~~  157 (225)
T PF09883_consen  125 --------QH----LPVEVEFVKVEDGIEARLTDEQVDRLYEWTR  157 (225)
T ss_pred             --------cC----CceEEEEEEcccCcccccCHHHHHHHHHHhh
Confidence                    10    1123344444444778999999998888875

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

Probab=90.96  E-value=0.34  Score=43.74  Aligned_cols=35  Identities=14%  Similarity=0.179  Sum_probs=32.7

Q ss_pred             CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      .|++++|+|+++++.|++|+++.++|+++.+++..
T Consensus        81 ~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~  115 (179)
T TIGR00448        81 LGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTD  115 (179)
T ss_pred             CCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCC
Confidence            69999999999999999999977999999999864

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

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

Probab=90.58  E-value=0.58  Score=50.82  Aligned_cols=71  Identities=10%  Similarity=0.080  Sum_probs=52.4

Q ss_pred             eecCCCceEEeHHHHH---HHH-HHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315          267 GRTLSGRPLLSTRRLF---RKM-AWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTE  337 (343)
Q Consensus       267 ~~de~G~I~LS~Krl~---~~~-aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nlee  337 (343)
                      .++++|.+.++-....   +.+ ..+.+....+.|++.+|+|+++.+.|.+|++ +|-.|+++.||++.. +.+.++
T Consensus       586 dieddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~d  662 (692)
T COG1185         586 DIEDDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVED  662 (692)
T ss_pred             EecCCCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccc
Confidence            3468898887764422   222 2233444578999999999999999999999 789999999999863 544443

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

Probab=90.53  E-value=1.2  Score=43.88  Aligned_cols=66  Identities=24%  Similarity=0.116  Sum_probs=53.9

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCC
Q 019315          172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPG  251 (343)
Q Consensus       172 ~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~  251 (343)
                      .++.|.|+|-+....|.||=+..+.-|+||.+|....                                           
T Consensus       155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~-------------------------------------------  191 (287)
T COG2996         155 KNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAE-------------------------------------------  191 (287)
T ss_pred             hcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhccc-------------------------------------------
Confidence            3999999999999999999998899999999997511                                           


Q ss_pred             CCceeccceEEEEEEeecCCCceEEeHHHHHH
Q 019315          252 RPVVETGTVLFAEVLGRTLSGRPLLSTRRLFR  283 (343)
Q Consensus       252 i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~  283 (343)
                         ..+|+.+.+.|+...++|+|-||.+....
T Consensus       192 ---prlG~~l~~rVi~~reDg~lnLSl~p~~~  220 (287)
T COG2996         192 ---PRLGERLTARVIGVREDGKLNLSLRPRAH  220 (287)
T ss_pred             ---ccCCceEEEEEEEEccCCeeecccccccH
Confidence               13456677788887789999999877554

>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]

Probab=89.63  E-value=0.86  Score=40.98  Aligned_cols=51  Identities=14%  Similarity=0.139  Sum_probs=42.7

Q ss_pred             chhHHHHhhccc---CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          156 DKVGEDKVSVEY---YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       156 ~~dFa~lLe~~~---~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      +..|+.||-.+.   -..-+|..|.|+|..|..+.+|||.|.|.-.++.+-++.
T Consensus        63 nqsFASlLRnSkl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~n  116 (173)
T KOG4078|consen   63 NQSFASLLRNSKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPALN  116 (173)
T ss_pred             hhhHHHHHhcCccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCcC
Confidence            589999996542   123469999999999999999999999999999887764

>PRK11642 exoribonuclease R; Provisional

Probab=87.58  E-value=1.2  Score=49.36  Aligned_cols=44  Identities=11%  Similarity=0.228  Sum_probs=36.1

Q ss_pred             HHHHHHHh-hCCCcEEEEEEEEecCeeEEEEC--CeEEEEeCCcccc
Q 019315          287 WHRVRQIK-QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS  330 (343)
Q Consensus       287 We~l~qa~-e~g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~  330 (343)
                      |...+-+. ..|++++|+|+++++.|++|+++  +++||+|.|++..
T Consensus       633 ~~~~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~  679 (813)
T PRK11642        633 WLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDN  679 (813)
T ss_pred             HHHHhhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCC
Confidence            44443333 58999999999999999999995  4999999998863

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=87.58  E-value=1.3  Score=45.05  Aligned_cols=35  Identities=14%  Similarity=0.251  Sum_probs=31.6

Q ss_pred             hCCCcEEEEEEEEec-CeeEEEECCeEEEEeCCccc
Q 019315          295 QLNEPIEVKFTEWNT-GGLLTRIEGLRAFLPKAELL  329 (343)
Q Consensus       295 e~g~~VeGkVve~nK-GGliVeIeGlrgFIP~SQl~  329 (343)
                      +.|++|+|+|.++.+ ++++|+++++.|+||.++.-
T Consensus       137 ~~Geiv~g~V~r~~~~~~i~vdlg~~ea~LP~~eqi  172 (374)
T PRK12328        137 KVGKIVFGTVVRVDNEENTFIEIDEIRAVLPMKNRI  172 (374)
T ss_pred             hcCcEEEEEEEEEecCCCEEEEcCCeEEEeCHHHcC
Confidence            589999999999996 56999999999999999875

>TIGR02063 RNase_R ribonuclease R

Probab=87.24  E-value=1.3  Score=48.12  Aligned_cols=35  Identities=17%  Similarity=0.276  Sum_probs=32.8

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC--CeEEEEeCCccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELL  329 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~  329 (343)
                      +.|++++|+|+++.+.|++|+++  |++||+|.|++.
T Consensus       626 ~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~  662 (709)
T TIGR02063       626 KIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLK  662 (709)
T ss_pred             cCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecC
Confidence            57999999999999999999995  699999999996

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.

>PRK11712 ribonuclease G; Provisional

Probab=86.48  E-value=0.85  Score=47.90  Aligned_cols=39  Identities=15%  Similarity=0.145  Sum_probs=34.8

Q ss_pred             CCCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEeccccC
Q 019315          168 YEPKPGDFVIGVVVSGNEN--KLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~--gv~VDIG~KsEG~IPisEls  206 (343)
                      .....|.|..|+|.+|.+.  .||||||.+..||+|++++.
T Consensus        34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~   74 (489)
T PRK11712         34 KRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIV   74 (489)
T ss_pred             cccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhcc
Confidence            3445899999999999884  99999999999999999985

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

Probab=86.38  E-value=2.9  Score=39.03  Aligned_cols=103  Identities=19%  Similarity=0.122  Sum_probs=63.5

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCC----C------eeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeec
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGA----D------LLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVK  237 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~----K------sEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~  237 (343)
                      .-+++|++|-|.|+++....+.|.|-.    .      ..|.+|++.+...+                       +    
T Consensus        60 ~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~-----------------------~----  112 (188)
T COG1096          60 PLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGY-----------------------V----  112 (188)
T ss_pred             CCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEeccccc-----------------------c----
Confidence            347889999999999999999999821    1      23555555554211                       1    


Q ss_pred             CCcceeccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEec--CeeEEE
Q 019315          238 DDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNT--GGLLTR  315 (343)
Q Consensus       238 ~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nK--GGliVe  315 (343)
                                 .-+.+-+.+||.+-+.|++..  -.+.||.+.=+                  -|.|.....  ++.++.
T Consensus       113 -----------~~~~d~f~~GDivrA~Vis~~--~~~~Lst~~~d------------------lGVI~A~CsrC~~~L~~  161 (188)
T COG1096         113 -----------EKLSDAFRIGDIVRARVISTG--DPIQLSTKGND------------------LGVIYARCSRCRAPLVK  161 (188)
T ss_pred             -----------cccccccccccEEEEEEEecC--CCeEEEecCCc------------------ceEEEEEccCCCcceEE
Confidence                       111233466777888887643  45777764422                  466666553  233444


Q ss_pred             ECCeEEEEeCCccc
Q 019315          316 IEGLRAFLPKAELL  329 (343)
Q Consensus       316 IeGlrgFIP~SQl~  329 (343)
                       .|..--+|..+.-
T Consensus       162 -~~~~l~Cp~Cg~t  174 (188)
T COG1096         162 -KGNMLKCPNCGNT  174 (188)
T ss_pred             -cCcEEECCCCCCE
Confidence             6777777777653

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

Probab=85.70  E-value=2  Score=46.44  Aligned_cols=36  Identities=11%  Similarity=0.318  Sum_probs=33.0

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC--CeEEEEeCCcccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAELLS  330 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl~~  330 (343)
                      +.|+.++|+|++++++|++|+++  |++||+|.|++..
T Consensus       571 ~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~  608 (654)
T TIGR00358       571 KVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHN  608 (654)
T ss_pred             CCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCC
Confidence            57999999999999999999995  7999999999864

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.

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

Probab=84.25  E-value=1.5  Score=42.85  Aligned_cols=41  Identities=22%  Similarity=0.441  Sum_probs=38.0

Q ss_pred             ccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       166 ~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      ..|.++.||+|.|+|+.|.....-||++.|.+++++++-+-
T Consensus        79 ~rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvN  119 (301)
T KOG3013|consen   79 SRYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVN  119 (301)
T ss_pred             hhcCCccCCEEEEEeeeeecceeEEecccccceEEEeeccc
Confidence            45788999999999999999999999999999999998875

>PRK10811 rne ribonuclease E; Reviewed

Probab=83.34  E-value=1.4  Score=49.87  Aligned_cols=37  Identities=22%  Similarity=0.234  Sum_probs=33.9

Q ss_pred             CCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEeccccC
Q 019315          170 PKPGDFVIGVVVSGNEN--KLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~--gv~VDIG~KsEG~IPisEls  206 (343)
                      ..+|+|..|+|.+|.++  ++|||||.+..|||+++++.
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~   74 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIA   74 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhcc
Confidence            45899999999999874  99999999999999999985

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=83.33  E-value=1.9  Score=32.49  Aligned_cols=34  Identities=21%  Similarity=0.204  Sum_probs=21.4

Q ss_pred             CCcEEEEEEEEecCeeEEEECC-eEEEEeCCcccc
Q 019315          297 NEPIEVKFTEWNTGGLLTRIEG-LRAFLPKAELLS  330 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeIeG-lrgFIP~SQl~~  330 (343)
                      |++.+.+|++.++.|++++.++ -+.|||.+++..
T Consensus         2 G~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~   36 (61)
T PF13509_consen    2 GQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPE   36 (61)
T ss_dssp             -------EEEE-SSEEEEEETT-EEEEEEGGG---
T ss_pred             CCCcceEEEEEeCCEEEEECCCCCEEEechHHcCC
Confidence            7788999999999999999864 899999999854

>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=81.87  E-value=2.1  Score=34.76  Aligned_cols=23  Identities=39%  Similarity=0.564  Sum_probs=18.6

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEe
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNV  192 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDI  192 (343)
                      +++|++|.|+|++++...++++|
T Consensus         2 P~vGdiV~~rVtrv~~~~a~v~I   24 (82)
T PF10447_consen    2 PKVGDIVIARVTRVNPRQAKVEI   24 (82)
T ss_dssp             --TT-EEEEEEEEE-SSEEEEEE
T ss_pred             CCCCCEEEEEEEEEeccEEEEEE
Confidence            57899999999999999999998

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	343
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-05

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 44.1 bits (103), Expect = 6e-05
 Identities = 35/219 (15%), Positives = 71/219 (32%), Gaps = 71/219 (32%)

Query: 38  QQSRKFHSFAASFRFLRSTHIVFCSQKDVFDDLSSA---QFPENVENEGLEGNEELELLN 94
           Q ++ +++F  S + L +T       K V D LS+A       +  +  L  +E   LL 
Sbjct: 254 QNAKAWNAFNLSCKILLTT-----RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL- 307

Query: 95  KPNLVPISNGVASEVDKKSEK-PDEEEALAPF-LKFFKPRDSAEEVEEEGSEVGVSRESI 152
                         +D + +  P E     P  L        AE + +     G++    
Sbjct: 308 -----------LKYLDCRPQDLPREVLTTNPRRLSII-----AESIRD-----GLAT--W 344

Query: 153 DVDDKVGEDKV------SVE---------YYEPKPGDFVIGVVVSGNENKL--DVNVGAD 195
           D    V  DK+      S+           ++       +               ++   
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD----RLSV----------FPPSAHIPTI 390

Query: 196 LLGT----MLTKEVLPLYDKEMDFLLCDLKKDAEEFMVR 230
           LL      ++  +V+ + +K   + L  ++K  +E  + 
Sbjct: 391 LLSLIWFDVIKSDVMVVVNKLHKYSL--VEKQPKESTIS 427

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	343
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.75
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	99.45
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	99.21
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	99.09
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	99.02
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	98.9
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	98.9
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	98.88
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	98.8
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	98.75
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	98.75
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	98.72
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.72
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	98.72
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	98.64
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	98.62
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	98.4
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	98.34
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	98.34
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.31
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	98.31
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	98.24
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	98.23
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.22
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.22
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	98.19
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	98.12
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	98.02
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	97.95
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	97.87
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.84
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	97.81
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	97.79
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	97.55
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.32
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	97.21
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	97.13
2bh8_A	101	1B11; transcription, molecular evolution, unique a	97.11
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	97.09
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	97.08
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	97.06
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	97.06
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	96.98
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	96.97
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	96.95
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	96.94
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	96.9
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	96.75
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	96.72
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	96.59
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	96.34
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	96.06
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	95.94
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	95.87
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	95.73
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	95.65
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	95.6
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	95.55
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	95.4
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	95.24
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	94.89
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	94.7
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	94.44
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	94.21
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	94.0
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	93.39
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	93.35
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	92.92
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	92.88
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	92.73
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	92.55
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	91.25
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	90.56
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	90.05
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	89.92
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	89.45
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	89.27
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	85.73
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	84.5
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	82.7
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	82.46
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	80.47
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	80.37

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=99.75  E-value=9.3e-19  Score=166.78  Aligned_cols=159  Identities=12%  Similarity=0.070  Sum_probs=129.0

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhh-hhhhh----------hhHhhhcceeeeec-C
Q 019315          171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLC-DLKKD----------AEEFMVRGKMGIVK-D  238 (343)
Q Consensus       171 k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~-d~~k~----------~ee~~VeGkV~~i~-~  238 (343)
                      ..|++++|+|++++++|+|||+| +.+|+||.+|+...-++++++.+. |....          ..+..+.|+|+.++ +
T Consensus         5 ~~G~~v~g~V~~~~~~G~fv~~~-g~egllp~se~~~~vGdevev~v~~d~~~r~iat~~~p~~~~G~~~~g~V~~v~~~   83 (285)
T 3go5_A            5 NLASFIVGLIIDENDRFYFVQKD-GQTYALAKEEGQHTVGDTVKGFAYTDMKQKLRLTTLEVTATQDQFGWGRVTEVRKD   83 (285)
T ss_dssp             TTTEEEEEEEEEECSSEEEEEET-TEEEEEEGGGCCCCTTSEEEEEEEECTTSCEEEECSCCCSCSSSCEEEEEEEEETT
T ss_pred             cCCCEEEEEEEEEECCEEEEEcC-CeEEEEEHHHCccccCCEEEEEEEECCCCCEEEecccccccCCCEEEEEEEEEccC
Confidence            47999999999999999999997 899999999995322344443222 22111          23578899999999 7


Q ss_pred             Ccc-eeccC-CCCCCCCceec----------cceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEE
Q 019315          239 DDA-IAMSG-GSGPGRPVVET----------GTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTE  306 (343)
Q Consensus       239 dga-V~Ig~-~ieg~i~v~ei----------Gd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve  306 (343)
                      +|+ |.+|. ++++|+|++++          |+++.+. +..|.++||.||+|++...++|......|+.|+.|+|+|++
T Consensus        84 ~GaFVdiG~~~~d~lvp~sel~~~~~~~~~~Gd~v~v~-l~iD~~~Ri~ls~k~~~~~~~~~~~~~~~~~G~~V~g~V~~  162 (285)
T 3go5_A           84 LGVFVDTGLPDKEIVVSLDILPELKELWPKKGDQLYIR-LEVDKKDRIWGLLAYQEDFQRLARPAYNNMQNQNWPAIVYR  162 (285)
T ss_dssp             TEEEEECSCTTCCEEEEGGGSCSSGGGSCCTTCEEEEE-EEECTTSCEEEEECCHHHHHHHCCCCCSCCTTCEEEEEEEE
T ss_pred             ceEEEEECCCCcEEEEEHHHCCcccccccCCCCEEEEE-EEECCCCcEEEEehhhhhcchhhhhhhhCCCCCEEEEEEEE
Confidence            999 99987 68999998866          6777543 56666789999998776678998877789999999999999


Q ss_pred             EecCeeEE-EE-CCeEEEEeCCccccC
Q 019315          307 WNTGGLLT-RI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       307 ~nKGGliV-eI-eGlrgFIP~SQl~~r  331 (343)
                      +...|++| .+ +|+.||||.|++...
T Consensus       163 i~~~G~fV~~i~~g~~Glih~SEl~~~  189 (285)
T 3go5_A          163 LKLSGTFVYLPENNMLGFIHPSERYAE  189 (285)
T ss_dssp             EETTEEEEEETTTTEEEEECGGGCSSC
T ss_pred             EeCCcEEEEEeCCCeEEEEEHHHcccc
Confidence            99999999 99 589999999999753

>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=99.45  E-value=1.1e-15  Score=137.40  Aligned_cols=120  Identities=16%  Similarity=0.085  Sum_probs=98.4

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEe--CCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNV--GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDI--G~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      +++|++++|+|++|+++|+||+|  ..+.+|+||++|+++.+                       +..        +   
T Consensus        13 p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~-----------------------v~~--------~---   58 (182)
T 1kl9_A           13 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRR-----------------------IRS--------I---   58 (182)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------------------------------------
T ss_pred             CCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcc-----------------------cCC--------H---
Confidence            48999999999999999999999  56899999999998431                       100        1   


Q ss_pred             CCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEec-CeeEEEE-CCeEEEEe
Q 019315          248 SGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNT-GGLLTRI-EGLRAFLP  324 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nK-GGliVeI-eGlrgFIP  324 (343)
                          ..++.+|+.+.+.|+..+ ++++|.||+|++. ..+|..+.+.|+.|..++|+|+.+.+ .|  |++ +|+.|++|
T Consensus        59 ----~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~~~-~~p~~~~~~~~~~g~~v~g~v~~i~~~~g--v~l~~giegl~h  131 (182)
T 1kl9_A           59 ----NKLIRIGRNECVVVIRVDKEKGYIDLSKRRVS-PEEAIKCEDKFTKSKTVYSILRHVAEVLE--YTKDEQLESLFQ  131 (182)
T ss_dssp             --------CTTCEEEEEEEEEETTTTEEEEESTTCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT--CCSHHHHHHHHH
T ss_pred             ----HHhcCCCCEEEEEEEEEECCCCEEEEEEeecC-cChHHHHHHhccCCCEEEEEEEEchhhcC--CcccCChhheEE
Confidence                234578899999999876 5799999999988 58999999999999999999999997 99  677 58999999


Q ss_pred             CCcccc
Q 019315          325 KAELLS  330 (343)
Q Consensus       325 ~SQl~~  330 (343)
                      .|.+++
T Consensus       132 ~s~~~~  137 (182)
T 1kl9_A          132 RTAWVF  137 (182)
T ss_dssp             HTHHHH
T ss_pred             eeecch
Confidence            998753

>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=99.21  E-value=2.3e-12  Score=114.95  Aligned_cols=103  Identities=17%  Similarity=0.092  Sum_probs=82.7

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315          171 KPGDFVIGVVVSGNENKLDVNVG--ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS  248 (343)
Q Consensus       171 k~GdiVeG~VVsI~~~gv~VDIG--~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i  248 (343)
                      ++|++++|+|++|.++|+||+|.  .+.+|+||++|+++.+                       +..        +    
T Consensus        14 ~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~-----------------------v~~--------~----   58 (175)
T 2a19_A           14 EIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRR-----------------------IRS--------I----   58 (175)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC-------------------------------C--------C----
T ss_pred             CCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcc-----------------------cCC--------H----
Confidence            48999999999999999999993  6799999999998431                       000        1    


Q ss_pred             CCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEe-cCee
Q 019315          249 GPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN-TGGL  312 (343)
Q Consensus       249 eg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~n-KGGl  312 (343)
                         ..++.+|+.+.+.|+..+ +.++|.||+|++. ..+|..+.+.|+.|..++|+|+.+. +.|+
T Consensus        59 ---~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~~~-~~~~~~~~~~~~~g~~v~g~V~~i~~~~G~  120 (175)
T 2a19_A           59 ---QKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVS-SEDIIKCEEKYQKSKTVHSILRYCAEKFQI  120 (175)
T ss_dssp             ---CCCCCTTSEEEEEEEEEETTTTEEEEESTTCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             ---HHcCCCCCEEEEEEEEEECCCCeEEEEEEecC-cChHHHHHHhccCCCcceEEEEEchhhcCC
Confidence               234578899999999876 5789999999988 4999999999999999999998888 6776

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=99.09  E-value=2.7e-11  Score=115.40  Aligned_cols=122  Identities=14%  Similarity=-0.074  Sum_probs=93.3

Q ss_pred             CCCCCCCEEEEEEEEEe-CCeEEEEeCC-CeeEEEeccccCccc------ccchh-hhhh----------------hhhh
Q 019315          168 YEPKPGDFVIGVVVSGN-ENKLDVNVGA-DLLGTMLTKEVLPLY------DKEMD-FLLC----------------DLKK  222 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~-~~gv~VDIG~-KsEG~IPisEls~~~------~ke~e-~l~~----------------d~~k  222 (343)
                      ..++.|+++.|+|++++ +.|||||+|. ..+|+||++|+++..      ++++. .+.+                +.|.
T Consensus        65 p~~~~G~~~~g~V~~v~~~~GaFVdiG~~~~d~lvp~sel~~~~~~~~~~Gd~v~v~l~iD~~~Ri~ls~k~~~~~~~~~  144 (285)
T 3go5_A           65 VTATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPELKELWPKKGDQLYIRLEVDKKDRIWGLLAYQEDFQRLA  144 (285)
T ss_dssp             CCSCSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGGSCSSGGGSCCTTCEEEEEEEECTTSCEEEEECCHHHHHHHC
T ss_pred             ccccCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHHCCcccccccCCCCEEEEEEEECCCCcEEEEehhhhhcchhh
Confidence            35678999999999999 7999999998 589999999997532      22221 0111                1221


Q ss_pred             h-----hhHhhhcceeeeecCCcc-e-eccCCCCCCCCceecc------ceEEEEEEeecC-CCceEEeHHHHHHHHHHH
Q 019315          223 D-----AEEFMVRGKMGIVKDDDA-I-AMSGGSGPGRPVVETG------TVLFAEVLGRTL-SGRPLLSTRRLFRKMAWH  288 (343)
Q Consensus       223 ~-----~ee~~VeGkV~~i~~dga-V-~Ig~~ieg~i~v~eiG------d~v~~eVl~~de-~G~I~LS~Krl~~~~aWe  288 (343)
                      .     ..+..|+|+|..++++|+ | .+.++++||+|++++.      +++.+.|+..++ +|+|.||+|++.. .+|+
T Consensus       145 ~~~~~~~~G~~V~g~V~~i~~~G~fV~~i~~g~~Glih~SEl~~~l~~Gd~v~~~V~~id~~d~kI~LSlk~~~~-~~~~  223 (285)
T 3go5_A          145 RPAYNNMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERYAEPRLGQVLDARVIGFREVDRTLNLSLKPRSF-EMLE  223 (285)
T ss_dssp             CCCCSCCTTCEEEEEEEEEETTEEEEEETTTTEEEEECGGGCSSCCCTTCEEEEEEEEEETTTTEEEEECSCCCC-CCCC
T ss_pred             hhhhhCCCCCEEEEEEEEEeCCcEEEEEeCCCeEEEEEHHHccccCCCCCEEEEEEEEEECCCCeEEEEeChhhh-hccc
Confidence            1     235789999999999999 9 9999999999987655      889999998765 8999999998653 3444


Q ss_pred             HH
Q 019315          289 RV  290 (343)
Q Consensus       289 ~l  290 (343)
                      ..
T Consensus       224 ~~  225 (285)
T 3go5_A          224 ND  225 (285)
T ss_dssp             HH
T ss_pred             hH
Confidence            43

>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=99.02  E-value=3.6e-11  Score=115.86  Aligned_cols=107  Identities=15%  Similarity=0.013  Sum_probs=89.6

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNVG--ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDIG--~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      .+++|++++|+|++|.++|+||+|+  .+.+|+||++|+++.+.                       .            
T Consensus        10 ~~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i-----------------------~------------   54 (308)
T 1q8k_A           10 FPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRI-----------------------R------------   54 (308)
T ss_dssp             CCSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSC-----------------------S------------
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccc-----------------------c------------
Confidence            3568999999999999999999997  68999999999985310                       0            


Q ss_pred             CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecC-eeEE
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTG-GLLT  314 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKG-GliV  314 (343)
                         -...++.+|+.+.+.|+..+ +.++|.||+|++. ..+|..+.+.|+.|..++|+|+++... |+++
T Consensus        55 ---~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~~-~~p~~~~~~~~~~G~~v~G~V~~v~~~~G~fi  120 (308)
T 1q8k_A           55 ---SINKLIRIGRNECVKVIRVDKEKGYIDLSKRRVS-PEEAIKCEDKFTKSKTVYSILRHVAEVLEYTK  120 (308)
T ss_dssp             ---CCTTTCSSSCEEEEEEEEEETTTTEEEEECSSCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCS
T ss_pred             ---CHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEecc-cChHHHHHHHccCCCeeEEEEEEcccccCCcc
Confidence               01234578899999999876 5799999999988 599999999999999999999999884 8754

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=98.90  E-value=3.5e-10  Score=93.59  Aligned_cols=87  Identities=18%  Similarity=0.106  Sum_probs=68.6

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      ...+++|++++|+|+++.++|+||+|+.+.+|+||++|+++..                      ++   ..     .  
T Consensus        25 ~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~----------------------~~---~~-----~--   72 (115)
T 2khi_A           25 AKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTN----------------------KN---IH-----P--   72 (115)
T ss_dssp             SCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSS----------------------TT---CS-----S--
T ss_pred             hhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccc----------------------cc---cC-----c--
Confidence            3578899999999999999999999998899999999997310                      00   00     0  


Q ss_pred             CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVR  291 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~  291 (343)
                           .....+|+.+.+.|+..+ ++++|.||+|++.. +||+++.
T Consensus        73 -----~~~~~vGd~V~vkV~~vd~~~~rI~lslk~~~~-~p~~~~~  112 (115)
T 2khi_A           73 -----SKVVNVGDVVEVMVLDIDEERRRISLGLKQCKA-NPWQQFA  112 (115)
T ss_dssp             -----TTTCCTTCEEEEEEEEEETTTTEEEECCCCCCS-SCCCCCC
T ss_pred             -----ccEECCCCEEEEEEEEEECCCCEEEEEEEecCc-CHHHHHH
Confidence                 123577889999999876 47899999998874 7897654

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A

Probab=98.90  E-value=2.8e-10  Score=108.04  Aligned_cols=105  Identities=19%  Similarity=0.166  Sum_probs=86.3

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNVG--ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDIG--~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      .+++|++|+|+|++|.++|+||+++  .+.+|+||++|+++.+                       +.   +     +  
T Consensus         8 ~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~-----------------------v~---~-----~--   54 (275)
T 3aev_A            8 YPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTW-----------------------VR---N-----I--   54 (275)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSC-----------------------CS---C-----G--
T ss_pred             CCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCccc-----------------------cc---C-----H--
Confidence            3568999999999999999999997  4799999999998431                       00   0     1  


Q ss_pred             CCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEe-cCee
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN-TGGL  312 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~n-KGGl  312 (343)
                           .....+|+.+.+.|+..+ ++++|.||+|++. ..+|....+.|+.|+.++|.|..+. +.|+
T Consensus        55 -----~~~~kvGd~V~vkVi~vD~~~~~I~LSlk~~~-~~~~~~~~~~~~~g~~v~g~v~~v~~~~G~  116 (275)
T 3aev_A           55 -----RDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVT-QQQRKAKLQEFKRAQKAENLLRLAAEKLGK  116 (275)
T ss_dssp             -----GGTCCTTCEEEEEEEEEETTTTEEEEESTTCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             -----HhccCCCCEEEEEEEEEECCCCEEEEEEeecC-cchhHHHHHhccCCCeEEEEEEEchhhcCC
Confidence                 123577889999999876 5799999999987 4899999999999999998888777 6665

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}

Probab=98.88  E-value=4e-09  Score=81.76  Aligned_cols=72  Identities=15%  Similarity=0.246  Sum_probs=59.8

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS  248 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i  248 (343)
                      .+++|++++|+|+++.++|+||+|+.+.+|++|++|+++.+                                  +    
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel~~~~----------------------------------~----   43 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLR----------------------------------L----   43 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSCC----------------------------------G----
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCccc----------------------------------c----
Confidence            47899999999999999999999998999999999997421                                  0    


Q ss_pred             CCCCCceeccceEEEEEEeecC-CCceEEeHHHHH
Q 019315          249 GPGRPVVETGTVLFAEVLGRTL-SGRPLLSTRRLF  282 (343)
Q Consensus       249 eg~i~v~eiGd~v~~eVl~~de-~G~I~LS~Krl~  282 (343)
                          ....+|+.+.+.|+..+. .|+|.||++++.
T Consensus        44 ----~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~~~   74 (80)
T 2k52_A           44 ----ENLNVGDEIIVQAIDVRPEKREIDFKYIPLE   74 (80)
T ss_dssp             ----GGCCTTCEEEEEEEEEETTTTEEEEEECSCC
T ss_pred             ----eeeCCCCEEEEEEEEEECCCCEEEEEEeecc
Confidence                124677888899998765 499999987755

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}

Probab=98.80  E-value=2.8e-08  Score=84.12  Aligned_cols=82  Identities=18%  Similarity=0.137  Sum_probs=65.7

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      ..+++|++++|+|++|.++|+||+|+.+.+|+||++|+++.+                       +.   +     +   
T Consensus         3 ~~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~-----------------------~~---~-----~---   48 (130)
T 2k4k_A            3 AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGF-----------------------VK---D-----I---   48 (130)
T ss_dssp             CCCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSC-----------------------CS---C-----G---
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCccc-----------------------cc---C-----c---
Confidence            458899999999999999999999988899999999997431                       00   0     1   


Q ss_pred             CCCCCCceeccceEEEEEEeecC-CCceEEeHHHHHHHHHHH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTL-SGRPLLSTRRLFRKMAWH  288 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de-~G~I~LS~Krl~~~~aWe  288 (343)
                          .....+|+.+.+.|+..+. +++|.||+|++.. .+|.
T Consensus        49 ----~~~~~vGd~V~vkV~~vd~~~~kI~LSlk~~~~-~p~~   85 (130)
T 2k4k_A           49 ----NEHLSVGDEVQVKVLAVDEEKGKISLSIRATQA-APEK   85 (130)
T ss_dssp             ----GGTCCTTCEEEEEEEEEETTTTEEEEESHHHHH-SCCC
T ss_pred             ----cccCCCCCEEEEEEEEEeCCCCEEEEEEeeccc-Cccc
Confidence                1235778899999998764 8999999999874 5654

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.75  E-value=9.1e-09  Score=83.65  Aligned_cols=84  Identities=21%  Similarity=0.122  Sum_probs=64.4

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCC---CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCccee
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGA---DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA  243 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~---KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~  243 (343)
                      ...++.|++++|+|++|.++|+||+|+.   +.+|+||++|+.+..                      ++.   .     
T Consensus         7 ~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~----------------------~~~---~-----   56 (103)
T 2eqs_A            7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREG----------------------RVA---N-----   56 (103)
T ss_dssp             CSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSS----------------------CCC---C-----
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCc----------------------ccC---C-----
Confidence            4568899999999999999999999985   899999999994210                      000   0     


Q ss_pred             ccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHH
Q 019315          244 MSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHR  289 (343)
Q Consensus       244 Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~  289 (343)
                      +       ..+..+|+.+.++|+..+. ++|.||+|++.. .+|+.
T Consensus        57 ~-------~~~~~~Gd~V~VkV~~vd~-~~i~LSlk~~~~-~~~~~   93 (103)
T 2eqs_A           57 V-------ADVVSKGQRVKVKVLSFTG-TKTSLSMKDVDQ-ETGED   93 (103)
T ss_dssp             H-------HHHCCTTCEEEEEEEEEET-TEEEEESTTBCT-TTCCB
T ss_pred             c-------ccEeCCCCEEEEEEEEEEC-CeeEEEEeeccc-CCchh
Confidence            0       1234678889999988765 699999998874 67754

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=98.75  E-value=9.4e-09  Score=84.02  Aligned_cols=78  Identities=21%  Similarity=0.126  Sum_probs=61.7

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      ...+++|++|+|+|++|.++|+||+|+.+.+|+||++|+++.+..                          .     +  
T Consensus        26 ~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~--------------------------~-----~--   72 (109)
T 2khj_A           26 VALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVE--------------------------D-----A--   72 (109)
T ss_dssp             TTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSS--------------------------S-----G--
T ss_pred             hhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCccccc--------------------------C-----h--
Confidence            357889999999999999999999999899999999999743100                          0     0  


Q ss_pred             CCCCCCCceeccceEEEEEEeecCC-CceEEeHHHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRTLS-GRPLLSTRRLF  282 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~de~-G~I~LS~Krl~  282 (343)
                           .....+|+.+.+.|+..+.+ ++|.||+|++.
T Consensus        73 -----~~~~~vGd~V~v~V~~vd~~~~ki~LS~k~~~  104 (109)
T 2khj_A           73 -----TLVLSVGDEVEAKFTGVDRKNRAISLSVRAKD  104 (109)
T ss_dssp             -----GGSCCTTCEEEEEEEEEETTTTEEEEETTSSS
T ss_pred             -----hhccCCCCEEEEEEEEEECCCCEEEEEEeecC
Confidence                 12346788899999987644 68999998754

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=98.72  E-value=9.2e-09  Score=81.89  Aligned_cols=80  Identities=15%  Similarity=0.192  Sum_probs=59.5

Q ss_pred             hhcccCCCCCCCEEEEEEEEEeCCeEEEEeCC--CeeEEEecc-ccCcccccchhhhhhhhhhhhhHhhhcceeeeecCC
Q 019315          163 VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGA--DLLGTMLTK-EVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDD  239 (343)
Q Consensus       163 Le~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~--KsEG~IPis-Els~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~d  239 (343)
                      |.-.+..+++|++++|+|+ |+++|+||+++.  +.+|++|++ |+++.+   +.    +.                   
T Consensus         2 ~~~~y~~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~---~~----~~-------------------   54 (88)
T 1luz_A            2 LAFCYSLPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDR---YV----EY-------------------   54 (88)
T ss_dssp             --CCSCCCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHH---HH----HH-------------------
T ss_pred             ceEEecCCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCccc---cc----CH-------------------
Confidence            4445667899999999999 999999999963  799999999 997421   00    00                   


Q ss_pred             cceeccCCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHH
Q 019315          240 DAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLF  282 (343)
Q Consensus       240 gaV~Ig~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~  282 (343)
                                  .... +|+.+.++|+..+ ++++|.||+|++.
T Consensus        55 ------------~~~~-~Gd~V~VkV~~vd~~~~kI~lslk~~~   85 (88)
T 1luz_A           55 ------------RDKL-VGKTVKVKVIRVDYTKGYIDVNYKRMC   85 (88)
T ss_dssp             ------------HHHH-TTCEEEEEEEEEETTTTEEEEEEEEEC
T ss_pred             ------------hHEe-CCCEEEEEEEEEECCCCEEEEEEeecC
Confidence                        0123 6778888898876 5789999987653

>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=98.72  E-value=1.5e-09  Score=102.30  Aligned_cols=98  Identities=14%  Similarity=0.124  Sum_probs=77.6

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceecc
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVG--ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS  245 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG--~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig  245 (343)
                      +.+++|++++|+|++|.++|+||+++  .+.+|+||++|+++.+..                       .        + 
T Consensus         7 ~~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~-----------------------~--------~-   54 (266)
T 3cw2_C            7 KLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVK-----------------------N--------I-   54 (266)
T ss_dssp             SSCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCC-----------------------C--------H-
T ss_pred             ccCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCccccc-----------------------C--------H-
Confidence            45789999999999999999999997  689999999999743100                       0        0 


Q ss_pred             CCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEE
Q 019315          246 GGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKF  304 (343)
Q Consensus       246 ~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkV  304 (343)
                            ...+.+|+.+.+.|+..+ ++|+|.||+|++. ..+|..+.+.|+.++.+.+.|
T Consensus        55 ------~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~~~-~~~~~~~~~~~~~~~~~~~iv  107 (266)
T 3cw2_C           55 ------RDVLKENRKVIVKVIRVDRRKGTVDVSLKKVT-DDERRKKNLQWKKIQRLDKIL  107 (266)
T ss_dssp             ------HHHSCTTCEEEEEECCCCSSSCCCBEESTTSC-TTHHHHHHHHHHHHHHHHHHH
T ss_pred             ------HHhCcCCCEEEEEEEEEeCCCCEEEEEEEecc-hhhHHHHHHhccccCccceee
Confidence                  123467888889998876 4799999999988 589999999888776554443

>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=98.72  E-value=3e-09  Score=88.99  Aligned_cols=85  Identities=12%  Similarity=0.115  Sum_probs=65.3

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~-KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      +.+++|++++|+|++|.++|+||+|+. +.+|+||++|+++.+...                               +  
T Consensus        18 ~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~-------------------------------~--   64 (119)
T 2cqo_A           18 NLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDK-------------------------------P--   64 (119)
T ss_dssp             CSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSC-------------------------------H--
T ss_pred             cccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccC-------------------------------h--
Confidence            568899999999999999999999954 579999999997431000                               0  


Q ss_pred             CCCCCCCceeccceEEEEEEeecC---CCceEEeHHHHHHHHHHHHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRTL---SGRPLLSTRRLFRKMAWHRVR  291 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~de---~G~I~LS~Krl~~~~aWe~l~  291 (343)
                           ..++.+|+.+.+.|+..+.   .++|.||+|++. ..+|+.+.
T Consensus        65 -----~~~~~~Gd~V~VkV~~vd~~~~~~~i~LSlk~~~-~~~~~~~~  106 (119)
T 2cqo_A           65 -----SEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVN-QGTGKDLD  106 (119)
T ss_dssp             -----HHHCCTTCEEEEEEEEEEECSSCEEEEEESTTBC-SSSCCBSC
T ss_pred             -----hhcCCCCCEEEEEEEEEeccccCceEEEEEeecc-cCCccccC
Confidence                 1234678888899987652   379999999987 47887653

>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=98.64  E-value=7.8e-08  Score=94.02  Aligned_cols=78  Identities=15%  Similarity=0.163  Sum_probs=63.0

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG  249 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie  249 (343)
                      .+.|++|+|+|.+++++++|||+| |+||+||++|+.+.                                         
T Consensus       132 ~~~GeIV~G~V~ri~~~~v~VDlG-k~EgiLp~sE~ip~-----------------------------------------  169 (344)
T 1hh2_P          132 ELKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKEWIPG-----------------------------------------  169 (344)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGSCTT-----------------------------------------
T ss_pred             hcCCCEEEEEEEEEecCcEEEEeC-CeEEEEeHHHcCCC-----------------------------------------
Confidence            348999999999999999999998 99999999999732                                         


Q ss_pred             CCCCceeccceEEEEEEeec---CCCceEEeHHHHHHHHHHHHHHH
Q 019315          250 PGRPVVETGTVLFAEVLGRT---LSGRPLLSTRRLFRKMAWHRVRQ  292 (343)
Q Consensus       250 g~i~v~eiGd~v~~eVl~~d---e~G~I~LS~Krl~~~~aWe~l~q  292 (343)
                         ....+|+.+.+.|+..+   ..+++.||+++......|-+++-
T Consensus       170 ---E~~~vGD~Vkv~V~~V~~~~kg~~I~LSRt~p~~lk~LfelEV  212 (344)
T 1hh2_P          170 ---EEIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVIGLMKLEI  212 (344)
T ss_dssp             ---CCCCTTCEEEEEEEEEEEETTEEEEEEESSSHHHHHHHHHHHC
T ss_pred             ---cCCCCCCEEEEEEEEEEcCCCCcEEEEEeeccHHHHHHHHhhc
Confidence               11255677777777542   34689999999998888987653

>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=98.62  E-value=5e-08  Score=90.20  Aligned_cols=93  Identities=19%  Similarity=0.282  Sum_probs=70.9

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      |.+++||+|.|+|+++.+++++||||++.+|+||++|+....   .                       ..+        
T Consensus        62 y~p~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~~~---~-----------------------~~~--------  107 (235)
T 2z0s_A           62 YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRP---F-----------------------NPA--------  107 (235)
T ss_dssp             CCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSC---C-----------------------CTT--------
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCCCc---c-----------------------ccc--------
Confidence            578999999999999999999999999999999999996210   0                       000        


Q ss_pred             CCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI  316 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI  316 (343)
                      ..-....+++||.+.++|+..++++++.||.|.                      ...++.++|+++.+
T Consensus       108 ~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k~----------------------~~lG~l~gG~vv~v  154 (235)
T 2z0s_A          108 VDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQG----------------------EGLGRIVRGKIVEI  154 (235)
T ss_dssp             TTCCTTSSCTTCEEEEEEEEECTTSCEEEECCS----------------------SSCEECCSSEEEEC
T ss_pred             hhhHhhcCCCCCEEEEEEEEECCCCcEEEEEec----------------------ccCccccCCEEEEE
Confidence            011134568899999999988777899999641                      12345588999987

>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=98.40  E-value=8e-07  Score=82.04  Aligned_cols=76  Identities=21%  Similarity=0.286  Sum_probs=61.2

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      |.+++||+|.|+|+.+.+++++|||+++.+|+||++|+.....                      +              
T Consensus        53 y~p~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~~~~----------------------~--------------   96 (229)
T 2ba0_A           53 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKP----------------------N--------------   96 (229)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCT----------------------T--------------
T ss_pred             ccCCCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHcccccc----------------------c--------------
Confidence            5689999999999999999999999999999999999972100                      0              


Q ss_pred             CCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr  280 (343)
                       .-..+.+++||.+.++|+..++++++.||.|+
T Consensus        97 -~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~  128 (229)
T 2ba0_A           97 -KKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKD  128 (229)
T ss_dssp             -SCGGGTCCTTCEEEEEEEEECTTCCEEEECCS
T ss_pred             -cchhcccCCCCEEEEEEEEECCCCcEEEEEcc
Confidence             00134467889999999988777899999753

>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=98.34  E-value=6.4e-07  Score=81.69  Aligned_cols=108  Identities=19%  Similarity=0.148  Sum_probs=74.8

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeC--------CCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVG--------ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKD  238 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG--------~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~  238 (343)
                      .+.+++||+|.|+|++|.+++++|||+        .+.+|+||++|+++.....                          
T Consensus        76 ~y~p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~--------------------------  129 (209)
T 2nn6_I           76 QLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDK--------------------------  129 (209)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCC--------------------------
T ss_pred             cCCCCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccc--------------------------
Confidence            367899999999999999999999985        4679999999997431000                          


Q ss_pred             CcceeccCCCCCCCCceeccceEEEEEEeecCC-CceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEec-CeeEEEE
Q 019315          239 DDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLS-GRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNT-GGLLTRI  316 (343)
Q Consensus       239 dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~de~-G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nK-GGliVeI  316 (343)
                         +.+       ...+++||.+.++|+..+++ +++.||.|+..                  -|+|..... |+.++.+
T Consensus       130 ---~~~-------~~~l~~GD~V~akVisi~~~~~~i~LS~k~~~------------------lGVv~A~c~~g~~m~~~  181 (209)
T 2nn6_I          130 ---VEI-------YKSFRPGDIVLAKVISLGDAQSNYLLTTAENE------------------LGVVVAHSESGIQMVPI  181 (209)
T ss_dssp             ---CCG-------GGTCCSSSEEEEEEEEEETTTTEEEEECCSSS------------------CEECCCBCSSSCBCEEE
T ss_pred             ---cch-------hhhcCCCCEEEEEEEEEeCCCCeEEEEEecCC------------------CcEEEEEcCCCCEEEEc
Confidence               001       23457889999999987644 57999988765                  356655554 4445555


Q ss_pred             CCeEEEEeCCcc
Q 019315          317 EGLRAFLPKAEL  328 (343)
Q Consensus       317 eGlrgFIP~SQl  328 (343)
                      .--.--+|..-.
T Consensus       182 ~~~~m~cp~cg~  193 (209)
T 2nn6_I          182 SWCEMQCPKTHT  193 (209)
T ss_dssp             ETTEEECTTTTC
T ss_pred             cCCEEECCCCCC
Confidence            322344565543

>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=98.34  E-value=7.1e-07  Score=83.56  Aligned_cols=79  Identities=23%  Similarity=0.263  Sum_probs=61.8

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      .|.+++||+|.|+|+++.+++++||||.+.+|+||++|+....                       +   ..+       
T Consensus        69 ~y~p~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei~~~~-----------------------~---~~~-------  115 (251)
T 2je6_I           69 FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRS-----------------------I---NVG-------  115 (251)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSC-----------------------C---CTT-------
T ss_pred             ccCCCCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCCc-----------------------c---ccc-------
Confidence            4678999999999999999999999999999999999996311                       0   000       


Q ss_pred             CCCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr  280 (343)
                        .-....+++||.+.++|+..++++++.||.|.
T Consensus       116 --~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r~  147 (251)
T 2je6_I          116 --EDLRRYLDVGDYVIARIENFDRSIDPVLSVKG  147 (251)
T ss_dssp             --CCCSSSCCTTCEEEEEEEEEETTEEEEEECCS
T ss_pred             --cchhhcCCCCCEEEEEEEEECCCCcEEEEEcc
Confidence              01134568889999999987777889999743

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=98.31  E-value=6.8e-08  Score=102.35  Aligned_cols=91  Identities=16%  Similarity=0.075  Sum_probs=0.0

Q ss_pred             hcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCccee
Q 019315          164 SVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA  243 (343)
Q Consensus       164 e~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~  243 (343)
                      +.....+++|++++|+|++|.++|+||+|..+.+|+||++|+++.+                       +..        
T Consensus       629 ~~i~~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~~r-----------------------v~~--------  677 (726)
T 4aid_A          629 KSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNER-----------------------VAK--------  677 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHhhhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCccc-----------------------ccC--------
Confidence            3334678999999999999999999999988899999999998431                       000        


Q ss_pred             ccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHH
Q 019315          244 MSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQI  293 (343)
Q Consensus       244 Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa  293 (343)
                      +       ..++++|+.+.++|+..+.+|+|.||+|++.. .+|+.+.+.
T Consensus       678 ~-------~d~~kvGD~V~VkVi~iD~~grI~LS~K~~~~-~~G~~~~~k  719 (726)
T 4aid_A          678 P-------SDVLKEGQMVKVKLLGFDDRGKTKLSMKVVDQ-ETGEDLSKK  719 (726)
T ss_dssp             --------------------------------------------------
T ss_pred             c-------cccCCCCCEEEEEEEEECCCCcEEEEEeeccc-Ccchhhhhh
Confidence            1       12357788888999987778999999999985 789888554

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=98.31  E-value=1.2e-06  Score=77.87  Aligned_cols=98  Identities=21%  Similarity=0.098  Sum_probs=73.0

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCC----------CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeec
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGA----------DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVK  237 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~----------KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~  237 (343)
                      +.++ ||+|.|+|++|.+++++|||+.          ..+|+||++|+++...                           
T Consensus        54 y~p~-GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~---------------------------  105 (179)
T 3m7n_A           54 EIVK-GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYV---------------------------  105 (179)
T ss_dssp             CCCT-TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCC---------------------------
T ss_pred             ccCC-CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchh---------------------------
Confidence            5678 9999999999999999999987          8999999999984310                           


Q ss_pred             CCcceeccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEe-c-CeeEEE
Q 019315          238 DDDAIAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWN-T-GGLLTR  315 (343)
Q Consensus       238 ~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~n-K-GGliVe  315 (343)
                                 +-..+.+++||.+.++|+.    +++.||.|..+                  -|+|.... + |..++.
T Consensus       106 -----------~~~~~~~~~GD~V~akVi~----~~i~LS~k~~~------------------lGvv~a~~~~~g~~m~~  152 (179)
T 3m7n_A          106 -----------KEISEAVGYLDILKARVIG----DNLRLSTKEEE------------------MGVLRALCSNCKTEMVR  152 (179)
T ss_dssp             -----------SSGGGTCCTTCEEEEEEEE----TTTEEECCSTT------------------CEEEECBCTTTCCBCEE
T ss_pred             -----------hCHhhcCCCCCEEEEEEEC----CeEEEEEecCC------------------CCEEEecccccCCceEE
Confidence                       0013456788999999986    88999987755                  47777775 3 445555


Q ss_pred             ECCeEEEEeCCc
Q 019315          316 IEGLRAFLPKAE  327 (343)
Q Consensus       316 IeGlrgFIP~SQ  327 (343)
                      +. -.--+|...
T Consensus       153 ~~-~~~~cp~~g  163 (179)
T 3m7n_A          153 EG-DILKCPECG  163 (179)
T ss_dssp             CS-SSEECSSSC
T ss_pred             CC-CEEECCCCC
Confidence            43 344555553

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=98.24  E-value=4e-07  Score=74.27  Aligned_cols=61  Identities=13%  Similarity=0.114  Sum_probs=45.2

Q ss_pred             EEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC-CCChh
Q 019315          275 LLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR-VNNFT  336 (343)
Q Consensus       275 ~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r-v~nle  336 (343)
                      .-|+|++. .+||+.+.+.++.|++++|+|+++...|++|+++ |++||||.|++... ..++.
T Consensus        11 ~~~iKq~~-~~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~~~~   73 (109)
T 2khj_A           11 SSGLVPRG-SHMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDAT   73 (109)
T ss_dssp             -----------CHHHHTTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSSSGG
T ss_pred             ccchhhcc-cCHHHHHhhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccccChh
Confidence            34788888 5999999999999999999999999999999995 89999999999753 33433

>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=98.23  E-value=8.9e-08  Score=101.86  Aligned_cols=90  Identities=14%  Similarity=0.047  Sum_probs=34.4

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEecccc----CcccccchhhhhhhhhhhhhHhhhcceeeeecCCccee
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEV----LPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIA  243 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEl----s~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~  243 (343)
                      ..+++|++++|+|++|.++|+||++..+.+|+||++|+    ++.+                       +..        
T Consensus       663 ~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s~~r-----------------------v~~--------  711 (757)
T 1e3p_A          663 TSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKR-----------------------VEN--------  711 (757)
T ss_dssp             ----------CBEEECC-CSCEECCC---CCCCC----------------------------------------------
T ss_pred             hhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccCCCc-----------------------ccC--------
Confidence            56789999999999999999999998889999999999    5321                       100        


Q ss_pred             ccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhhC
Q 019315          244 MSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQL  296 (343)
Q Consensus       244 Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e~  296 (343)
                      +       ..+..+|+++.++|+..+.+|+|.||+|++. ..+|....+.|.+
T Consensus       712 ~-------~~~~~vGd~V~VkVi~vd~~grI~LS~k~~~-~~pw~~~~~~~~~  756 (757)
T 1e3p_A          712 V-------EDVLGVGQKVQVEIAEIDSRGKLSLIPVIEG-EEAASDEKKDDAE  756 (757)
T ss_dssp             -----------CCSSCBCCCCCCCCCSSCC-----------------------
T ss_pred             c-------ccccCCCCEEEEEEEEECCCCCEEEEEecCC-CCchhhhhhcccC
Confidence            0       1234667777788887766899999999988 5899998877653

>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=98.22  E-value=2.5e-06  Score=70.54  Aligned_cols=79  Identities=18%  Similarity=0.098  Sum_probs=57.9

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeC-CCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceecc
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVG-ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS  245 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG-~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig  245 (343)
                      ...+++|++++|+|.+|.++|+||+|+ .+.+|++|.++...       +...+.                       . 
T Consensus        16 ~~~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~-------~~~~~~-----------------------~-   64 (119)
T 1wi5_A           16 AEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQE-------YIRQKN-----------------------K-   64 (119)
T ss_dssp             TTTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHH-------HHHHHS-----------------------S-
T ss_pred             HhcCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccc-------cccccC-----------------------c-
Confidence            357899999999999999999999998 57888888776420       100000                       0 


Q ss_pred             CCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHH
Q 019315          246 GGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLF  282 (343)
Q Consensus       246 ~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~  282 (343)
                            .....+|+.+.++|+..+ +.++|.||+|+..
T Consensus        65 ------~~~~~~Gd~V~vkV~~vd~~~~~i~Lslk~~~   96 (119)
T 1wi5_A           65 ------GAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSE   96 (119)
T ss_dssp             ------SCCCCTTCEEEEEEEECCTTSCEEEEECCCCC
T ss_pred             ------cCEeCCCCEEEEEEEEEeCCCCEEEEEEchhh
Confidence                  123577888999999876 4589999987643

>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=98.22  E-value=3.3e-06  Score=74.63  Aligned_cols=95  Identities=24%  Similarity=0.374  Sum_probs=63.8

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      ..++++|++++|+|++++++|+||+++. .+|++|++++.+.+   +.   .|.                 ....+ ++.
T Consensus        76 ~~~~~~Gev~~G~V~~v~~~G~fV~l~~-~eglvhis~l~~~~---~~---~d~-----------------~~~~~-~~~  130 (187)
T 1go3_E           76 VYIPEMYELIEGEVVDVVEFGSFVRLGP-LDGLIHVSQIMDDY---VS---YDP-----------------KREAI-IGK  130 (187)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECSS-SEEEEEGGGSCSSC---EE---ECC-----------------C--CE-EET
T ss_pred             EEccCCCCEEEEEEEEEeCcEEEEEEcC-ccEEEEhHHhCCCc---ce---ECC-----------------ccceE-Eec
Confidence            4678999999999999999999999986 89999999997432   11   010                 00000 111


Q ss_pred             CCCCCCCceeccceEEEEEEeecC------CCceEEeHHHHH-HHHHHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRTL------SGRPLLSTRRLF-RKMAWHR  289 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~de------~G~I~LS~Krl~-~~~aWe~  289 (343)
                      .   .....++|+.+.+.|++.+.      .++|.||++... ....|-.
T Consensus       131 ~---~~~~~~~Gd~V~vkV~~vd~~~~~p~~~~I~lS~k~~~LG~~~w~~  177 (187)
T 1go3_E          131 E---TGKVLEIGDYVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIE  177 (187)
T ss_dssp             T---TCCEECTTCEEEEEEEEEECCC-----CEEEEECCSTTCEEHHHHH
T ss_pred             C---CCeEEcCCCEEEEEEEEEEcccCCCCccEEEEEEcCCCCCcHHHHh
Confidence            0   12456788899999987542      358999998832 1245543

>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=98.19  E-value=3.6e-06  Score=79.18  Aligned_cols=78  Identities=22%  Similarity=0.230  Sum_probs=59.5

Q ss_pred             CCCCCCCEEEEEEEE----EeCCeEEEEeCC---CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCc
Q 019315          168 YEPKPGDFVIGVVVS----GNENKLDVNVGA---DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDD  240 (343)
Q Consensus       168 ~~~k~GdiVeG~VVs----I~~~gv~VDIG~---KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dg  240 (343)
                      |.-+.|++|+|+|.+    ++++.++||+|+   |.||+||.+|+.+.                                
T Consensus         3 ~~~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqip~--------------------------------   50 (251)
T 2asb_A            3 FSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVPG--------------------------------   50 (251)
T ss_dssp             -CCCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSCTT--------------------------------
T ss_pred             hhhcCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcCCC--------------------------------
Confidence            344689999999999    899999999998   79999999998742                                


Q ss_pred             ceeccCCCCCCCCceeccceEEEEEEeec---CCCceEEeHHHHHHHHHHHH
Q 019315          241 AIAMSGGSGPGRPVVETGTVLFAEVLGRT---LSGRPLLSTRRLFRKMAWHR  289 (343)
Q Consensus       241 aV~Ig~~ieg~i~v~eiGd~v~~eVl~~d---e~G~I~LS~Krl~~~~aWe~  289 (343)
                                  .....|+.+.+.|+..+   ..++|.||+.+......|=+
T Consensus        51 ------------E~~~~GDrIkayV~~V~~~~~gpqIiLSRt~p~lvk~Lfe   90 (251)
T 2asb_A           51 ------------ESYEHGNRLRCYVVGVTRGAREPLITLSRTHPNLVRKLFS   90 (251)
T ss_dssp             ------------CCCCTTCEEEEEEEEEECCSSSCEEEEESSCHHHHHHHHH
T ss_pred             ------------ccCCCCCEEEEEEEEEEcCCCCCEEEEEeccHHHHHHHHH
Confidence                        11255677777777532   34799999988776555543

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=98.12  E-value=3.3e-07  Score=97.14  Aligned_cols=87  Identities=16%  Similarity=0.090  Sum_probs=0.0

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      ...+++|++++|+|++|.++|+||+++.+.+|+||++|+++.+                       +..        +  
T Consensus       622 ~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~~~~-----------------------v~~--------~--  668 (723)
T 3cdi_A          622 TAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKR-----------------------VEK--------V--  668 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCcc-----------------------ccC--------c--
Confidence            4578899999999999999999999988899999999997421                       100        0  


Q ss_pred             CCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQ  292 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~q  292 (343)
                           ..+..+|+.+.++|+..+.+|+|.||+|.+. ..+|..+.-
T Consensus       669 -----~~~~~vGd~V~VkVi~vd~~grI~LS~k~~~-~~~g~~~~p  708 (723)
T 3cdi_A          669 -----TDYLQMGQEVPVKVLEVDRQGRIRLSIKEAT-EQSQPAAAP  708 (723)
T ss_dssp             ----------------------------------------------
T ss_pred             -----ccccCCCCEEEEEEEEECCCCcEEEEEEecc-CCCCcccCc
Confidence                 1234678888889988766899999999987 478887643

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}

Probab=98.02  E-value=9.9e-06  Score=90.07  Aligned_cols=85  Identities=12%  Similarity=-0.092  Sum_probs=66.2

Q ss_pred             cccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceec
Q 019315          165 VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAM  244 (343)
Q Consensus       165 ~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~I  244 (343)
                      +....+++|++|+|+|++|+++|+||+|+.+.+|+||++++++..      ...+                        .
T Consensus       895 et~~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~------~v~~------------------------p  944 (1219)
T 3psi_A          895 ESEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQ------LRRP------------------------A  944 (1219)
T ss_dssp             CCTTTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTT------SCSC------------------------S
T ss_pred             CcHhhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCc------ccCC------------------------H
Confidence            456789999999999999999999999998999999999998431      0000                        0


Q ss_pred             cCCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHH
Q 019315          245 SGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMA  286 (343)
Q Consensus       245 g~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~a  286 (343)
                             ..++.+|+.+.++|+..+ +.++|.||+|.-+.+.+
T Consensus       945 -------~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~dl~~~  980 (1219)
T 3psi_A          945 -------NEIYEIGKTYPAKVIYIDYANITAEVSLLDHDVKQQ  980 (1219)
T ss_dssp             -------TTTSCTTCEEEEEEEEEEGGGTEEEEECCHHHHC--
T ss_pred             -------HHcCCCCCEEEEEEEEEECCCCEEEEEecHHHhcch
Confidence                   234678899999999876 67999999987654333

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=97.95  E-value=2.4e-06  Score=70.47  Aligned_cols=54  Identities=15%  Similarity=0.130  Sum_probs=41.3

Q ss_pred             EeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCcccc
Q 019315          276 LSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLS  330 (343)
Q Consensus       276 LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~  330 (343)
                      -|+|++. ..+|+.+...++.|++++|+|+++...|++|++ +|++||||.|++..
T Consensus        11 ~~~k~~~-~~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~   65 (115)
T 2khi_A           11 SSGLVPR-GSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDW   65 (115)
T ss_dssp             -----------CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSC
T ss_pred             cchhhcc-cCCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCc
Confidence            3677777 589999888899999999999999999999999 48999999999975

>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=97.87  E-value=7.3e-06  Score=87.59  Aligned_cols=76  Identities=24%  Similarity=0.231  Sum_probs=57.7

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      ...+++|++++|+|++|+++|+||+||.+.+|+||++++++.+.       .|.                          
T Consensus       649 ~~~l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v-------~d~--------------------------  695 (785)
T 3bzc_A          649 LKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFV-------KDP--------------------------  695 (785)
T ss_dssp             STTCCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCC-------SCH--------------------------
T ss_pred             hhhcCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCcccc-------CCh--------------------------
Confidence            45688999999999999999999999999999999999984310       000                          


Q ss_pred             CCCCCCCceeccceEEEEEEeec-CCCceEEeHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRR  280 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Kr  280 (343)
                           ..++.+|+.+.++|+..+ +.++|.||.|.
T Consensus       696 -----~~~~~vGd~V~VkVi~VD~~~~rI~LSlk~  725 (785)
T 3bzc_A          696 -----YEVVKAGDIVKVKVMEVDIPRNRVGLSMRM  725 (785)
T ss_dssp             -----HHHCCTTCCCCCBEEEEETTTTEEEECCSS
T ss_pred             -----hheeCCCCEEEEEEEEEECCCCEEEEEEec
Confidence                 112355666677777765 56889998864

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=97.84  E-value=2.2e-05  Score=77.38  Aligned_cols=39  Identities=23%  Similarity=0.444  Sum_probs=35.4

Q ss_pred             CCCCCCEEEEEEEE----EeCCeEEEEeCC---CeeEEEeccccCc
Q 019315          169 EPKPGDFVIGVVVS----GNENKLDVNVGA---DLLGTMLTKEVLP  207 (343)
Q Consensus       169 ~~k~GdiVeG~VVs----I~~~gv~VDIG~---KsEG~IPisEls~  207 (343)
                      .-+.|++|+|+|.+    ++++++|||+|.   +.||+||.+|+.|
T Consensus       127 ~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~EqiP  172 (366)
T 1k0r_A          127 STREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVP  172 (366)
T ss_dssp             CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSCT
T ss_pred             HhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcCC
Confidence            34599999999999    999999999997   6999999999874

>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=97.81  E-value=8.9e-05  Score=65.12  Aligned_cols=88  Identities=20%  Similarity=0.235  Sum_probs=59.6

Q ss_pred             cccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceec
Q 019315          165 VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAM  244 (343)
Q Consensus       165 ~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~I  244 (343)
                      .-..++.+|++++|+|++++++|+||++|. .+|++|++++.+.+   +.   .|..                 ... -+
T Consensus        74 ~iv~~p~~Gev~~G~V~~v~~~G~fv~l~~-~~glvh~s~l~~d~---~~---~d~~-----------------~~~-~~  128 (180)
T 4ayb_E           74 MITYVPVVQEVVEGEVLQVDNYGVFVNLGP-MDGLVHISQITDDT---LK---YDNV-----------------RGI-IF  128 (180)
T ss_dssp             EEEECCCTTCEEEEEEEEEETTEEEEECSS-SEEEEEGGGSCSSC---EE---ECSS-----------------SCC-EE
T ss_pred             eeeeeccCCCEEEEEEeeeccceEEEEECC-ccceEEeeecCCCc---cc---cchh-----------------cce-EE
Confidence            334678999999999999999999999985 79999999998532   10   0100                 000 01


Q ss_pred             cCCCCCCCCceeccceEEEEEEeec-----CCCceEEeHHH
Q 019315          245 SGGSGPGRPVVETGTVLFAEVLGRT-----LSGRPLLSTRR  280 (343)
Q Consensus       245 g~~ieg~i~v~eiGd~v~~eVl~~d-----e~G~I~LS~Kr  280 (343)
                      +...   ..+.++|+.+.+.|+..+     ..++|.||.|+
T Consensus       129 g~~~---~~~~~~Gd~VrvkV~~v~~~~~~~~~rI~ls~k~  166 (180)
T 4ayb_E          129 GEKS---KKVIQKGDKVRARVISVASTVTGRLPRIALTMRQ  166 (180)
T ss_dssp             ETTT---CCCCCTTCEEEEEEEEECC-------CEEEECCS
T ss_pred             Eecc---CeEECCCCEEEEEEEEEeCCCCcccCcEEEEcCC
Confidence            1111   234578888999998643     34689999987

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}

Probab=97.79  E-value=4.1e-06  Score=91.80  Aligned_cols=87  Identities=11%  Similarity=-0.081  Sum_probs=0.8

Q ss_pred             cccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceec
Q 019315          165 VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAM  244 (343)
Q Consensus       165 ~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~I  244 (343)
                      .....+++|++|+|+|++|+++|+||+|+.+.+|+||++++++..      ...+                        .
T Consensus       898 et~~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~------~v~~------------------------~  947 (1030)
T 3psf_A          898 ESEKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQ------LRRP------------------------A  947 (1030)
T ss_dssp             CC------------------------------------------------------------------------------
T ss_pred             ccHHHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCCc------ccCC------------------------H
Confidence            345789999999999999999999999998999999999998421      0000                        0


Q ss_pred             cCCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHH
Q 019315          245 SGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWH  288 (343)
Q Consensus       245 g~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe  288 (343)
                             ..++.+|+.+.++|+..+ +.++|.||.|.-+.+.+|.
T Consensus       948 -------~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~dl~~~~~  985 (1030)
T 3psf_A          948 -------NEIYEIGKTYPAKVIYIDYANITAEVSLLDHDVKQQYV  985 (1030)
T ss_dssp             ---------------------------------------------
T ss_pred             -------HHcCCCCCEEEEEEEEEECCCCEEEEEechHHhccccc
Confidence                   134567788888888876 6799999999877666664

>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=97.55  E-value=0.0004  Score=61.80  Aligned_cols=39  Identities=23%  Similarity=0.347  Sum_probs=36.5

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCC-CeeEEEeccccC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVL  206 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~-KsEG~IPisEls  206 (343)
                      |.+++||+|.|+|+.+..++++||||. ..+|++|++.+.
T Consensus         3 Y~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~   42 (175)
T 2ja9_A            3 YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFP   42 (175)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSST
T ss_pred             ccCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCC
Confidence            678899999999999999999999999 899999999874

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}

Probab=97.32  E-value=0.00016  Score=58.64  Aligned_cols=41  Identities=17%  Similarity=0.181  Sum_probs=38.0

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcc
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPL  208 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~  208 (343)
                      ..++.|++|+|+|..++++|+||+|....+|+||++|+++.
T Consensus        57 ~~l~~Ge~V~g~V~~i~~fG~fv~l~~~~eGlvhis~i~~~   97 (101)
T 2bh8_A           57 GNPQQGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISWA   97 (101)
T ss_dssp             CCCCTTCEEEEEEEECCSEEEEECTTSCEEEEEEEEEEEEC
T ss_pred             cCCCCCCEEEEEEEEeCCcEEEEEcCCCceEEEEHHHCccC
Confidence            57899999999999999999999997789999999999853

>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=97.21  E-value=0.00054  Score=59.91  Aligned_cols=41  Identities=24%  Similarity=0.361  Sum_probs=37.3

Q ss_pred             cccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          165 VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       165 ~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      .-..++++|++++|+|++++++|+||++|. .+|++|++++.
T Consensus        76 ~~~~~~~~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l~  116 (171)
T 1y14_B           76 AVVFKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMP  116 (171)
T ss_dssp             EEEECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSC
T ss_pred             EEEccCCCCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHCC
Confidence            334678899999999999999999999998 99999999985

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}

Probab=97.13  E-value=0.00062  Score=52.28  Aligned_cols=37  Identities=14%  Similarity=0.186  Sum_probs=34.0

Q ss_pred             hhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCcccc
Q 019315          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLS  330 (343)
Q Consensus       294 ~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~  330 (343)
                      ++.|++++|+|+++...|++|+++ |++||||.|++..
T Consensus         3 ~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel~~   40 (80)
T 2k52_A            3 VEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMIS   40 (80)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSS
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCc
Confidence            467999999999999999999995 9999999999964

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}

Probab=97.11  E-value=0.0004  Score=56.27  Aligned_cols=37  Identities=14%  Similarity=0.248  Sum_probs=34.0

Q ss_pred             hCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      +.|+.|+++|+...+.|++|++ .+++|+||.|+++..
T Consensus        60 ~~Ge~V~g~V~~i~~fG~fv~l~~~~eGlvhis~i~~~   97 (101)
T 2bh8_A           60 QQGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISWA   97 (101)
T ss_dssp             CTTCEEEEEEEECCSEEEEECTTSCEEEEEEEEEEEEC
T ss_pred             CCCCEEEEEEEEeCCcEEEEEcCCCceEEEEHHHCccC
Confidence            4799999999999999999999 689999999999864

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}

Probab=97.09  E-value=0.00086  Score=56.41  Aligned_cols=45  Identities=16%  Similarity=0.177  Sum_probs=38.0

Q ss_pred             HhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315          293 IKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTE  337 (343)
Q Consensus       293 a~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nlee  337 (343)
                      .++.|++++|+|+++...|++|++ +|++||||.|++... +.++.+
T Consensus         4 ~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~~~~~~   50 (130)
T 2k4k_A            4 KFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINE   50 (130)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCCSCGGG
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccccCccc
Confidence            356899999999999999999999 799999999999754 444433

>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=97.08  E-value=0.00041  Score=66.81  Aligned_cols=85  Identities=24%  Similarity=0.288  Sum_probs=58.9

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      |.+++||+|.|+|+.+..++++|||+...+|+++++++....+    .+               +...+. +. ..    
T Consensus        91 Y~P~vGDvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~gg----~i---------------R~~~~~-D~-~~----  145 (308)
T 2nn6_H           91 YIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGG----EL---------------RRRSAE-DE-LA----  145 (308)
T ss_dssp             CCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC---------------------------------C-HH----
T ss_pred             cCCCCCCEEEEEEEEEeCceEEEEECCCcCCceechhhccccc----ee---------------ecccch-hh-hh----
Confidence            5789999999999999999999999988899999999852100    00               000000 00 00    


Q ss_pred             CCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr  280 (343)
                         ..+.+++||.+.++|+..+.++.+.||.|+
T Consensus       146 ---m~~~l~vGDlV~ArVisv~~~~~i~LStr~  175 (308)
T 2nn6_H          146 ---MRGFLQEGDLISAEVQAVFSDGAVSLHTRS  175 (308)
T ss_dssp             ---HHHHSCSSCEECCEEEEEETTTEEEEECCS
T ss_pred             ---hhccCCCCCEEEEEEEEcCCCCCEEEEecC
Confidence               124567788888888877777889998764

>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=97.06  E-value=0.00059  Score=66.75  Aligned_cols=73  Identities=14%  Similarity=0.104  Sum_probs=50.7

Q ss_pred             eccceEEEEEEeecCCCceEEeHHHHHHHHHHHHH-----HHHhh--CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcc
Q 019315          256 ETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRV-----RQIKQ--LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAEL  328 (343)
Q Consensus       256 eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l-----~qa~e--~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl  328 (343)
                      ++|+.+.+++...+-+.....+.|+... ..|.+.     .+.|+  .|++|+|+|+++.++|++|++++++||||.+++
T Consensus        88 ~vGd~ie~~I~~~dfgR~aa~~aKqvi~-qkireaere~i~~e~~~~~GeIV~G~V~ri~~~~v~VDlGk~EgiLp~sE~  166 (344)
T 1hh2_P           88 EVGSIVKKELNVKNFGRIAAQTAKQVLI-QRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEW  166 (344)
T ss_dssp             CTTCEEEEECCCCCSSSCSGGGHHHHHH-HHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEETTEEEEEEGGGS
T ss_pred             cCCCEEEEEEccccCccHHHHHHHHHHH-HHHHHHHHHHHHHHHhhcCCCEEEEEEEEEecCcEEEEeCCeEEEEeHHHc
Confidence            5677777766543332333445455442 222222     12244  799999999999999999999999999999998


Q ss_pred             c
Q 019315          329 L  329 (343)
Q Consensus       329 ~  329 (343)
                      .
T Consensus       167 i  167 (344)
T 1hh2_P          167 I  167 (344)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=97.06  E-value=8.4e-05  Score=61.89  Aligned_cols=53  Identities=13%  Similarity=0.152  Sum_probs=43.0

Q ss_pred             HHHHHHHHHhhCCCcEEEEEEEEecCeeEEEECCe--EEEEeCCccccC-CCChhh
Q 019315          285 MAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRIEGL--RAFLPKAELLSR-VNNFTE  337 (343)
Q Consensus       285 ~aWe~l~qa~e~g~~VeGkVve~nKGGliVeIeGl--rgFIP~SQl~~r-v~nlee  337 (343)
                      ..|+.+...++.|++++|+|+++...|++|+++|+  +||||.|++... +.++.+
T Consensus        11 ~~~~~~~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~   66 (119)
T 2cqo_A           11 GRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSE   66 (119)
T ss_dssp             CCCCCSCCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHH
T ss_pred             cchhhhhcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhh
Confidence            45665656678999999999999999999999765  999999999754 445443

>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=96.98  E-value=0.00068  Score=62.06  Aligned_cols=43  Identities=23%  Similarity=0.334  Sum_probs=38.1

Q ss_pred             hhcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          163 VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       163 Le~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      +.....++++|++++|+|++++++|+||++|. .+|+||++++.
T Consensus        74 ~~~i~~~p~vGev~~G~V~~vt~fG~FVelg~-~dGlVhiS~l~  116 (215)
T 2b8k_G           74 YRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMP  116 (215)
T ss_dssp             CCEEEECCCTTEEEEEEEEEEETTEEEEECTT-SEEEEEGGGSC
T ss_pred             hhhheeccCCCCEEEEEEEEEecceEEEEecC-cEEEEEHHHCC
Confidence            33344678899999999999999999999998 89999999996

>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=96.97  E-value=0.00094  Score=53.87  Aligned_cols=45  Identities=18%  Similarity=0.183  Sum_probs=37.2

Q ss_pred             HhhCCCcEEEEEEEEecCeeEEEEC----CeEEEEeCCcc-ccC-CCChhh
Q 019315          293 IKQLNEPIEVKFTEWNTGGLLTRIE----GLRAFLPKAEL-LSR-VNNFTE  337 (343)
Q Consensus       293 a~e~g~~VeGkVve~nKGGliVeIe----GlrgFIP~SQl-~~r-v~nlee  337 (343)
                      .++.|++++|+|+++...|++|+++    +++||||.|++ +.. ++++.+
T Consensus         9 ~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~   59 (103)
T 2eqs_A            9 EPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVAD   59 (103)
T ss_dssp             SCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHH
T ss_pred             cCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCccc
Confidence            3568999999999999999999996    79999999999 432 444443

>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=96.95  E-value=0.00086  Score=59.49  Aligned_cols=43  Identities=14%  Similarity=0.356  Sum_probs=32.4

Q ss_pred             CCCcEEEEEEEEecCeeEEEE---CCeEEEEeCCccccC-CCChhhh
Q 019315          296 LNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAELLSR-VNNFTEL  338 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeI---eGlrgFIP~SQl~~r-v~nleel  338 (343)
                      .|++++|+|+++...|++|++   +|++||||.|+++.+ ++++.++
T Consensus        15 ~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~   61 (175)
T 2a19_A           15 IDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKL   61 (175)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--------CCCCC
T ss_pred             CCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHc
Confidence            899999999999999999999   689999999999864 5554443

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=96.94  E-value=0.00038  Score=55.08  Aligned_cols=36  Identities=11%  Similarity=0.081  Sum_probs=32.7

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC---CeEEEEeCC-ccccC
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKA-ELLSR  331 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe---GlrgFIP~S-Ql~~r  331 (343)
                      +.|++++|+|+ +...|++|+++   |++||+|.| +++.+
T Consensus        10 ~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~   49 (88)
T 1luz_A           10 NAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMD   49 (88)
T ss_dssp             CTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHH
T ss_pred             CCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcc
Confidence            57999999999 99999999994   799999999 99753

>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=96.90  E-value=0.00091  Score=59.78  Aligned_cols=44  Identities=14%  Similarity=0.305  Sum_probs=32.7

Q ss_pred             hCCCcEEEEEEEEecCeeEEEE---CCeEEEEeCCccccC-CCChhhh
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRI---EGLRAFLPKAELLSR-VNNFTEL  338 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeI---eGlrgFIP~SQl~~r-v~nleel  338 (343)
                      +.|++++|+|+++...|++|++   +|++||||.|+++.+ ++++.++
T Consensus        14 ~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~   61 (182)
T 1kl9_A           14 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKL   61 (182)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC-----------
T ss_pred             CCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHh
Confidence            6899999999999999999999   689999999999864 5555543

>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=96.75  E-value=0.0016  Score=56.84  Aligned_cols=43  Identities=19%  Similarity=0.220  Sum_probs=37.0

Q ss_pred             hhcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          163 VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       163 Le~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      +.....++++|++++|+|++++++|+||++|. .+|++|++++.
T Consensus        72 ~~~~~~~~~~Gev~~G~V~~v~~fG~fV~l~~-~~glvhis~l~  114 (172)
T 2c35_B           72 YKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGP-MSCFISRHSIP  114 (172)
T ss_dssp             EEEEEECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSC
T ss_pred             EEEEEeeCCCCCEEEEEEEEEeCCEEEEEECC-EEEEEEHHHCC
Confidence            33345678899999999999999999999974 66999999985

>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=96.72  E-value=0.0053  Score=62.96  Aligned_cols=40  Identities=23%  Similarity=0.221  Sum_probs=37.1

Q ss_pred             CCCCCCCEEEEEEEEEeCC--eEEEEeCCCeeEEEeccccCc
Q 019315          168 YEPKPGDFVIGVVVSGNEN--KLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~--gv~VDIG~KsEG~IPisEls~  207 (343)
                      ....+|++..|+|++|.+.  ++|||||.+..||+|++|+.+
T Consensus        41 ~~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~   82 (517)
T 2bx2_L           41 HEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAR   82 (517)
T ss_dssp             SCCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCG
T ss_pred             CcCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcCh
Confidence            4577899999999999999  999999999999999999974

>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=96.59  E-value=0.0071  Score=57.77  Aligned_cols=39  Identities=28%  Similarity=0.457  Sum_probs=36.4

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      |-+++||+|.|+|+.+..+.+.|||+....|+||.+++.
T Consensus       123 YiP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~  161 (289)
T 2nn6_G          123 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFE  161 (289)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSS
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcC
Confidence            678999999999999999999999999999999998875

>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=96.34  E-value=0.00029  Score=75.13  Aligned_cols=112  Identities=11%  Similarity=0.161  Sum_probs=48.2

Q ss_pred             CCCEE--EEEEEE--EeCCeEEEEeCCCeeEEEeccccCcccccc----hhhhhhhhhhhhhHhhhcceeeeecCCcc-e
Q 019315          172 PGDFV--IGVVVS--GNENKLDVNVGADLLGTMLTKEVLPLYDKE----MDFLLCDLKKDAEEFMVRGKMGIVKDDDA-I  242 (343)
Q Consensus       172 ~GdiV--eG~VVs--I~~~gv~VDIG~KsEG~IPisEls~~~~ke----~e~l~~d~~k~~ee~~VeGkV~~i~~dga-V  242 (343)
                      .|+++  .|++++  +.+.|++|||+.  +|.++++...+...+.    ++.+ .+..+...+..++|+|+.++++|+ |
T Consensus       609 i~~vIG~gGk~Ik~I~~~~G~~IdI~~--dG~v~Is~~~~~~~~~a~~~i~~i-~~p~~~~vG~i~~G~V~~i~~fGaFV  685 (757)
T 1e3p_A          609 IGEVIGPKRQMINQIQEDTGAEITIED--DGTIYIGAADGPAAEAARATINGI-ANPTSPEVGERILGSVVKTTTFGAFV  685 (757)
T ss_dssp             ------------CTTCCCCCSCC----------CCCBSSHHHHCC----------------------CBEEECC-CSCEE
T ss_pred             eehcccccceeeehhhHhhCCEEEecC--CceEEEecCCHHHHHHHHHHHHHh-cchhhcccccEEEEEEEEccccEEEE
Confidence            36665  477887  567899999984  8999999876331110    1111 111233346889999999999999 9


Q ss_pred             eccCCCCCCCCceec----cceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEEEEEEEecCe
Q 019315          243 AMSGGSGPGRPVVET----GTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEVKFTEWNTGG  311 (343)
Q Consensus       243 ~Ig~~ieg~i~v~ei----Gd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeGkVve~nKGG  311 (343)
                      .+.++++||+|++++    +..            +             .++..+.++.|+.|+++|.++.+.|
T Consensus       686 ~l~~g~eGLvHiSel~~~~s~~------------r-------------v~~~~~~~~vGd~V~VkVi~vd~~g  733 (757)
T 1e3p_A          686 SLLPGKDGLLHISQIRKLAGGK------------R-------------VENVEDVLGVGQKVQVEIAEIDSRG  733 (757)
T ss_dssp             CCC---CCCCC--------------------------------------------CCSSCBCCCCCCCCCSSC
T ss_pred             EEcCCcEEEEEhHHhccccCCC------------c-------------ccCcccccCCCCEEEEEEEEECCCC
Confidence            998889999999876    210            1             1344567889999999999998654

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=96.06  E-value=0.0019  Score=56.68  Aligned_cols=43  Identities=21%  Similarity=0.215  Sum_probs=37.7

Q ss_pred             hhcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccC
Q 019315          163 VSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVL  206 (343)
Q Consensus       163 Le~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls  206 (343)
                      +..-..++.+|++++|+|+++++.|+||++|. .+|++|++++.
T Consensus        75 f~~ivf~p~~Gev~~G~V~~v~~fG~FV~l~~-~~glVh~s~l~  117 (172)
T 3h0g_G           75 YRAVLWRPFRGEVVDAIVTTVNKMGFFANIGP-LNVFVSSHLVP  117 (172)
T ss_dssp             EEEEEECCCTTCEEECCCCEEETTEEECCBTT-BCCEEEGGGSC
T ss_pred             EEEeeeccCCCCEEEEEEEEEEcceEEEEeCC-eEEEEEHHHCC
Confidence            44445678999999999999999999999985 67999999995

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=95.94  E-value=0.0012  Score=69.99  Aligned_cols=71  Identities=11%  Similarity=0.077  Sum_probs=0.0

Q ss_pred             eecCCCceEEeHHHHHH----HHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315          267 GRTLSGRPLLSTRRLFR----KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTE  337 (343)
Q Consensus       267 ~~de~G~I~LS~Krl~~----~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nlee  337 (343)
                      .++++|.+.+|......    ...|+.+...++.|++++|+|+++...|++|++ +|++||||.|+++.+ ++++++
T Consensus       594 dI~~dg~v~I~~~~~~~~~~a~~~i~~i~~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~~~~v~~~~~  670 (723)
T 3cdi_A          594 EIEDDGTVKIAATDGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTD  670 (723)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             EecCCccEEEecCCHHHHHHHHHHHHHHhhhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCccccCccc
Confidence            34567888887654432    234666666788999999999999999999999 589999999999763 444433

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=95.87  E-value=0.0012  Score=70.20  Aligned_cols=70  Identities=7%  Similarity=0.022  Sum_probs=3.6

Q ss_pred             ecCCCceEEeHH---HHH-HHHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhh
Q 019315          268 RTLSGRPLLSTR---RLF-RKMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTE  337 (343)
Q Consensus       268 ~de~G~I~LS~K---rl~-~~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nlee  337 (343)
                      ++++|.+.++-.   .++ .+..|+.+...++.|++++|+|+++..+|++|++ +|++||||.|+++.+ +.++++
T Consensus       605 i~ddG~v~I~~~~~~~~~~A~~~i~~i~~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~~rv~~~~d  680 (726)
T 4aid_A          605 INDDGVVKVSASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSD  680 (726)
T ss_dssp             ---------CCSCHHHHHHHHHC-----------------------------------------------------
T ss_pred             EECCceEEEEeCCHHHHHHHHHHHHHHhhhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCcccccCccc
Confidence            356677766542   222 2345777878889999999999999999999999 689999999999864 555444

>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=95.73  E-value=0.009  Score=57.48  Aligned_cols=44  Identities=14%  Similarity=0.294  Sum_probs=37.6

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC---CeEEEEeCCccccC-CCChhhh
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAELLSR-VNNFTEL  338 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe---GlrgFIP~SQl~~r-v~nleel  338 (343)
                      +.|++++|+|+++...|++|+++   |++||||.|+++++ ++++.++
T Consensus        12 ~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~   59 (308)
T 1q8k_A           12 EVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKL   59 (308)
T ss_dssp             SSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCSCCTTT
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccccCHHHh
Confidence            47999999999999999999994   89999999999864 5555544

>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=95.65  E-value=0.014  Score=50.71  Aligned_cols=35  Identities=26%  Similarity=0.399  Sum_probs=33.0

Q ss_pred             CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      .|++++|+|+++++.|++|+++.++||+|.|+++.
T Consensus        81 ~Gev~~G~V~~v~~fG~fV~l~~~~glvhis~l~~  115 (172)
T 2c35_B           81 KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPS  115 (172)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCT
T ss_pred             CCCEEEEEEEEEeCCEEEEEECCEEEEEEHHHCCC
Confidence            79999999999999999999988999999999963

>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=95.60  E-value=0.015  Score=50.63  Aligned_cols=36  Identities=11%  Similarity=0.203  Sum_probs=33.2

Q ss_pred             hCCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      ..|++++|+|+++++.|++|+++.++||+|.|+++.
T Consensus        82 ~~Gev~~G~V~~v~~fG~FV~l~~~dglvhis~l~~  117 (171)
T 1y14_B           82 FKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQ  117 (171)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCT
T ss_pred             CCCCEEEEEEEEEecCEEEEEecCeEEEEEHHHCCC
Confidence            379999999999999999999966999999999963

>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=95.55  E-value=0.013  Score=51.49  Aligned_cols=36  Identities=17%  Similarity=0.273  Sum_probs=33.6

Q ss_pred             hCCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      ..|++++|+|+++.+.|++|++.+++||+|.|++..
T Consensus        80 ~~Gev~~G~V~~v~~~G~fV~l~~~eglvhis~l~~  115 (187)
T 1go3_E           80 EMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMD  115 (187)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCS
T ss_pred             CCCCEEEEEEEEEeCcEEEEEEcCccEEEEhHHhCC
Confidence            479999999999999999999988999999999964

>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=95.40  E-value=0.036  Score=57.84  Aligned_cols=85  Identities=14%  Similarity=0.181  Sum_probs=56.9

Q ss_pred             CCCCCCC--EEEEEEEEEeCCeEEEEe-CCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceec
Q 019315          168 YEPKPGD--FVIGVVVSGNENKLDVNV-GADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAM  244 (343)
Q Consensus       168 ~~~k~Gd--iVeG~VVsI~~~gv~VDI-G~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~I  244 (343)
                      .+-+.|+  +.+|+|++|+++|+||.| ..+.+|+||++++....    +++.+|..        .+.+.. ..      
T Consensus       554 l~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~----d~~~~d~~--------~~~l~~-~~------  614 (644)
T 2id0_A          554 LKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVR----DELVCSQE--------NGTVQI-KG------  614 (644)
T ss_dssp             HGGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCG----GGEEEETT--------TTEEEE-TT------
T ss_pred             hhhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcC----ceeEEccc--------ccEEEe-cC------
Confidence            3456899  999999999999999999 57899999999996310    01111110        011100 00      


Q ss_pred             cCCCCCCCCceeccceEEEEEEeec-CCCceEEeH
Q 019315          245 SGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLST  278 (343)
Q Consensus       245 g~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~  278 (343)
                             .....+|+.+.++|+..+ ..++|.+|.
T Consensus       615 -------~~~~~lGD~V~VkV~~vd~~~~~I~~~l  642 (644)
T 2id0_A          615 -------ETVYKVTDVIDVTIAEVRMETRSIIARP  642 (644)
T ss_dssp             -------EEEEETTCEEEEEEEEEETTTTEEEEEE
T ss_pred             -------CCEeCCCCEEEEEEEEEeCCCCEEEEEE
Confidence                   123577888888888765 568888874

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=95.24  E-value=0.026  Score=49.77  Aligned_cols=42  Identities=10%  Similarity=0.079  Sum_probs=35.9

Q ss_pred             CCcEEEEEEEEecCeeEEEE-C----------CeEEEEeCCccccC-CCChhhh
Q 019315          297 NEPIEVKFTEWNTGGLLTRI-E----------GLRAFLPKAELLSR-VNNFTEL  338 (343)
Q Consensus       297 g~~VeGkVve~nKGGliVeI-e----------GlrgFIP~SQl~~r-v~nleel  338 (343)
                      |++|.|+|+++...|++|+| .          ++.|+||.|++... ++++.++
T Consensus        58 GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~  111 (179)
T 3m7n_A           58 GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEA  111 (179)
T ss_dssp             TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGT
T ss_pred             CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhc
Confidence            99999999999999999999 4          68999999999764 4555444

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=94.89  E-value=0.027  Score=50.63  Aligned_cols=42  Identities=19%  Similarity=0.328  Sum_probs=37.3

Q ss_pred             ccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcc
Q 019315          166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPL  208 (343)
Q Consensus       166 ~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~  208 (343)
                      .+.++.+|++++|+|.++++.|+||.+| ..+|+++.+++.+.
T Consensus        75 ~~f~p~~GEv~~G~Vs~vt~~GifV~lg-~~eglv~~~~l~~d  116 (203)
T 3ayh_B           75 IIFRPFRGEVMLGKIKSCSEEGIRVTIS-FFDDIFIPKDMLFD  116 (203)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEECS-SCCCEEEEGGGBCT
T ss_pred             EEEccCCCCEEEEEEEEEeccEEEEEEe-CceEEEEcHHhCCC
Confidence            3467889999999999999999999997 68999999999743

>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=94.70  E-value=0.033  Score=48.65  Aligned_cols=36  Identities=8%  Similarity=0.219  Sum_probs=33.9

Q ss_pred             hCCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      ..|++++|+|+++++.|++|+++.+.||+|.|++..
T Consensus        80 ~~Gev~~G~V~~v~~~G~fv~l~~~~glvh~s~l~~  115 (180)
T 4ayb_E           80 VVQEVVEGEVLQVDNYGVFVNLGPMDGLVHISQITD  115 (180)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCS
T ss_pred             cCCCEEEEEEeeeccceEEEEECCccceEEeeecCC
Confidence            489999999999999999999988999999999964

>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=94.44  E-value=0.03  Score=51.17  Aligned_cols=36  Identities=11%  Similarity=0.203  Sum_probs=33.3

Q ss_pred             hCCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      ..|++++|+|+++++.|++|+++.++||+|.|+|+.
T Consensus        82 ~vGev~~G~V~~vt~fG~FVelg~~dGlVhiS~l~d  117 (215)
T 2b8k_G           82 FKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQ  117 (215)
T ss_dssp             CTTEEEEEEEEEEETTEEEEECTTSEEEEEGGGSCS
T ss_pred             CCCCEEEEEEEEEecceEEEEecCcEEEEEHHHCCc
Confidence            579999999999999999999965999999999974

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=94.21  E-value=0.01  Score=52.03  Aligned_cols=35  Identities=20%  Similarity=0.261  Sum_probs=33.0

Q ss_pred             CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      .|++++|+|+++++.|++|+++.++||+|.|+++.
T Consensus        84 ~Gev~~G~V~~v~~fG~FV~l~~~~glVh~s~l~~  118 (172)
T 3h0g_G           84 RGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPP  118 (172)
T ss_dssp             TTCEEECCCCEEETTEEECCBTTBCCEEEGGGSCT
T ss_pred             CCCEEEEEEEEEEcceEEEEeCCeEEEEEHHHCCC
Confidence            79999999999999999999988999999999964

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=94.00  E-value=0.061  Score=49.14  Aligned_cols=44  Identities=14%  Similarity=0.215  Sum_probs=37.9

Q ss_pred             cccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcc
Q 019315          165 VEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPL  208 (343)
Q Consensus       165 ~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~  208 (343)
                      ..+.+..+|++++|+|.++++.|+||.+....+|+++.+++.+.
T Consensus        74 ~~~f~p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d  117 (218)
T 2ckz_B           74 AVVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFE  117 (218)
T ss_dssp             EEEECCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCT
T ss_pred             EEEecCCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCC
Confidence            34567889999999999999999999993368999999999743

>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=93.39  E-value=0.045  Score=44.78  Aligned_cols=36  Identities=25%  Similarity=0.314  Sum_probs=32.1

Q ss_pred             HhhCCCcEEEEEEEEecCeeEEEEC--CeEEEEeCCcc
Q 019315          293 IKQLNEPIEVKFTEWNTGGLLTRIE--GLRAFLPKAEL  328 (343)
Q Consensus       293 a~e~g~~VeGkVve~nKGGliVeIe--GlrgFIP~SQl  328 (343)
                      .++.|++++|+|+++...|++|+++  ++.||+|.+.+
T Consensus        18 ~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~   55 (119)
T 1wi5_A           18 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKA   55 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHH
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecc
Confidence            3568999999999999999999996  78999998775

>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=93.35  E-value=0.23  Score=52.83  Aligned_cols=85  Identities=13%  Similarity=-0.049  Sum_probs=49.5

Q ss_pred             CEEEEEEEEEeCCeEEEEeCC-CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCCCCC
Q 019315          174 DFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSGPGR  252 (343)
Q Consensus       174 diVeG~VVsI~~~gv~VDIG~-KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ieg~i  252 (343)
                      ++.+|+|++|.++|+||.|.. +.||+||++++....    ++...|..        +..+.. ...     +.   ...
T Consensus       671 ~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~----d~~~fd~~--------~~~l~g-~~~-----~~---~~~  729 (760)
T 2vnu_D          671 STETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDP----NSAAFDEV--------EYKLTF-VPT-----NS---DKP  729 (760)
T ss_dssp             SEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCG----GGCEEETT--------TTEEEE-CCT-----TC---SSC
T ss_pred             eEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCC----ceeEEccc--------ccEEEE-ecC-----CC---ccC
Confidence            799999999999999999965 799999999995110    01111110        001100 000     00   012


Q ss_pred             CceeccceEEEEEEeecC----CCceEEeHH
Q 019315          253 PVVETGTVLFAEVLGRTL----SGRPLLSTR  279 (343)
Q Consensus       253 ~v~eiGd~v~~eVl~~de----~G~I~LS~K  279 (343)
                      .+..+|+.+.+.|+..+.    .++|.||+|
T Consensus       730 ~~~~lGD~V~VkV~~vd~~~~~~~kI~lslk  760 (760)
T 2vnu_D          730 RDVYVFDKVEVQVRSVMDPITSKRKAELLLK  760 (760)
T ss_dssp             EEEETTCEEEEEEC--------CCEEEC---
T ss_pred             cEEecCCEEEEEEEEEECccccCCcEEEEeC
Confidence            356788889998887653    389999875

>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=92.92  E-value=0.056  Score=48.99  Aligned_cols=45  Identities=11%  Similarity=0.128  Sum_probs=37.0

Q ss_pred             hhCCCcEEEEEEEEecCeeEEEEC---------CeEEEEeCCccccC-CC--Chhhh
Q 019315          294 KQLNEPIEVKFTEWNTGGLLTRIE---------GLRAFLPKAELLSR-VN--NFTEL  338 (343)
Q Consensus       294 ~e~g~~VeGkVve~nKGGliVeIe---------GlrgFIP~SQl~~r-v~--nleel  338 (343)
                      .+.|++|.|+|+++...|++|+|.         +++|+||.|++... ++  ++.++
T Consensus        79 p~vGDvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~  135 (209)
T 2nn6_I           79 PDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKS  135 (209)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGT
T ss_pred             CCCCCEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhh
Confidence            468999999999999999999984         56899999999754 44  45444

>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=92.88  E-value=0.064  Score=57.48  Aligned_cols=45  Identities=16%  Similarity=0.090  Sum_probs=38.3

Q ss_pred             hhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC-CCChhhh
Q 019315          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR-VNNFTEL  338 (343)
Q Consensus       294 ~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r-v~nleel  338 (343)
                      ++.|++++|+|+++.++|++|+++ ++.||||.|+++.+ +.++.+.
T Consensus       652 l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v~d~~~~  698 (785)
T 3bzc_A          652 LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEV  698 (785)
T ss_dssp             CCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCCSCHHHH
T ss_pred             cCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCccccCChhhe
Confidence            568999999999999999999995 78999999999864 5555443

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=92.73  E-value=0.08  Score=57.97  Aligned_cols=34  Identities=18%  Similarity=0.113  Sum_probs=32.0

Q ss_pred             CCEEEEEEEEEeCCeEEEEeCC-CeeEEEeccccC
Q 019315          173 GDFVIGVVVSGNENKLDVNVGA-DLLGTMLTKEVL  206 (343)
Q Consensus       173 GdiVeG~VVsI~~~gv~VDIG~-KsEG~IPisEls  206 (343)
                      |++.+|+|++|.++|+||.|.. +.||+||++++.
T Consensus       887 ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~  921 (977)
T 2wp8_J          887 ESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLT  921 (977)
T ss_dssp             TCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTC
T ss_pred             ceEEEEEEEEEcCCeEEEEEcCCCeEEEEEecccc
Confidence            9999999999999999999964 899999999996

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}

Probab=92.55  E-value=0.1  Score=58.39  Aligned_cols=46  Identities=7%  Similarity=0.047  Sum_probs=39.1

Q ss_pred             HhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC--CCChhhh
Q 019315          293 IKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR--VNNFTEL  338 (343)
Q Consensus       293 a~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r--v~nleel  338 (343)
                      .++.|++|+|+|+++...|++|+++ |+.|+||.|+++.+  +.++.+.
T Consensus       899 ~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~p~~v  947 (1219)
T 3psi_A          899 TFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEI  947 (1219)
T ss_dssp             TSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTTSCSCSTTT
T ss_pred             hCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCcccCCHHHc
Confidence            4678999999999999999999995 99999999999864  4555543

>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=91.25  E-value=0.23  Score=45.54  Aligned_cols=36  Identities=22%  Similarity=0.236  Sum_probs=33.6

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCcccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLS  330 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~  330 (343)
                      +.|++|.|+|+++...|++|+++ ...|+||.|++..
T Consensus        56 ~~GDiV~G~V~~v~~~~a~V~I~~~~~g~l~isev~~   92 (229)
T 2ba0_A           56 SVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPE   92 (229)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTT
T ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHccc
Confidence            68999999999999999999996 5999999999984

>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=90.56  E-value=0.14  Score=47.75  Aligned_cols=37  Identities=24%  Similarity=0.425  Sum_probs=33.8

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR  331 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r  331 (343)
                      +.|++|.|+|+++...|++|+++ +..|+||.|++..+
T Consensus        73 ~~GDiV~G~V~~v~~~ga~VdI~~~~~GlL~isei~~~  110 (251)
T 2je6_I           73 KINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGR  110 (251)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTS
T ss_pred             CCCCEEEEEEEEEeCceEEEEcCCCeEEEEEHHHhcCC
Confidence            68999999999999999999996 69999999999743

>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=90.05  E-value=0.16  Score=50.13  Aligned_cols=41  Identities=17%  Similarity=0.112  Sum_probs=32.8

Q ss_pred             HHHHhh--CCCcEEEEEEE----EecCeeEEEECC----eEEEEeCCcccc
Q 019315          290 VRQIKQ--LNEPIEVKFTE----WNTGGLLTRIEG----LRAFLPKAELLS  330 (343)
Q Consensus       290 l~qa~e--~g~~VeGkVve----~nKGGliVeIeG----lrgFIP~SQl~~  330 (343)
                      +.+.|+  .|++|+|+|.+    +.+++++|++++    ++|+||.+++..
T Consensus       122 i~~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~EqiP  172 (366)
T 1k0r_A          122 TYGEFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVP  172 (366)
T ss_dssp             -----CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSCT
T ss_pred             HHHHHHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcCC
Confidence            334454  99999999999    999999999976    999999998853

>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=89.92  E-value=0.15  Score=46.68  Aligned_cols=36  Identities=14%  Similarity=0.090  Sum_probs=33.7

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCcccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLS  330 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~  330 (343)
                      +.|++|.|+|+++...|++|+++ +..|+||.|++..
T Consensus        65 ~~GDiV~G~V~~v~~~~~~V~I~~~~~g~l~isei~~  101 (235)
T 2z0s_A           65 QAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLG  101 (235)
T ss_dssp             CTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHT
T ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeEEEEEHHHhCC
Confidence            79999999999999999999996 6999999999964

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}

Probab=89.45  E-value=0.068  Score=58.90  Aligned_cols=46  Identities=7%  Similarity=0.038  Sum_probs=0.0

Q ss_pred             HHhhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC--CCChhh
Q 019315          292 QIKQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR--VNNFTE  337 (343)
Q Consensus       292 qa~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r--v~nlee  337 (343)
                      +.++.|++|+|+|+++..+|++|+++ |+.|+||.|+++.+  +.++.+
T Consensus       901 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~~~~  949 (1030)
T 3psf_A          901 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANE  949 (1030)
T ss_dssp             -------------------------------------------------
T ss_pred             HHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCCcccCCHHH
Confidence            35678999999999999999999995 89999999999754  344443

>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=89.27  E-value=0.71  Score=48.10  Aligned_cols=35  Identities=23%  Similarity=0.455  Sum_probs=32.4

Q ss_pred             hCCC--cEEEEEEEEecCeeEEEE--CCeEEEEeCCccc
Q 019315          295 QLNE--PIEVKFTEWNTGGLLTRI--EGLRAFLPKAELL  329 (343)
Q Consensus       295 e~g~--~VeGkVve~nKGGliVeI--eGlrgFIP~SQl~  329 (343)
                      +.|+  .++|+|+++.+.|++|++  .|++||||.|++.
T Consensus       557 ~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~  595 (644)
T 2id0_A          557 KAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLH  595 (644)
T ss_dssp             GTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTC
T ss_pred             ccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhcc
Confidence            5788  999999999999999999  4899999999995

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=85.73  E-value=0.55  Score=42.05  Aligned_cols=35  Identities=14%  Similarity=0.132  Sum_probs=31.1

Q ss_pred             hCCCcEEEEEEEEecCeeEEEECCeEEEEeCCccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL  329 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~  329 (343)
                      ..|++++|+|+++++.|++|+++.+.|+++.|++.
T Consensus        80 ~~GEv~~G~Vs~vt~~GifV~lg~~eglv~~~~l~  114 (203)
T 3ayh_B           80 FRGEVMLGKIKSCSEEGIRVTISFFDDIFIPKDML  114 (203)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSCCCEEEEGGGB
T ss_pred             CCCCEEEEEEEEEeccEEEEEEeCceEEEEcHHhC
Confidence            47999999999999999999997688888888774

>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=84.50  E-value=0.26  Score=46.10  Aligned_cols=59  Identities=17%  Similarity=0.196  Sum_probs=47.3

Q ss_pred             HhhhcceeeeecCCcc-eecc--CCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEE
Q 019315          226 EFMVRGKMGIVKDDDA-IAMS--GGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEV  302 (343)
Q Consensus       226 e~~VeGkV~~i~~dga-V~Ig--~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeG  302 (343)
                      +..+.|+|..++++|+ |.++  ++++||+|+++++.            +++             ..+.+.++.|+.|.+
T Consensus        12 G~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~------------~~v-------------~~~~~~~~vGd~V~V   66 (266)
T 3cw2_C           12 GEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSS------------KWV-------------KNIRDVLKENRKVIV   66 (266)
T ss_dssp             TCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSC------------SSC-------------CCHHHHSCTTCEEEE
T ss_pred             CCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCc------------ccc-------------cCHHHhCcCCCEEEE
Confidence            4578899999999999 9997  78999999998841            111             124567889999999


Q ss_pred             EEEEEec
Q 019315          303 KFTEWNT  309 (343)
Q Consensus       303 kVve~nK  309 (343)
                      +|+++..
T Consensus        67 kVi~vd~   73 (266)
T 3cw2_C           67 KVIRVDR   73 (266)
T ss_dssp             EECCCCS
T ss_pred             EEEEEeC
Confidence            9999875

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=82.70  E-value=0.95  Score=41.20  Aligned_cols=34  Identities=12%  Similarity=0.177  Sum_probs=30.2

Q ss_pred             CCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccc
Q 019315          296 LNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELL  329 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~  329 (343)
                      .|++++|+|+++++.|++|++ +-+.|+++.|++.
T Consensus        81 vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~  115 (218)
T 2ckz_B           81 LGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNML  115 (218)
T ss_dssp             TTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTS
T ss_pred             CCCEEEEEEEEEccCcEEEEccCccceEEEcHHHC
Confidence            799999999999999999999 4578888888874

>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=82.46  E-value=0.94  Score=46.43  Aligned_cols=35  Identities=17%  Similarity=0.194  Sum_probs=32.1

Q ss_pred             hCCCcEEEEEEEEecC--eeEEEEC-CeEEEEeCCccc
Q 019315          295 QLNEPIEVKFTEWNTG--GLLTRIE-GLRAFLPKAELL  329 (343)
Q Consensus       295 e~g~~VeGkVve~nKG--GliVeIe-GlrgFIP~SQl~  329 (343)
                      ..|.+..|+|+++.++  |++|+++ |-.||||.|++.
T Consensus        44 ~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~   81 (517)
T 2bx2_L           44 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIA   81 (517)
T ss_dssp             CTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSC
T ss_pred             CCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcC
Confidence            4699999999999999  9999994 888999999985

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A

Probab=80.47  E-value=0.32  Score=45.85  Aligned_cols=62  Identities=11%  Similarity=0.123  Sum_probs=47.5

Q ss_pred             HhhhcceeeeecCCcc-eecc--CCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHHHHHHHhhCCCcEEE
Q 019315          226 EFMVRGKMGIVKDDDA-IAMS--GGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWHRVRQIKQLNEPIEV  302 (343)
Q Consensus       226 e~~VeGkV~~i~~dga-V~Ig--~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe~l~qa~e~g~~VeG  302 (343)
                      +..+.|+|+.++++|+ |.++  ++++||+|+++++...            +.             ...+.++.|+.|.+
T Consensus        12 Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~------------v~-------------~~~~~~kvGd~V~v   66 (275)
T 3aev_A           12 GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTW------------VR-------------NIRDYLKEGQKVVA   66 (275)
T ss_dssp             TCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSC------------CS-------------CGGGTCCTTCEEEE
T ss_pred             CCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCccc------------cc-------------CHHhccCCCCEEEE
Confidence            4578899999999999 9997  5899999999884211            10             12346789999999


Q ss_pred             EEEEEec-Cee
Q 019315          303 KFTEWNT-GGL  312 (343)
Q Consensus       303 kVve~nK-GGl  312 (343)
                      +|.++.. .|-
T Consensus        67 kVi~vD~~~~~   77 (275)
T 3aev_A           67 KVIRVDPRKGH   77 (275)
T ss_dssp             EEEEEETTTTE
T ss_pred             EEEEEECCCCE
Confidence            9999986 443

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=80.37  E-value=2.2  Score=46.76  Aligned_cols=35  Identities=9%  Similarity=0.138  Sum_probs=32.2

Q ss_pred             hCCCcEEEEEEEEecCeeEEEE-C-CeEEEEeCCccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRI-E-GLRAFLPKAELL  329 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeI-e-GlrgFIP~SQl~  329 (343)
                      ..|+..+|.|+++.+.|++|.+ + |++|+||.|++.
T Consensus       885 ~~ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~  921 (977)
T 2wp8_J          885 NNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLT  921 (977)
T ss_dssp             HTTCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTC
T ss_pred             ccceEEEEEEEEEcCCeEEEEEcCCCeEEEEEecccc
Confidence            4599999999999999999999 4 899999999985

---

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	343
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	0.001

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 88

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 13/65 (20%), Positives = 26/65 (40%)

Query: 166 EYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAE 225
           E Y P+ GD VIG++ S       V++ +  +  +  ++ L          +  L K  +
Sbjct: 1   EIYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGD 60

Query: 226 EFMVR 230
               +
Sbjct: 61  YIKAK 65

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	343
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.19
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.14
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.13
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.09
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.08
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	99.05
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.99
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	98.76
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	98.75
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	98.67
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.55
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.23
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.2
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	97.94
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	97.91
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	97.84
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	97.74
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	97.73
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	97.42
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	97.33
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.31
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	97.04
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	96.97
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	96.87
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	96.87
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	96.85
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	96.69
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	96.65
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	96.49
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	96.33
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	96.32
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	96.3
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	95.95
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	95.34
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	94.91
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	92.81
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	89.14
d1k3ra1	71	Hypothetical protein MTH1 (MT0001), insert domain	87.65
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	83.16

>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=99.19  E-value=8.6e-12  Score=94.80  Aligned_cols=74  Identities=19%  Similarity=0.160  Sum_probs=61.0

Q ss_pred             CCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCC
Q 019315          169 EPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGS  248 (343)
Q Consensus       169 ~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~i  248 (343)
                      .+++|++++|+|+++.++|+||+++.+.+|+||++|+++.+.+.                               +    
T Consensus         2 d~kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~~~~~~-------------------------------~----   46 (76)
T d1sroa_           2 EIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEK-------------------------------V----   46 (76)
T ss_dssp             CCCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCSC-------------------------------H----
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccCC-------------------------------H----
Confidence            47899999999999999999999999999999999998642110                               0    


Q ss_pred             CCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315          249 GPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (343)
Q Consensus       249 eg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr  280 (343)
                         ..++.+|+++.+.|+..+.++++.||+|+
T Consensus        47 ---~~~~~~G~~v~v~Vi~id~~~ri~LS~k~   75 (76)
T d1sroa_          47 ---TDYLQMGQEVPVKVLEVDRQGRIRLSIKE   75 (76)
T ss_dssp             ---HHHCCTTCEEEEEEEECCTTCCCEEEECC
T ss_pred             ---HHccCCCCEEEEEEEEECCCCCEEEEEEc
Confidence               12346788889999988777899999875

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.14  E-value=4.3e-11  Score=92.68  Aligned_cols=80  Identities=23%  Similarity=0.225  Sum_probs=64.4

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      .|.+++||+|.|+|++++++|+||||+...+|+||++|+++....                                   
T Consensus         2 ~Y~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~~-----------------------------------   46 (87)
T d2je6i1           2 FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSIN-----------------------------------   46 (87)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCC-----------------------------------
T ss_pred             cccCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceec-----------------------------------
Confidence            577899999999999999999999999999999999999743100                                   


Q ss_pred             CCCCCCCceeccceEEEEEEeecCCCceEEeHHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl  281 (343)
                      ........+.+|+.+.++|+..++++++.||.|..
T Consensus        47 ~~~~~~~~~~~Gd~v~~kV~~vd~~~~i~LS~k~~   81 (87)
T d2je6i1          47 VGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGK   81 (87)
T ss_dssp             TTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCST
T ss_pred             cccccchhhcccceEEEEEEEECCCCCEEEEEecC
Confidence            00011345688999999999888888999998653

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.13  E-value=9.3e-11  Score=89.78  Aligned_cols=77  Identities=21%  Similarity=0.278  Sum_probs=62.8

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      |.+++||+|.|+|.+++++|+||+|+...+|+||++|+++...                                 ..  
T Consensus         1 Y~Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~---------------------------------~~--   45 (83)
T d2ba0a1           1 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKP---------------------------------NK--   45 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCT---------------------------------TS--
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEecCCCeeEEEeccccccccc---------------------------------cc--
Confidence            4578999999999999999999999999999999999984310                                 00  


Q ss_pred             CCCCCCceeccceEEEEEEeecCCCceEEeHHHH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRL  281 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl  281 (343)
                        -....+.+|+.+.+.|+..+++++|.||.|.+
T Consensus        46 --~~~~~~~vGd~V~~kV~~vd~~~~i~LS~k~~   77 (83)
T d2ba0a1          46 --KPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDR   77 (83)
T ss_dssp             --CGGGTCCTTCEEEEEEEEECTTCCEEEECCSS
T ss_pred             --ChhhhcccccEEEEEEEEECCCCCEEEEecCC
Confidence              00234578899999999888789999998764

>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=99.09  E-value=1.1e-10  Score=90.36  Aligned_cols=80  Identities=20%  Similarity=0.297  Sum_probs=64.4

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      .|.+++||+|.|+|++++++|+||+|+...+|+||.+|+++...+                                  .
T Consensus         2 ~Y~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~~~----------------------------------~   47 (88)
T d2z0sa1           2 IYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFN----------------------------------P   47 (88)
T ss_dssp             CCCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCC----------------------------------T
T ss_pred             CcCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCccccc----------------------------------c
Confidence            367899999999999999999999999999999999999743100                                  0


Q ss_pred             CCCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr  280 (343)
                      -.....+.+++|+.+.++|+..+.++++.||.|.
T Consensus        48 ~~~~~~~~~~vGd~V~~kV~~vd~~~~i~Ls~k~   81 (88)
T d2z0sa1          48 AVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQG   81 (88)
T ss_dssp             TTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCS
T ss_pred             cccchhhhcccCcEEEEEEEEECCCCCEEEEEec
Confidence            0011245678899999999998888999999864

>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=99.08  E-value=1.5e-10  Score=89.40  Aligned_cols=73  Identities=23%  Similarity=0.171  Sum_probs=54.9

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeC--CCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNVG--ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDIG--~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      +++|++|+|+|++|+++|+||++.  .+.+|+||++|+++.+..                       .        +   
T Consensus        11 p~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~~~-----------------------~--------~---   56 (86)
T d1kl9a2          11 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIR-----------------------S--------I---   56 (86)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------------------------------------
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccc-----------------------c--------c---
Confidence            468999999999999999999996  379999999999853210                       0        0   


Q ss_pred             CCCCCCceeccceEEEEEEeec-CCCceEEeHHH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRR  280 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Kr  280 (343)
                          ...+.+|+.+.+.|+..+ ++++|.||+||
T Consensus        57 ----~~~~~~Gd~v~~kV~~vd~~~~ki~LS~Kq   86 (86)
T d1kl9a2          57 ----NKLIRIGRNECVVVIRVDKEKGYIDLSKRR   86 (86)
T ss_dssp             --------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             ----eEEeecccEEEEEEEEEECCCCEEEEEeeC
Confidence                123467888999999865 77999999885

>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=99.05  E-value=1.6e-10  Score=90.86  Aligned_cols=86  Identities=22%  Similarity=0.194  Sum_probs=67.7

Q ss_pred             hHHHHhhcccCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeec
Q 019315          158 VGEDKVSVEYYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVK  237 (343)
Q Consensus       158 dFa~lLe~~~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~  237 (343)
                      +|.+.++ ....+++|++|+|+|++++++|+||+++.+.+|+||++|+++.+...                         
T Consensus         5 ~~~~~ie-~~~~~k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~-------------------------   58 (94)
T d3bzka4           5 EFQEGVE-SLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKD-------------------------   58 (94)
T ss_dssp             HHHHTCC-CGGGCCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSC-------------------------
T ss_pred             HHHhhhh-HHhcCCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccC-------------------------
Confidence            4555554 35779999999999999999999999999999999999998542100                         


Q ss_pred             CCcceeccCCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHH
Q 019315          238 DDDAIAMSGGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLF  282 (343)
Q Consensus       238 ~dgaV~Ig~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~  282 (343)
                            +       ..++.+|+.+.+.|+..+ ++++|.||+|+.+
T Consensus        59 ------~-------~~~~~vGq~v~~~V~~id~~~~~i~LS~K~~e   91 (94)
T d3bzka4          59 ------P-------YEVVKAGDIVKVKVMEVDIPRNRVGLSMRMSD   91 (94)
T ss_dssp             ------H-------HHHCCTTCEEEEEEEEEETTTTEEEEESCTTC
T ss_pred             ------h-------hhhhccCcEEEEEEEEEECCCCEEEEEEeccC
Confidence                  0       123467888899999876 7799999998653

>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=98.99  E-value=2.4e-10  Score=87.62  Aligned_cols=75  Identities=19%  Similarity=0.213  Sum_probs=57.4

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCC--CeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceecc
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGA--DLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS  245 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~--KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig  245 (343)
                      .-+++|++|+|+|.+|+++|+||+++.  +.+|+||.+|+++.....                               + 
T Consensus         7 ~~p~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~-------------------------------~-   54 (84)
T d2ahob2           7 KLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKN-------------------------------I-   54 (84)
T ss_dssp             SSCCTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----C-------------------------------H-
T ss_pred             cCCCCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccc-------------------------------c-
Confidence            345789999999999999999999974  689999999998542110                               0 


Q ss_pred             CCCCCCCCceeccceEEEEEEeec-CCCceEEeHHH
Q 019315          246 GGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRR  280 (343)
Q Consensus       246 ~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Kr  280 (343)
                            .....+|+++.+.|+..+ +++++.||+||
T Consensus        55 ------~~~~~~G~~v~~kV~~vd~~~~~i~LS~Kq   84 (84)
T d2ahob2          55 ------RDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (84)
T ss_dssp             ------HHHTCSSCEEECEEEEEETTTTEEEEESSS
T ss_pred             ------ceEeecccEEEEEEEEEECCCCEEEEEEcC
Confidence                  122467788889999865 77999999874

>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=98.76  E-value=1.2e-09  Score=89.27  Aligned_cols=87  Identities=17%  Similarity=0.046  Sum_probs=66.5

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeC-CCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceecc
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVG-ADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMS  245 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG-~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig  245 (343)
                      ...+++|++|+|+|.+|+++|+||++| .+.+||||++|+++..      ...+.                         
T Consensus        16 ~~~l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~~------~~~~~-------------------------   64 (119)
T d1wi5a_          16 AEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYI------RQKNK-------------------------   64 (119)
T ss_dssp             TTTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHH------HHHSS-------------------------
T ss_pred             HhhcCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhcccc------ccCCH-------------------------
Confidence            467999999999999999999999998 5689999999997320      00000                         


Q ss_pred             CCCCCCCCceeccceEEEEEEeec-CCCceEEeHHHHHHHHHHHHH
Q 019315          246 GGSGPGRPVVETGTVLFAEVLGRT-LSGRPLLSTRRLFRKMAWHRV  290 (343)
Q Consensus       246 ~~ieg~i~v~eiGd~v~~eVl~~d-e~G~I~LS~Krl~~~~aWe~l  290 (343)
                            ...+.+|+.+.+.|+..+ ..+++.||+|+.....+|...
T Consensus        65 ------~~~~~vGq~v~~~V~~vd~~~~~i~LS~k~~~~~~~~~~~  104 (119)
T d1wi5a_          65 ------GAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEVSTAIATE  104 (119)
T ss_dssp             ------SCCCCTTCEEEEEEEECCTTSCEEEEECCCCCSCCCCCCS
T ss_pred             ------HHhcccceEEEEEEEEEeCCCCEEEEEecHHHhhhhhhhh
Confidence                  123467888999999876 568899999987766666543

>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=98.75  E-value=2.8e-09  Score=83.96  Aligned_cols=86  Identities=20%  Similarity=0.204  Sum_probs=62.0

Q ss_pred             cCCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccC
Q 019315          167 YYEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSG  246 (343)
Q Consensus       167 ~~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~  246 (343)
                      .|.+++||+|.|+|+++.+++++|||+...+|+||++|+.+.....                      +.....-  +  
T Consensus         3 ~Y~P~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~~~~----------------------rr~~~~~--~--   56 (95)
T d2nn6h1           3 RYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGEL----------------------RRRSAED--E--   56 (95)
T ss_dssp             CCCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------------------------------C--
T ss_pred             cccCCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHcccccccc----------------------ccccchh--h--
Confidence            4678899999999999999999999999999999999997431000                      0000000  0  


Q ss_pred             CCCCCCCceeccceEEEEEEeecCCCceEEeHHH
Q 019315          247 GSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRR  280 (343)
Q Consensus       247 ~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Kr  280 (343)
                        .-+.++.++|+.+.++|+..+.+|++.||.|.
T Consensus        57 --~~~~~~~~~Gd~V~~kV~~v~~dg~i~Ls~r~   88 (95)
T d2nn6h1          57 --LAMRGFLQEGDLISAEVQAVFSDGAVSLHTRS   88 (95)
T ss_dssp             --HHHHHHSCSSCEECCEEEEEETTTEEEEECCS
T ss_pred             --hhhhhhcccccEEEEEEEEECCCCCEEEEecc
Confidence              00134567888899999988888999999764

>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=98.67  E-value=2.4e-08  Score=80.00  Aligned_cols=97  Identities=21%  Similarity=0.258  Sum_probs=66.9

Q ss_pred             CCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCCCC
Q 019315          170 PKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGGSG  249 (343)
Q Consensus       170 ~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~ie  249 (343)
                      ++.|++++|+|++|+++|+||+|+ +.+|+||++++++.+   +.   .+.                 ....+ ++..  
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~-~ieGlv~~s~l~~~~---~~---~~~-----------------~~~~~-~~~~--   53 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLG-PLDGLIHVSQIMDDY---VS---YDP-----------------KREAI-IGKE--   53 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSCSSC---EE---ECC-----------------C--CE-EETT--
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEee-CeEEEEEeecccCce---ee---ecc-----------------ceeEE-eecc--
Confidence            578999999999999999999997 599999999998431   00   000                 00000 1110  


Q ss_pred             CCCCceeccceEEEEEEeec-CCC-----ceEEeHHHHHHHHHHHHHHHHhh
Q 019315          250 PGRPVVETGTVLFAEVLGRT-LSG-----RPLLSTRRLFRKMAWHRVRQIKQ  295 (343)
Q Consensus       250 g~i~v~eiGd~v~~eVl~~d-e~G-----~I~LS~Krl~~~~aWe~l~qa~e  295 (343)
                       -.....+|+.+.+.|+..+ +.+     ++.||.|+.. ..+|+.+.+.++
T Consensus        54 -~~~~~~~Gd~v~vkV~~vd~~~~~~~~~~i~ls~K~~~-~~~~e~~~~~~~  103 (106)
T d1go3e1          54 -TGKVLEIGDYVRARIVAISLKAERKRGSKIALTMRQPY-LGKLEWIEEEKA  103 (106)
T ss_dssp             -TCCEECTTCEEEEEEEEEECCC-----CEEEEECCSTT-CEEHHHHHHHHH
T ss_pred             -cccceeecceEEEEEEEEchhhccccCceeecccccCC-CCcchhhhhHhh
Confidence             0235678889999998765 333     4889988876 478988887664

>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=98.55  E-value=1.5e-07  Score=73.49  Aligned_cols=72  Identities=22%  Similarity=0.380  Sum_probs=60.6

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      |.+++||+|.|+|+.+..++++|||+...+|+||+++|...                        +.             
T Consensus         2 Y~P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~g~------------------------~k-------------   44 (88)
T d2nn6g1           2 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGA------------------------TK-------------   44 (88)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCC------------------------SS-------------
T ss_pred             CcCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcCcc------------------------cc-------------
Confidence            56889999999999999999999999999999999998521                        10             


Q ss_pred             CCCCCCceeccceEEEEEEeecCCCceEEeH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLST  278 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~  278 (343)
                        ...+..++||.+.++|...+.++.+.||.
T Consensus        45 --~~r~~l~~GD~V~arV~~v~~~~~~~Lsc   73 (88)
T d2nn6g1          45 --RNRPNVQVGDLIYGQFVVANKDMEPEMVC   73 (88)
T ss_dssp             --CSSSSSCTTCEEEEEEEECCTTSCCEEEC
T ss_pred             --ccCcccCCCCEEEEEEEEeCCCCCEEEEE
Confidence              11456688999999999888889999985

>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=98.23  E-value=3e-06  Score=66.12  Aligned_cols=73  Identities=22%  Similarity=0.340  Sum_probs=59.8

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCcccccchhhhhhhhhhhhhHhhhcceeeeecCCcceeccCC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLPLYDKEMDFLLCDLKKDAEEFMVRGKMGIVKDDDAIAMSGG  247 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~~~~ke~e~l~~d~~k~~ee~~VeGkV~~i~~dgaV~Ig~~  247 (343)
                      |.+++||+|.|+|+.+..++++||||....|++|.++..+.                       .+              
T Consensus         3 Y~P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g-----------------------~~--------------   45 (90)
T d2ja9a1           3 YIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPN-----------------------AS--------------   45 (90)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTT-----------------------CC--------------
T ss_pred             ccCCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCc-----------------------cc--------------
Confidence            56889999999999999999999999999999998776421                       11              


Q ss_pred             CCCCCCceeccceEEEEEEeecCCCceEEeH
Q 019315          248 SGPGRPVVETGTVLFAEVLGRTLSGRPLLST  278 (343)
Q Consensus       248 ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~  278 (343)
                       ....+..++||.+.++|...+.++.+.||.
T Consensus        46 -k~~r~~l~~GDlV~arV~~v~~~~~~~Lsc   75 (90)
T d2ja9a1          46 -KKNRPTLQVGDLVYARVCTAEKELEAEIEC   75 (90)
T ss_dssp             -SSSCCCCCTTCEEEEEEEECCTTSCCEEES
T ss_pred             -cccCCccCCCCEEEEEEEEECCCCCEEEEE
Confidence             112456688999999999888889999985

>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=98.20  E-value=3.2e-06  Score=63.58  Aligned_cols=39  Identities=23%  Similarity=0.336  Sum_probs=35.1

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      +.=+.|++|+|+|.+++++.++||+| ++||+||.+|..+
T Consensus         4 f~~~~geiv~G~V~r~~~~~~~Vdlg-~~eaiLp~~eqip   42 (72)
T d1hh2p1           4 YSELKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKEWIP   42 (72)
T ss_dssp             TTCCTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGSCT
T ss_pred             HhhccCcEEEEEEEEEcCCCEEEEEC-CcEEECCHHHcCC
Confidence            34468999999999999999999998 7999999999874

>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=97.94  E-value=3e-07  Score=67.14  Aligned_cols=30  Identities=17%  Similarity=0.065  Sum_probs=19.5

Q ss_pred             EEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          178 GVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       178 G~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      |+|.+|.++|+||+++.+.+|+||++|+++
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~   30 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRK   30 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC------
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHccc
Confidence            799999999999999999999999999984

>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=97.91  E-value=6.1e-06  Score=62.82  Aligned_cols=44  Identities=14%  Similarity=0.277  Sum_probs=32.1

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC---CeEEEEeCCccccC-CCChhhh
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAELLSR-VNNFTEL  338 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe---GlrgFIP~SQl~~r-v~nleel  338 (343)
                      +.|++|+|+|+++.+.|++|++.   |++||||.|++++. ..++.++
T Consensus        12 ~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~   59 (86)
T d1kl9a2          12 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKL   59 (86)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC-----------
T ss_pred             CCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEE
Confidence            47999999999999999999994   79999999999875 5565554

>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=97.84  E-value=3.6e-06  Score=65.37  Aligned_cols=54  Identities=13%  Similarity=0.059  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHhhCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC-CCChhhh
Q 019315          284 KMAWHRVRQIKQLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR-VNNFTEL  338 (343)
Q Consensus       284 ~~aWe~l~qa~e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r-v~nleel  338 (343)
                      +.+|+.+. .++.|++++|+|+++.+.|++|++ +|++||||.++++.+ ..++.++
T Consensus         7 ~~~ie~~~-~~k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~   62 (94)
T d3bzka4           7 QEGVESLK-DLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEV   62 (94)
T ss_dssp             HHTCCCGG-GCCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSCHHHH
T ss_pred             HhhhhHHh-cCCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccChhhh
Confidence            34554443 467899999999999999999999 589999999999876 5676655

>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=97.74  E-value=8.8e-06  Score=60.80  Aligned_cols=45  Identities=16%  Similarity=0.204  Sum_probs=39.8

Q ss_pred             hhCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC-CCChhhh
Q 019315          294 KQLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR-VNNFTEL  338 (343)
Q Consensus       294 ~e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r-v~nleel  338 (343)
                      ++.|++++|+|+++.+.|++|+++ |++||||.|+++.. .++++++
T Consensus         3 ~kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~~~~~~~~~~   49 (76)
T d1sroa_           3 IEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDY   49 (76)
T ss_dssp             CCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCSCHHHH
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccCCHHHc
Confidence            468999999999999999999994 89999999999876 6677665

>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=97.73  E-value=1.7e-05  Score=59.86  Aligned_cols=44  Identities=27%  Similarity=0.405  Sum_probs=35.8

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC---CeEEEEeCCccccC-CCChhhh
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE---GLRAFLPKAELLSR-VNNFTEL  338 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe---GlrgFIP~SQl~~r-v~nleel  338 (343)
                      +.|++|+|+|+++...|++|++.   |++||||.|+++.. ..++.++
T Consensus        10 ~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~   57 (84)
T d2ahob2          10 SEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDV   57 (84)
T ss_dssp             CTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----CHHHH
T ss_pred             CCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccccceE
Confidence            36999999999999999999994   89999999999876 5666654

>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=97.42  E-value=6.3e-05  Score=59.48  Aligned_cols=36  Identities=17%  Similarity=0.273  Sum_probs=33.9

Q ss_pred             hCCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      +.|++++|+|+++++.|++|++++++||+|.|+|..
T Consensus         2 ~~gei~~g~V~~v~~~G~FVel~~ieGlv~~s~l~~   37 (106)
T d1go3e1           2 EMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMD   37 (106)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSSEEEEEGGGSCS
T ss_pred             CCCCEEEEEEEEEeeeEEEEEeeCeEEEEEeecccC
Confidence            368999999999999999999999999999999974

>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=97.33  E-value=0.00011  Score=55.10  Aligned_cols=43  Identities=21%  Similarity=0.183  Sum_probs=36.5

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC--CCChhh
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR--VNNFTE  337 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r--v~nlee  337 (343)
                      +.|++|.|+|+++...|++|+++ ++.||||.|+++.+  ..++.+
T Consensus         4 k~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~   49 (83)
T d2ba0a1           4 SVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNE   49 (83)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGG
T ss_pred             CCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccccccccChhh
Confidence            47999999999999999999994 79999999999754  344444

>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=97.31  E-value=0.00019  Score=54.14  Aligned_cols=37  Identities=24%  Similarity=0.458  Sum_probs=31.7

Q ss_pred             CCCCEEEEEEEEEeCC----eEEEEeC---CCeeEEEeccccCc
Q 019315          171 KPGDFVIGVVVSGNEN----KLDVNVG---ADLLGTMLTKEVLP  207 (343)
Q Consensus       171 k~GdiVeG~VVsI~~~----gv~VDIG---~KsEG~IPisEls~  207 (343)
                      +.|++|+|+|-+++.+    .++||+|   .+.||+||.+|..|
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqip   46 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQVP   46 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSCT
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcCC
Confidence            5799999999998754    4899998   36999999999874

>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=97.04  E-value=0.00016  Score=54.76  Aligned_cols=37  Identities=24%  Similarity=0.415  Sum_probs=33.9

Q ss_pred             hCCCcEEEEEEEEecCeeEEEE-CCeEEEEeCCccccC
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRI-EGLRAFLPKAELLSR  331 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeI-eGlrgFIP~SQl~~r  331 (343)
                      +.|++|.|+|+++...|++|++ +++.||||.|++..+
T Consensus         6 k~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~   43 (87)
T d2je6i1           6 KINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGR   43 (87)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTS
T ss_pred             CCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCc
Confidence            4699999999999999999999 479999999999764

>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=96.97  E-value=0.00056  Score=51.95  Aligned_cols=35  Identities=11%  Similarity=0.233  Sum_probs=32.9

Q ss_pred             CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      .|++++|+|+++++.|++|+++.++||+|.+++..
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg~~eg~i~~~~l~~   37 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQ   37 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCT
T ss_pred             CCCEEEEEEEEEEeeEEEEEEcCeEEEEEhhhcCc
Confidence            58999999999999999999988999999999964

>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=96.87  E-value=0.00019  Score=57.65  Aligned_cols=38  Identities=24%  Similarity=0.316  Sum_probs=34.2

Q ss_pred             HhhCCCcEEEEEEEEecCeeEEEE--CCeEEEEeCCcccc
Q 019315          293 IKQLNEPIEVKFTEWNTGGLLTRI--EGLRAFLPKAELLS  330 (343)
Q Consensus       293 a~e~g~~VeGkVve~nKGGliVeI--eGlrgFIP~SQl~~  330 (343)
                      .++.|.+|+|+|+++.+.|++|++  .+++||||.+++..
T Consensus        18 ~l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~   57 (119)
T d1wi5a_          18 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQE   57 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHH
T ss_pred             hcCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhcc
Confidence            356899999999999999999999  48999999999864

>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=96.87  E-value=0.00093  Score=50.68  Aligned_cols=35  Identities=26%  Similarity=0.338  Sum_probs=32.6

Q ss_pred             CCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          172 PGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       172 ~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      +|+++.|+|+++++.|+||++| ..+|+||++.+.+
T Consensus         3 ~Gev~~g~I~~v~~~G~fv~lg-~~eg~i~~~~l~~   37 (91)
T d1y14b1           3 KGEVVDGTVVSCSQHGFEVQVG-PMKVFVTKHLMPQ   37 (91)
T ss_dssp             TTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCT
T ss_pred             CCCEEEEEEEEEEeeEEEEEEc-CeEEEEEhhhcCc
Confidence            6999999999999999999998 5899999999963

>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=96.85  E-value=0.003  Score=48.20  Aligned_cols=36  Identities=6%  Similarity=0.024  Sum_probs=32.3

Q ss_pred             CCCEEEEEEEEEeCCeEEEEe-CCCeeEEEeccccCc
Q 019315          172 PGDFVIGVVVSGNENKLDVNV-GADLLGTMLTKEVLP  207 (343)
Q Consensus       172 ~GdiVeG~VVsI~~~gv~VDI-G~KsEG~IPisEls~  207 (343)
                      .++.-+|+|++|++.|+||.+ ..+.+|+||++.|.+
T Consensus         3 ~~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~   39 (87)
T d2ix0a3           3 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHA   39 (87)
T ss_dssp             SCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCS
T ss_pred             CCCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCCC
Confidence            467889999999999999999 557999999999974

>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=96.69  E-value=0.0012  Score=50.43  Aligned_cols=35  Identities=26%  Similarity=0.399  Sum_probs=32.9

Q ss_pred             CCCcEEEEEEEEecCeeEEEECCeEEEEeCCcccc
Q 019315          296 LNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELLS  330 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~~  330 (343)
                      .|++++|+|+++++.|++|+++.++||+|.+++..
T Consensus         4 ~Gev~~g~V~~v~~~G~fv~lg~~~~~v~~~~l~~   38 (94)
T d2c35b1           4 KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPS   38 (94)
T ss_dssp             TTCEEEEEEEEEETTEEEEEETTEEEEEEGGGSCT
T ss_pred             CCCEEEEEEEEEEeeEEEEEecCceEEEEhhhcCc
Confidence            58999999999999999999988999999999964

>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=96.65  E-value=0.0017  Score=49.54  Aligned_cols=36  Identities=19%  Similarity=0.179  Sum_probs=33.0

Q ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCeeEEEeccccCc
Q 019315          171 KPGDFVIGVVVSGNENKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       171 k~GdiVeG~VVsI~~~gv~VDIG~KsEG~IPisEls~  207 (343)
                      =.|++++|+|.++++.|+||++| ..+|++|.+.+.+
T Consensus         3 f~Gev~~g~V~~v~~~G~fv~lg-~~~~~v~~~~l~~   38 (94)
T d2c35b1           3 FKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPS   38 (94)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCT
T ss_pred             CCCCEEEEEEEEEEeeEEEEEec-CceEEEEhhhcCc
Confidence            36999999999999999999998 5899999999873

>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=96.49  E-value=0.00059  Score=51.50  Aligned_cols=37  Identities=16%  Similarity=0.130  Sum_probs=33.8

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccC
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSR  331 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~r  331 (343)
                      +.|++|.|+|+++...|++|+|+ ++.||||.|+++..
T Consensus         6 k~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~   43 (88)
T d2z0sa1           6 QAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGR   43 (88)
T ss_dssp             CTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTS
T ss_pred             CCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcc
Confidence            47999999999999999999994 79999999999754

>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=96.33  E-value=0.00023  Score=51.31  Aligned_cols=57  Identities=12%  Similarity=0.193  Sum_probs=33.5

Q ss_pred             ceeeeecCCcc-eeccCCCCCCCCceeccceEEEEEEeecCCCceEEeHHHHHHHHHHH---HHHHHhhCCCcEEEEEEE
Q 019315          231 GKMGIVKDDDA-IAMSGGSGPGRPVVETGTVLFAEVLGRTLSGRPLLSTRRLFRKMAWH---RVRQIKQLNEPIEVKFTE  306 (343)
Q Consensus       231 GkV~~i~~dga-V~Ig~~ieg~i~v~eiGd~v~~eVl~~de~G~I~LS~Krl~~~~aWe---~l~qa~e~g~~VeGkVve  306 (343)
                      |+|+.++++|+ |++..+++||+|+++++..                        .+|+   +..+.++.|+.|+++|++
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~------------------------~~~~~v~~~~~~~~~G~~V~vkV~~   56 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKL------------------------AGGKRVENVEDVLGVGQKVQVEIAE   56 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC-------------------------------------------CCSSCBCCCCCCC
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHcccc------------------------cccccccCHHHhcCCCCEEEEEEEE
Confidence            78999999999 9999999999999887311                        1222   345568899999999998


Q ss_pred             EecCe
Q 019315          307 WNTGG  311 (343)
Q Consensus       307 ~nKGG  311 (343)
                      +++.|
T Consensus        57 iD~~~   61 (62)
T d1e3pa2          57 IDSRG   61 (62)
T ss_dssp             CCSSC
T ss_pred             EcCCC
Confidence            87654

>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=96.32  E-value=0.0024  Score=47.34  Aligned_cols=35  Identities=20%  Similarity=0.074  Sum_probs=33.0

Q ss_pred             hCCCcEEEEEEEEecCeeEEEECCeEEEEeCCccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIEGLRAFLPKAELL  329 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIeGlrgFIP~SQl~  329 (343)
                      ++|++|+|.|..+.+++++|++++++|+||.++.-
T Consensus         7 ~~geiv~G~V~r~~~~~~~Vdlg~~eaiLp~~eqi   41 (72)
T d1hh2p1           7 LKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWI   41 (72)
T ss_dssp             CTTCEEEEEEEEECSSEEEEEETTEEEEEEGGGSC
T ss_pred             ccCcEEEEEEEEEcCCCEEEEECCcEEECCHHHcC
Confidence            48999999999999999999999999999999874

>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=96.30  E-value=0.0027  Score=48.49  Aligned_cols=35  Identities=23%  Similarity=0.485  Sum_probs=31.6

Q ss_pred             CCCcEEEEEEEEecCeeEEEE-C-CeEEEEeCCcccc
Q 019315          296 LNEPIEVKFTEWNTGGLLTRI-E-GLRAFLPKAELLS  330 (343)
Q Consensus       296 ~g~~VeGkVve~nKGGliVeI-e-GlrgFIP~SQl~~  330 (343)
                      .++..+|.|+++.+.|++|++ + |++||||.|.|..
T Consensus         3 ~~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~   39 (87)
T d2ix0a3           3 TDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHA   39 (87)
T ss_dssp             SCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCS
T ss_pred             CCCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCCC
Confidence            478899999999999999999 3 7999999999964

>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=95.95  E-value=0.017  Score=46.53  Aligned_cols=39  Identities=26%  Similarity=0.227  Sum_probs=31.3

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCC--------CeeEEEeccccC
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGA--------DLLGTMLTKEVL  206 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~--------KsEG~IPisEls  206 (343)
                      +-+++||+|.|+|+++....++|+|..        ...|+++.+++.
T Consensus         3 ~vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr   49 (125)
T d2nn6i1           3 LLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVR   49 (125)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGG
T ss_pred             cCCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcc
Confidence            447899999999999999999999933        355677766664

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=95.34  E-value=0.041  Score=41.80  Aligned_cols=34  Identities=21%  Similarity=0.217  Sum_probs=30.8

Q ss_pred             CEEEEEEEEEeC--CeEEEEeCCCeeEEEeccccCc
Q 019315          174 DFVIGVVVSGNE--NKLDVNVGADLLGTMLTKEVLP  207 (343)
Q Consensus       174 diVeG~VVsI~~--~gv~VDIG~KsEG~IPisEls~  207 (343)
                      +|..|+|.+|.+  +.||||||....||+|++|+.+
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~   37 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAR   37 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCG
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccce
Confidence            577899999988  5999999999999999999874

>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=94.91  E-value=0.008  Score=46.03  Aligned_cols=36  Identities=11%  Similarity=0.077  Sum_probs=32.5

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCcccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLS  330 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~  330 (343)
                      +.|++|.|+|+++...|++|+|+ +..||||.|++..
T Consensus         7 ~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~   43 (95)
T d2nn6h1           7 EVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNL   43 (95)
T ss_dssp             CSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-
T ss_pred             CCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccc
Confidence            47999999999999999999995 6899999999964

>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=92.81  E-value=0.043  Score=41.61  Aligned_cols=39  Identities=8%  Similarity=-0.106  Sum_probs=34.0

Q ss_pred             hCCCcEEEEEEEEecCeeEEEEC-CeEEEEeCCccccCCC
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIE-GLRAFLPKAELLSRVN  333 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIe-GlrgFIP~SQl~~rv~  333 (343)
                      +.|+.|-|+|+++...|++|+|+ ...|+||.|++..+.+
T Consensus         5 ~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~g~~k   44 (88)
T d2nn6g1           5 VKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATK   44 (88)
T ss_dssp             CSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCSS
T ss_pred             CCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcCcccc
Confidence            47899999999999999999994 6899999999875543

>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=89.14  E-value=0.082  Score=39.17  Aligned_cols=35  Identities=17%  Similarity=0.222  Sum_probs=29.4

Q ss_pred             hCCCcEEEEEEEEecCe----eEEEEC----CeEEEEeCCccc
Q 019315          295 QLNEPIEVKFTEWNTGG----LLTRIE----GLRAFLPKAELL  329 (343)
Q Consensus       295 e~g~~VeGkVve~nKGG----liVeIe----GlrgFIP~SQl~  329 (343)
                      ++|++|+|.|..+.++.    ++|+++    +++|+||.++.-
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eqi   45 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV   45 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHcC
Confidence            47999999999987654    789993    699999999874

>d1k3ra1 b.40.4.10 (A:93-163) Hypothetical protein MTH1 (MT0001), insert domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Hypothetical protein MTH1 (MT0001), insert domain
domain: Hypothetical protein MTH1 (MT0001), insert domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=87.65  E-value=0.34  Score=35.54  Aligned_cols=33  Identities=27%  Similarity=0.411  Sum_probs=28.1

Q ss_pred             CCCCCCCEEEEEEEEEeCCeEEEEeCCCeeEEE
Q 019315          168 YEPKPGDFVIGVVVSGNENKLDVNVGADLLGTM  200 (343)
Q Consensus       168 ~~~k~GdiVeG~VVsI~~~gv~VDIG~KsEG~I  200 (343)
                      .+++.|++-+|.+++...+|+|||||....+++
T Consensus         6 g~p~vGEiReG~~~rr~~~g~~vDiGlD~la~~   38 (71)
T d1k3ra1           6 GKPVTGEYRQGLTVKRVKKGTLVDIGADKLALC   38 (71)
T ss_dssp             SSCCTTCEEEEEEEEECSSSEEEESSSSCEEEC
T ss_pred             CCCcccceeeEEEEEecCCcEEEEecCCceeee
Confidence            358899999999999999999999997655543

>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=83.16  E-value=0.52  Score=35.44  Aligned_cols=35  Identities=3%  Similarity=-0.103  Sum_probs=30.3

Q ss_pred             hCCCcEEEEEEEEecCeeEEEECC-eEEEEeCCccc
Q 019315          295 QLNEPIEVKFTEWNTGGLLTRIEG-LRAFLPKAELL  329 (343)
Q Consensus       295 e~g~~VeGkVve~nKGGliVeIeG-lrgFIP~SQl~  329 (343)
                      +.|++|-|+|+++...|++|+|.+ ..|++|.|..-
T Consensus         6 ~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f   41 (90)
T d2ja9a1           6 SVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAF   41 (90)
T ss_dssp             CTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSS
T ss_pred             CCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhcc
Confidence            479999999999999999999964 78998876553